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Sample components

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Component type:    
Scientific name:   e.g. Human rhinovirus A
NCBI taxonomy identifier:   e.g. 9913 (autocompleted field)
Alternative names: e.g. Common cold virus
Experimental weight (MDa): e.g. 3 (in megadaltons)
Theoretical weight (MDa): e.g. 3 (in megadaltons)
Virus type:    
Virus isolate type:    
Virus strain:   e.g. Mahoney
Is the virus enveloped?:    
Is the virus empty?:    
Details: e.g. 1.4 nanometer gold particles were attached to specific cysteine residues on the virus surface.

Natural host of the virus

Host category:    
Host organism:   e.g. Homo sapiens
NCBI taxonomy identifier:   e.g. 9913 (autocompleted field)
Host organism strain: e.g. BMH 71-18

Expression system for the virus

Has the virus been expressed in a different organism than the natural host?:    

Virus shell

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Shell name: e.g. M1
Diameter of shell (Å): e.g. 1234.56 (in angstroms)
Triangulation number: e.g. 50

Sample components

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Component type:    
Scientific name:   e.g. Ribulose-1,5-bisphosphate carboxylase oxygenase
Alternative names: e.g. RuBisCO
Experimental weight (MDa): e.g. 3 (in megadaltons)
Theoretical weight (MDa): e.g. 3 (in megadaltons)
Number of copies: e.g. 2
Oligomeric state: e.g. Dimer
UniProt identifier: e.g. A4Q8T1
Gene ontology (GO) identifier list: e.g. 0005876, 0005877
InterPro (IPR) identifier list: e.g. IPR001304, IPR001205
Details: e.g. 1.4 nanometer gold particles were attached to specific cysteine residues on the protein surface.

Natural source of the component

Scientific organism name:   e.g. Homo sapiens
NCBI taxonomy identifier:   e.g. 9913 (autocompleted field)
Common organism name: e.g. Human
Organism strain name: e.g. BMH 71-18
Organ/tissue: e.g. Cartilage
Cell type: e.g. Chondroblasts
Organelle: e.g. Nucleus
Cellular location: e.g. Plasma membrane

Recombinant expression system of the component

Is the protein recombinantly expressed?:    

Component type

A description of each type of component of the sample.

Example: For Golgi apparatus the component type is CELLULAR-COMPONENT.
Example: For 5 nm Gold the assembly type is LABEL.
Example: For Kyrromycin the assembly type is SMALL MOLECULE.
Example: For DNA or RNA the assembly type is NUCLEIC ACID.
Example: For Actin assembly type is PROTEIN.
Example: For Semliki-forest the assembly type is VIRUS.
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Scientific name of the sample component

The scientific name of the sample component.

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Synonym name of sample component

Alternative name of the sample component.

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Experimental molecular weight of component

The value of the experimentally determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
close

Theoretical molecular weight of component

The value of the theoretically determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
close

Number copies of the cellular-component

The number of copies of the cellular-component.

Example: 2
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Oligomeric state of the cellular-component

The oligomeric state of the cellular-component.

Example: Trimer
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Gene Ontology (GO) identifier for the cellular-component

The GO id is the appropriate identifier used by the Gene Ontology Consortium. Reference: Nature Genetics 2000 (25) 25-29.

Example: GO:0005876
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InterPro (IPR) identifier for the cellular-component

The IPR identifier is the appropriate identifier used by the Interpro Resource. Reference: Nucleic Acid Research 2001 (1) 37-40.

Example: IPR001304
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Additional details about the component

Details that provide extra information about the component.

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Scientific species name

The scientific name of the species of the natural organism from which the cellular-component was obtained.

Example: Gallus gallus
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NCBI taxonomy identifier

The NCBI taxonomy identifier (see http://www.ncbi.nlm.nih.gov/Taxonomy).

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Common species name

The common name of the species of the natural organism from which the cellular-component was obtained.

Example: Chicken

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Organism strain name

The strain of the natural organism from which the cellular-component was obtained.

Example: BMH 71-18
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Organ/tissue source of cellular-component

The organ or tissue of the natural organism from which the component was obtained.

Example: Bone
close

Cell type of the cellular-component

Name the specific line of cells from which this component has been derived.

Example: Murine hybridoma
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Organelle source of cellular-component

The organelle from which the component was obtained.

Example: Mitochondrion
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Cellular location of cellular-component

The cellular location of the component.

Example: Cell membrane
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Cellular-component recombinant expression

A cellular-component is considered to be recombinantly expressed if the genes from the original organism are inserted using molecular cloning and transformation technologies into a foreign organism.

Example: NO
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Expression system for cellular-component

The expression system used to produce the cellular-component.

Example: Saccharomyces cerevisiae.
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NCBI taxonomy identifier

The NCBI taxonomy identifier (see http://www.ncbi.nlm.nih.gov/Taxonomy).

close

Organism strain name

The strain of the organism used as expression system.

Example: BMH 71-18
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Cell line

Name the specific line of cells from which this component has been derived.

Example: Murine hybridoma
close

Plasmid used in expression system for cellular-component

The plasmid used in the expression system used to produce the component.

Example: pBR322
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Scientific name of the sample component

The scientific name of the sample component.

close

Synonym name of sample component

Alternative name of the sample component.

close

Experimental molecular weight of component

The value of the experimentally determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
close

Theoretical molecular weight of component

The value of the theoretically determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
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Number copies of the label

Example: 2
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Oligomeric State of the label

The oligomeric state of the label.

Example: Trimer
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Chemical formula of label

The chemical formula of the label. Examples of gold labels could include the following.
Gold clusters are gold compounds with a core of gold atoms and organic groups covalently bound to the surface gold atoms. An example is undecagold, Au11(P(C6H5)3)7, whose structure was solved by X-ray crystallography. These differ from colloidal gold, which are suspensions of metal particles, usually formed by metal ion reduction; although the particles may be approximately the same size, they vary due to the statistical process of formation. Gold clusters are compounds with a definite formula, and should all be perfectly identical. However, it is known that there is a family of stable gold cluster compounds, such as Au6, Au11, Au13, Au55, Au67, etc. In a given preparation of gold clusters, there is usually some mixture of these, thus leading to some size variation. Methods such as gel filtration column chromatography and ultrafiltration can be used to separate most of these species, so that relatively pure preparations may be achieved. The UV-Vis spectra of the different clusters are also usually significantly different, aiding in identification of the various clusters. Since the larger nuclearity clusters (>= Au55) have not been crystallized, their exact structure has not been determined.

Example: Au11(P(C6H5)3)7
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Additional details about the component

Details that provide extra information about the component.

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Scientific name of the sample component

The scientific name of the sample component.

close

Synonym name of sample component

Alternative name of the sample component.

close

Experimental molecular weight of component

The value of the experimentally determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
close

Theoretical molecular weight of component

The value of the theoretically determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
close

Number copies of the ligand

Example: 2
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Oligomeric state of the ligand

The oligomeric state of the ligand.

Example: Trimer
close

Gene Ontology (GO) identifier for the ligand

The GO id is the appropriate identifier used by the Gene Ontology Consortium. Reference: Nature Genetics 2000 (25) 25-29.

Example: GO:0005876
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InterPro (IPR) identifier for the ligand

The IPR identifier is the appropriate identifier used by the Interpro Resource. Reference: Nucleic Acid Research 2001 (1) 37-40.

Example: IPR001304
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Additional details about the component

Details that provide extra information about the component.

close

Scientific species name

The scientific name of the species of the natural organism from which the ligand was obtained.

Example: Gallus gallus
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NCBI taxonomy identifier

The NCBI taxonomy identifier (see http://www.ncbi.nlm.nih.gov/Taxonomy).

close

Common species name

The common name of the species of the natural organism from which the ligand was obtained.

Example: Chicken
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Organism strain name

The strain of the natural organism from which the ligand was obtained.

Example: BMH 71-18.
close

Organ/tissue source of ligand

The organ or tissue of the natural organism from which the ligand was obtained.

Example: Bone
close

Cell type of the ligand

Name the specific line of cells from which this component has been derived.

Example: Murine hybridoma
close

Organelle source of the ligand

The organelle from which the ligand was obtained.

Example: Mitochondrion
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Cellular location of ligand

The cellular location of the ligand.

Example: Cell membrane
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Ligand recombinant expression

A ligand is considered to be recombinantly expressed if the genes from the original organism are inserted using molecular cloning and transformation technologies into a foreign organism.

Example: NO
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Expression system for the ligand

The expression system used to produce the ligand.

Example: Saccharomyces cerevisiae
close

NCBI taxonomy identifier

The NCBI taxonomy identifier (see http://www.ncbi.nlm.nih.gov/Taxonomy).

close

Organism strain name

The strain of the organism used as expression system.

Example: BMH 71-18
close

Cell line

Name the specific line of cells from which this component has been derived.

Example: Murine hybridoma
close

Plasmid used in expression system for the ligand

The plasmid used in the expression system used to produce the ligand.

Example: pBR322
close

Scientific name of the sample component

The scientific name of the sample component.

close

Synonym name of sample component

Alternative name of the sample component.

close

Experimental molecular weight of component

The value of the experimentally determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
close

Theoretical molecular weight of component

The value of the theoretically determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
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Nucleic acid type

Select the category of nucleic acid from the drop down menu.

Example: PEPTIDE NUCLEIC ACID DNA
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Alternative nucleic acid type

If the nucleci acid type is not found in the drop-down list, report it in this text area.

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Nucleic acid description

Select the structural description of nucleic acid from the drop down menu.

Example: DOUBLE HELIX
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Alternative nucleic acid structure

If the nucleci acid structure is not found in the drop-down list, report it in this text area.

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Sequence of nucleotides

The nucleotide sequence in sigle letter code. Nucleic Acids are polymers of nucleotides. The four nucleotides in DNA contain the bases Adenine (A), Guanine (G), Cytocine (C) and Thymine (T). The four nucleotides in RNA contain the bases Adenine (A), Guanine (G), Cytocine (C) and Uracil (U).

Example: ACUGGCU
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Additional details about the component

Details that provide extra information about the component.

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Scientific organism name

The scientific name of the species of the natural organism from which the nucleic-acid was obtained.

Example: Gallus gallus
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NCBI taxonomy identifier

The NCBI taxonomy identifier (see http://www.ncbi.nlm.nih.gov/Taxonomy).

close

Common organism name

The common name of the species of the natural organism from which the nucleic-acid was obtained.

Example: Chicken
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Organism strain name

The strain of the natural organism from which the nucleic acid was obtained.

Example: BMH 71-18
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Nucleotide origin

If the nucleotide sequence is from a non biological source then select "YES".

Example: YES
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Scientific name of the sample component

The scientific name of the sample component.

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Synonym name of sample component

Alternative name of the sample component.

close

Experimental molecular weight of component

The value of the experimentally determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
close

Theoretical molecular weight of component

The value of the theoretically determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
close

Number copies of the protein

The number of copies of the protein.

Example: 2
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Oligomeric sate of the protein

The oligomeric state of the protein.

Example: Trimer
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UniProt identifier for the protein

The UniProt id is the appropriate identifier used by the UniProt Consortium. Reference: Nucleic Acids Res. 40:D71-D75 (2012).

Example: A4Q8T1
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Gene Ontology (GO) identifier for the protein

The GO id is the appropriate identifier used by the Gene Ontology Consortium. Reference: Nature Genetics 2000 (25) 25-29.

Example: GO:0005876
close

InterPro (IPR) identifier for the protein

The IPR identifier is the appropriate identifier used by the Interpro Resource. Reference: Nucleic Acid Research 2001 (1) 37-40.

Example: IPR001304
close

Additional details about the component

Details that provide extra information about the component.

close

Scientific organism name

The scientific name of the species of the natural organism from which the protein was obtained.

Example: Gallus gallus
close

NCBI taxonomy identifier

The NCBI taxonomy identifier (see http://www.ncbi.nlm.nih.gov/Taxonomy).

close

Common species name

The common name of the species of the natural organism from which the protein was obtained.

Example: Chicken
close

Organism strain name

The strain of the natural organism from which the protein was obtained.

Example: BMH 71-18
close

Organ/tissue source of protein

The organ or tissue of the natural organism from which the protein was obtained.

Example: Bone
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Cell type of the the protein

The cell from which the protein was obtained.

Example: 3T3 fibroblasts
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Organelle source of the protein

The organelle from which the protein was obtained.

Example: Mitochondrion
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Cellular location of the protein

The cellular location of the protein.

Example: Cell membrane
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Protein recombinant expression

A protein is considered to be recombinantly expressed if the genes from the original organism are inserted using molecular cloning and transformation technologies into a foreign organism.

Example: NO
close

Expression system for the protein

The expression system used to produce the protein.

Example: Saccharomyces cerevisiae
close

NCBI taxonomy identifier

The NCBI taxonomy identifier (see http://www.ncbi.nlm.nih.gov/Taxonomy).

close

Organism strain name

The strain of the organism used as expression system.

Example: BMH 71-18
close

Cell line

Name the specific line of cells from which this component has been derived.

Example: Murine hybridoma
close

Plasmid used in expression system for the protein

The plasmid used in the expression system used to produce the component.

Example: pBR322
close

Scientific name of the sample component

The scientific name of the sample component.

close

NCBI taxonomy identifier

The NCBI taxonomy identifier (see http://www.ncbi.nlm.nih.gov/Taxonomy).

close

Synonym name of sample component

Alternative name of the sample component.

close

Experimental molecular weight of component

The value of the experimentally determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
close

Theoretical molecular weight of component

The value of the theoretically determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
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Virus type

The prevailing characteristic of the virus.
Virion: morphologically complete virus particle.

Example: VIROID
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Alternative virus type

If the virus type is not found in the drop-down list, report it in this text area.

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Virus isolate type

The isolate from which the virus was obtained.

Example: SUBSPECIES
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Virus serocomplex

Serocomplex of the virus.

Example: JEV
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Virus serotype

Serotype of the virus.

Example: EV-95
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Virus strain

Strain of the virus.

Example: Mahoney
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Virus subspecies

Subspecies of the virus.

Example: B1
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Alternative virus isolate

If the virus isolate is not found in the drop-down list, report it in this text area.

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Virus envelope

A flag to indicate if the virus is enveloped or not. The nucleocapsid may be invested with an envelope.

Example: YES
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Virus empty

A flag to indicate if the virus is empty or not. The capsid may contain no nucleic acid.

Example: YES
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Additional details about the component

Details that provide extra information about the component.

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Virus host

The host category description for the virus.

Example: FUNGI
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Alternative host category

If the host category is not found in the drop-down list, report it in this text area.

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Host species

The host species from which the virus was isolated.

Example: Homo sapiens
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NCBI taxonomy identifier

The NCBI taxonomy identifier (see http://www.ncbi.nlm.nih.gov/Taxonomy).

close

Organism strain name

The strain of the natural host organism.

Example: BMH 71-18
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Expression of the virus

Indicate if the virus has been produced in the natural host organism or in another organism.

Example: NO
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Expression system for the virus

The expression system used to produce the virus.

Example: Saccharomyces cerevisiae
close

NCBI taxonomy identifier

The NCBI taxonomy identifier (see http://www.ncbi.nlm.nih.gov/Taxonomy).

close

Organism strain name

The strain of the organism used as expression system.

Example: BMH 71-18
close

Cell line

Name the specific line of cells from which this component has been derived.

Example: Murine hybridoma
close

Plasmid used in expression system for the virus

The plasmid used in the expression system used to produce the component.

Example: pBR322
close

Scientific name of the sample component

The scientific name of the sample component.

close

Synonym name of sample component

Alternative name of the sample component.

close

Experimental molecular weight of component

The value of the experimentally determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
close

Theoretical molecular weight of component

The value of the theoretically determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
close

Eukaryotic ribosome components

Select the eukaryotic ribosome sample component(s).

Example: ALL
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Gene Ontology (GO) identifier for the ribosome

The GO id is the appropriate identifier used by the Gene Ontology Consortium. Reference: Nature Genetics 2000 (25) 25-29.

Example: GO:0005876
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InterPro (IPR) identifier for the ribosome

The IPR identifier is the appropriate identifier used by the Interpro Resource. Reference: Nucleic Acid Research 2001 (1) 37-40.

Example: IPR001304
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Additional details about the component

Details that provide extra information about the component.

close

Scientific species name

The scientific name of the species of the natural organism from which the ribosome was obtained.

Example: Gallus gallus
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NCBI taxonomy identifier

The NCBI taxonomy identifier (see http://www.ncbi.nlm.nih.gov/Taxonomy).

close

Common species name

The common name of the species of the natural organism from which the ribosome was obtained.

Example: Chicken

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Organism strain name

The strain of the natural organism from which the ribosome was obtained.

Example: BMH 71-18
close

Organ/tissue source of ribosome

The organ or tissue of the natural organism from which the component was obtained.

Example: Bone
close

Cell type of the ribosome

Name the specific line of cells from which this component has been derived.

Example: Murine hybridoma
close

Organelle source of ribosome

The organelle from which the component was obtained.

Example: Mitochondrion
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Cellular location of ribosome

The cellular location of the component.

Example: Cell membrane
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Ribosome recombinant expression

A ribosome is considered to be recombinantly expressed if the genes from the original organism are inserted using molecular cloning and transformation technologies into a foreign organism.

Example: NO
close

Expression system for ribosome

The expression system used to produce the ribosome.

Example: Saccharomyces cerevisiae.
close

NCBI taxonomy identifier

The NCBI taxonomy identifier (see http://www.ncbi.nlm.nih.gov/Taxonomy).

close

Organism strain name

The strain of the organism used as expression system

Example: BMH 71-18
close

Cell line

Name the specific line of cells from which this component has been derived.

Example: Murine hybridoma
close

Plasmid used in expression system for ribosome

The plasmid used in the expression system used to produce the component.

Example: pBR322
close

Scientific name of the sample component

The scientific name of the sample component.

close

Synonym name of sample component

Alternative name of the sample component.

close

Experimental molecular weight of component

The value of the experimentally determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
close

Theoretical molecular weight of component

The value of the theoretically determined molecular weight of the component (in megadaltons).

In the case of a virus, please specify the molecular weight of the whole virus, not just the molecular weight of the asymmetric unit.

Example: 1.20
Range: 0.001 to 1000000000.0 (in megadaltons)
close

Prokaryotic ribosome components

Select the prokaryotic ribosome sample component(s).

Example: ALL
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Gene Ontology (GO) identifier for the ribosome

The GO id is the appropriate identifier used by the Gene Ontology Consortium. Reference: Nature Genetics 2000 (25) 25-29.

Example: GO:0005876
close

InterPro (IPR) identifier for the ribosome

The IPR identifier is the appropriate identifier used by the Interpro Resource. Reference: Nucleic Acid Research 2001 (1) 37-40.

Example: IPR001304
close

Additional details about the component

Details that provide extra information about the component.

close

Scientific species name

The scientific name of the species of the natural organism from which the ribosome was obtained.

Example: Gallus gallus
close

NCBI taxonomy identifier

The NCBI taxonomy identifier (see http://www.ncbi.nlm.nih.gov/Taxonomy).

close

Common species name

The common name of the species of the natural organism from which the ribosome was obtained.

Example: Chicken

close

Organism strain name

The strain of the natural organism from which the ribosome was obtained.

Example: BMH 71-18
close

Organ/tissue source of ribosome

The organ or tissue of the natural organism from which the component was obtained.

Example: Bone
close

Cell type of the ribosome

Name the specific line of cells from which this component has been derived.

Example: Murine hybridoma
close

Organelle source of ribosome

The organelle from which the component was obtained.

Example: Mitochondrion
close

Cellular location of ribosome

The cellular location of the component.

Example: Cell membrane
close

Ribosome recombinant expression

A ribosome is considered to be recombinantly expressed if the genes from the original organism are inserted using molecular cloning and transformation technologies into a foreign organism.

Example: NO
close

Expression system for ribosome

The expression system used to produce the ribosome.

Example: Saccharomyces cerevisiae.
close

NCBI taxonomy identifier

The NCBI taxonomy identifier (see http://www.ncbi.nlm.nih.gov/Taxonomy).

close

Organism strain name

The strain of the organism used as expression system

Example: BMH 71-18
close

Cell line

Name the specific line of cells from which this component has been derived.

Example: Murine hybridoma
close

Plasmid used in expression system for ribosome

The plasmid used in the expression system used to produce the component.

Example: pBR322
close

Shell name

Virus capsids can have more than one layer.
For example rotaviruses have a triple layered capsid formed by three concentric protein layers. Proteins forming capsid are VP2 internal layer with a triangulation T=1, VP6 (intermediate layer, T=13 symmetry), VP7 (external layer, T=13) and VP4 which forms a spike inserted in the outermost two layers.

Example: VP2
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Diameter of capsid shell

Enter the diameter of the shell in angstroms.

Example: 354
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Triangulation number

The triangulation number gives a geometric concept which refers to the organisation of the geometric figure. The simplest icosahedral has only equivalent units; all bonds are identical and all vertices have identical bonding. The larger icosahedra have hexagons between the pentagons and can be visualised as replacing the original triangular faces with larger ones formed from equilateral triangles. The number of triangles replacing the original one is the triangulation number. More precisely, the triangulation number is given by the following relationship:

T = h*2 + hk + k*2

where h and k are positive integers which define the position of the five fold vertex on the original hexagonal net.
For example, a T = 4 virus will have 4 different subunit environments and 60 * T or 240 subunits.

Example: 4
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