REMARK 3 REMARK 3 REFINEMENT REMARK 3 SOFTWARE PACKAGES : MRC SUITE, SPIDER, EMBL ICOS PACKAGE REMARK 3 RECONSTRUCTION SCHEMA : SPHERICAL HARMONICS REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : X-RAY DIFFRACTION STRUCTURES REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY REFINEMENT REMARK 3 REFINEMENT TARGET : R-FACTOR REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : THE CRYSTAL STRUCTURE OF THE CAPSID REMARK 3 PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359 REMARK 3 (SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM REMARK 3 DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED REMARK 3 INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE REMARK 3 FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET REMARK 3 OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED REMARK 3 BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT REMARK 3 (CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT REMARK 3 CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563 REMARK 3 ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE REMARK 3 AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5 REMARK 3 SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222 REMARK 3 ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN REMARK 3 DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE REMARK 3 PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS REMARK 3 GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER REMARK 3 OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY REMARK 3 THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE REMARK 3 DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE REMARK 3 MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE REMARK 3 ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE REMARK 3 HIGHEST PSEUDO TEMPERATURE FACTORS. REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 2.64 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : 2.52 REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 9.0 REMARK 3 NUMBER OF PARTICLES : 5267 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: THE PIXEL SIZE REMARK 3 OF THE CRYO-EM MAP WAS CALIBRATED AGAINST THE ATOMIC MODEL OF REMARK 3 THE NUCLEOCAPSID. DENSITIES WERE COMPARED BY CROSS-CORRELATION REMARK 3 WITHIN A SPHERICAL SHELL OF INTERNAL RADIUS 169 ANGSTROMS AND REMARK 3 EXTERNAL RADIUS 198 ANGSTROMS. REMARK 3 REMARK 3 OTHER DETAILS: THE COORDINATES ARE IN THE P, Q, R FRAME IN REMARK 3 ANGSTROM UNITS AND CORRESPOND TO ICOSAHEDRAL SYMMETRY AXES. REMARK 3 THE ORIGIN IS CHOSEN AT THE CENTER OF THE VIRUS WITH P, Q REMARK 3 AND R ALONG MUTUALLY PERPENDICULAR TWO-FOLD AXES OF THE REMARK 3 ICOSAHEDRON. THEY SHOULD REMAIN IN THAT FRAME FOR THE EASE REMARK 3 OF THE USER IN CREATING THE BIOLOGICALLY SIGNIFICANT VIRAL REMARK 3 COMPLEX PARTICLE USING THE 60 ICOSAHEDRAL SYMMETRY OPERATORS REMARK 3 RESIDUES NOT VISIBLE IN THE ORIGINAL CRYSTAL STRUCTURES ARE REMARK 3 NOT INCLUDED IN THE CRYO-EM STRUCTURE MODEL. FOR EXAMPLE, REMARK 3 C RESIDUES 1-118, ARE NOT VISIBLE IN THE CRYSTAL STRUCTURE REMARK 3 (PDB ENTRY 1VCQ) AND THEREFORE ARE NOT INCLUDED IN THE REMARK 3 COORDINATES BELOW. REMARK 3
REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 REMARK 245 EXPERIMENT TYPE : CRYO-ELECTRON MICROSCOPY REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE AGGREGATION STATE : HELICAL REMARK 245 NAME OF SAMPLE : KINESIN DECORATED MICROTUBULE REMARK 245 SAMPLE CONCENTRATION : 3.5 REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : PLUNGED INTO ETHANE REMARK 245 SAMPLE BUFFER : PHOSPHATE REMARK 245 PH : 7.4 REMARK 245 SAMPLE DETAILS: THE SAMPLE CONSISTS OF A KINESIN-DECORATED REMARK 245 MICROTUBULE. THE EXPERIMENT DESCRIBES A MICROTUBULE-RELATED REMARK 245 PROCESS. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 15 JUNE 1998 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 48 REMARK 245 TEMPERATURE (KELVIN) : 95 REMARK 245 MICROSCOPE MODEL : PHILIPS CM200 FEG REMARK 245 DETECTOR TYPE : SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 975 REMARK 245 MAXIMUM DEFOCUS (NM) : 7600 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0 REMARK 245 NOMINAL CS : 2 REMARK 245 IMAGING MODE : LOW DOSE REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 1000 REMARK 245 ILLUMINATION MODE : BRIGHT FIELD REMARK 245 NOMINAL MAGNIFICATION : 50000 REMARK 245 CALIBRATED MAGNIFICATION : 50050 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN REMARK 245 TEMPERATURES IN THE ELECTRON MICROSCOPE. REMARK 245
REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS
EXAMPLE 1 REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS 4 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 300 REMARK 300 ASSEMBLY COMPONENTS REMARK 300 COM_ID: 1; REMARK 300 NAME: MICROTUBULE; REMARK 300 GO_ID: 0005874; REMARK 300 OTHER DETAILS: MICROTUBULES ISOLATED AS TUBULIN FROM COW REMARK 300 BRAIN (BOS TAURUS) AND FORMED 15:4 HELICES. REMARK 300 THE TUBULIN PROTOFILAMENTS CONSISITING OF REMARK 300 POLYMERISED ALTERNATING ALPHA AND BETA SUBUNITS; REMARK 300 COM_ID: 2; REMARK 300 NAME: KINESIN; REMARK 300 GO_ID: 0005871; REMARK 300 OTHER DETAILS: KINESIN FROM DROSOPHILA WAS EXPRESSED IN REMARK 300 ESCHERICIA COLI. A TRUNCATED AMINO-TERMINAL REMARK 300 REGION (RESIDUES 1-392) EXTENDING BEYOND THE REMARK 300 MINIMAL MOTOR DOMAIN FORMED A HOMODIMER REMARK 300 EXAMPLE 2 REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE UNIQUE VIRAL REPEAT UNIT, REMARK 300 WHICH CONSISTS OF 5 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 300 REMARK 300 ASSEMBLY COMPONENTS REMARK 300 COM_ID: 1; REMARK 300 NAME: FAB; REMARK 300 IPR_ID: NULL; REMARK 300 GO_ID: NULL; REMARK 300 OTHER_DETAILS: ANTIBODY FRAGMENT; REMARK 300 COM_ID: 2; REMARK 300 NAME: VIRUS; REMARK 300 IPR_ID: NULL; REMARK 300 GO_ID: NULL; REMARK 300 OTHER DETAILS: NULL REMARK 300 REMARK 300 VIRUS PARTICULARS REMARK 300 COM_ID: 2; REMARK 300 VIRUS_HOST_CATEGORY: VERTEBRATES ; REMARK 300 VIRUS_HOST_SPECIES: GALLUS GALLUS ; REMARK 300 VIRUS_HOST_GROWTH_CELL: GIZZARD ; REMARK 300 VIRUS_TYPE: VIRUS; REMARK 300 VIRUS_ISOLATE: SPECIES ; REMARK 300 ICTVDB_ID: 1.0.2.0.001 REMARK 300
NOTE: for SubKey Items in the Electron Microscopy REMARK 300,
* The REMARK 300 record for Electron Microscopy entries specifies the
nature of the biological components at a macro cellular component
level. Each component represents a discrete macromolecular entity
contained within the sample studied, for instance VIRUS, PROTEIN,
NUCLEIC ACID, LIGAND, LABEL or CELLULAR COMPONENT
* Only the relevant tokens need to appear in an entry.
* As in COMPND and SOURCE records where MOL_ID indicates that subsequent
specifications are related to a particular molecule, in the REMARK 300
records COM_ID: is used in a similar manner.
* COM_ID: Numbers each component of the sample studied.
* NAME: Name of the macromolecule sub component
* IPR_ID: The InterPro (IPR) identifier for the component.
* GO_ID: The Gene Ontology (GO) identifier for the component.
* OTHER_DETAILS: Additional comments.
* VIRUS_HOST_CATEGORY: The host category description for the virus.
Choose from: ALGAE, ARCHAEA, BACTERIA(EUBACTERIA), FUNGI
INVERTEBRATES, PLANTAE (HIGHER PLANTS), PROTOZOA,
or VERTEBRATES
* VIRUS_HOST_SPECIES: The host species from which the virus was isolated.
* VIRUS_HOST_GROWTH_CELL: The host cell from which the virus was isolated.
* VIRUS_TYPE:The type of virus. Choose from:
VIRION, SATELLITE, PRION, VIROID, VIRUS-LIKE PARTICLE or OTHER
* VIRUS_ISOLATE:The isolate from which the virus was obtained.
Choose from: STRAIN, SEROTYPE, SEROCOMPLEX, SUBSPECIES, or SPECIES
* ICTVDB_ID: The International Committee on Taxonomy of Viruses
(ICTV) Taxon Identifier is the Virus Code used throughout the
ICTV database (ICTVdb). The ICTVdb id is the appropriate
identifier used by the International Committee on Taxonomy of Viruses
Resource. Reference: Virus Taxonomy, Academic Press (1999).
ISBN:0123702003.
The project is funded by the European Commission as the IIMS,
contract-no. QLRI-CT-2000-31237 under the RTD programme
"Quality of Life and Management of Living Resources"