EMD-4729

Single-particle
3.0 Å
EMD-4729 Deposition: 25/03/2019
Map released: 10/07/2019
Last modified: 30/10/2019
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-4729

Structure of XBP1u-paused ribosome nascent chain complex (post-state)

EMD-4729

Single-particle
3.0 Å
EMD-4729 Deposition: 25/03/2019
Map released: 10/07/2019
Last modified: 30/10/2019
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Name: Structure of XBP1u-paused ribosome nascent chain complex (post-state).
Complex [5]
Name: Structure of XBP1u-paused ribosome nascent chain complex (post-state).
Name: ribosome
Natural source [1]
Name: tRNA
Natural source [1]
Name: X-box-binding protein 1
Natural source [1]
Organism: Homo sapiens
Recombinant Expression [1]
Organism Strain Cell Plasmid
Oryctolagus cuniculus - - -
Name: mRNA
Natural source [1]
Organism: Homo sapiens
Recombinant Expression [1]
Organism Strain Cell Plasmid
synthetic construct - - -
RNA [7]
Name: E-tRNA
Number of copies: 1
Natural source
Molecular weight
Experimental Theoretical Method
- 24 kDa -
Name: P-tRNA
Number of copies: 1
Natural source
Molecular weight
Experimental Theoretical Method
- 24 kDa -
Name: 28S ribosomal RNA
Number of copies: 1
Natural source
Molecular weight
Experimental Theoretical Method
- 1 MDa -
Name: 5S rRNA
Number of copies: 1
Natural source
Molecular weight
Experimental Theoretical Method
- 38 kDa -
Name: 5.8S ribosomal RNA
Number of copies: 1
Natural source
Molecular weight
Experimental Theoretical Method
- 48 kDa -
Name: 18S ribosomal RNA
Number of copies: 1
Natural source
Molecular weight
Experimental Theoretical Method
- 548 kDa -
Name: mRNA
Number of copies: 1
Natural source
Organism: Homo sapiens
Molecular weight
Experimental Theoretical Method
- 1 kDa -
Protein [78]
Name: X-box-binding protein 1
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Homo sapiens
Molecular weight
Experimental Theoretical Method
- 2 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Oryctolagus cuniculus - - -
Name: uL2
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 26 kDa -
Name: uL3
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 45 kDa -
Name: uL4
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 41 kDa -
Name: 60S ribosomal protein L5
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 34 kDa -
Name: 60S ribosomal protein L6
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribosome
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 28 kDa -
Name: uL30
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 26 kDa -
Name: eL8
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 26 kDa -
Name: uL6
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 21 kDa -
Name: Ribosomal protein L10 (Predicted)
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 23 kDa -
Name: Ribosomal protein L11
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribonucleoprotein complex ribosome cytoplasm
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 19 kDa -
Name: 60S ribosomal protein L13
Number of copies: 1
UniProtKB UniProtKB UniProtKB UniProtKB PDBe-KB PDBe-KB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 24 kDa -
Name: Ribosomal protein L14
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
translation
Molecular function:
RNA binding structural constituent of ribosome
Cellular location:
ribosome
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 16 kDa -
Name: Ribosomal protein L15
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [7]
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 24 kDa -
Name: uL13
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Molecular weight
Experimental Theoretical Method
- 23 kDa -
Name: uL22
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 17 kDa -
Name: eL18
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 21 kDa -
Name: eL19
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Molecular weight
Experimental Theoretical Method
- 21 kDa -
Name: eL20
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Molecular weight
Experimental Theoretical Method
- 20 kDa -
Name: eL21
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 18 kDa -
Name: eL22
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Molecular weight
Experimental Theoretical Method
- 11 kDa -
Name: eL14
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 13 kDa -
Name: Ribosomal protein L24
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 14 kDa -
Name: uL23
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 13 kDa -
Name: Ribosomal protein L26
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 15 kDa -
Name: 60S ribosomal protein L27
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 15 kDa -
Name: uL15
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 16 kDa -
Name: eL29
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 12 kDa -
Name: eL30
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 10 kDa -
Name: eL31
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 12 kDa -
Name: eL32
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 15 kDa -
Name: eL33
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 12 kDa -
Name: eL34
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 12 kDa -
Name: uL29
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 14 kDa -
Name: 60S ribosomal protein L36
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribosome
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 11 kDa -
Name: Ribosomal protein L37
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribosome
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 10 kDa -
Name: eL38
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Molecular weight
Experimental Theoretical Method
- 8 kDa -
Name: eL39
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 6 kDa -
Name: eL40
Number of copies: 1
Natural source
Molecular weight
Experimental Theoretical Method
- 6 kDa -
Name: 60s ribosomal protein l41
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribonucleoprotein complex ribosome
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 3 kDa -
Name: eL42
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 12 kDa -
Name: ribosomal protein eL43
Number of copies: 1
UniProtKB UniProtKB UniProtKB PDBe-KB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 10 kDa -
Name: eL28
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 14 kDa -
Name: 60S acidic ribosomal protein P0
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 21 kDa -
Name: uL11
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 16 kDa -
Name: uS2
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Molecular weight
Experimental Theoretical Method
- 24 kDa -
Name: 40S ribosomal protein S3a
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [2]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 24 kDa -
Name: uS5
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Molecular weight
Experimental Theoretical Method
- 24 kDa -
Name: Ribosomal protein S3
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 25 kDa -
Name: 40S ribosomal protein S4
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
translation
Molecular function:
structural constituent of ribosome rRNA binding
Cellular location:
ribonucleoprotein complex ribosome
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 29 kDa -
Name: Ribosomal protein S5
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
translation
Molecular function:
RNA binding structural constituent of ribosome
Cellular location:
small ribosomal subunit
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 21 kDa -
Name: 40S ribosomal protein S6
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribosome
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 27 kDa -
Name: 40S ribosomal protein S7
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
centrosome ribonucleoprotein complex ribosome
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 21 kDa -
Name: 40S ribosomal protein S8
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribonucleoprotein complex ribosome cytosolic ribosome
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 24 kDa -
Name: Ribosomal protein S9 (Predicted)
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 21 kDa -
Name: eS10
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 11 kDa -
Name: Ribosomal protein S11
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 17 kDa -
Name: 40S ribosomal protein S12
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribosome
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 13 kDa -
Name: ribosomal protein uS15
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 17 kDa -
Name: uS11
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 14 kDa -
Name: uS17
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 14 kDa -
Name: Ribosomal protein S16
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 16 kDa -
Name: eS17
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 15 kDa -
Name: uS13
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 16 kDa -
Name: eS19
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 15 kDa -
Name: uS10
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Molecular weight
Experimental Theoretical Method
- 11 kDa -
Name: eS21
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Molecular weight
Experimental Theoretical Method
- 9 kDa -
Name: Ribosomal protein S15a
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribonucleoprotein complex ribosome
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 14 kDa -
Name: Ribosomal protein S23
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [4]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
rough endoplasmic reticulum small ribosomal subunit
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 15 kDa -
Name: eS24
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Molecular weight
Experimental Theoretical Method
- 14 kDa -
Name: ribosomal protein eS25
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 8 kDa -
Name: eS26
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Molecular weight
Experimental Theoretical Method
- 11 kDa -
Name: 40S ribosomal protein S27
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 9 kDa -
Name: Ribosomal protein S28
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Domains
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 7 kDa -
Name: uS14
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 6 kDa -
Name: eS31
Number of copies: 1
UniProtKB PDBe-KB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 7 kDa -
Name: ribosomal protein RACK1
Number of copies: 1
UniProtKB UniProtKB UniProtKB PDBe-KB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB AlphaFold DB
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 34 kDa -
Name: 40S ribosomal protein S30
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [3]
Biological process:
translation
Molecular function:
structural constituent of ribosome
Cellular location:
ribosome
Natural source
Organism: Rabbit
Molecular weight
Experimental Theoretical Method
- 6 kDa -
Ligand [2]
Name: MAGNESIUM ION
HET code: MG
Number of copies: 299
ChEBI DrugBank
Molecular weight
Experimental Theoretical Method
- 24 Da -
Name: ZINC ION
HET code: ZN
Number of copies: 6
ChEMBL ChEBI DrugBank
Molecular weight
Experimental Theoretical Method
- 65 Da -