 |
An Information Portal to Biological Macromolecular Structures |
|
PDB Home |
Contact Us 
|
 |
Validation & Deposition Services Home |
|
|
||
|
An Information Portal to Biological Macromolecular Structures |
|
|
PDB Home |
Contact Us
|
|
Validation & Deposition Services Home |
|
|
||
EXPDTA CRYO-ELECTRON MICROSCOPY REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : EM REFINEMENT REMARK 3 SOFTWARE PACKAGES : MRC SUITE, SPIDER, EMBL ICOS PACKAGE REMARK 3 RECONSTRUCTION SCHEMA : SPHERICAL HARMONICS REMARK 3 REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 ATOMIC MODELS : 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 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 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE AGGREGATION STATE : HELICAL REMARK 245 NAME OF SAMPLE : KINESIN DECORATED MICROTUBULE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 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 OTHER_DETAILS: THE SAMPLE CONSISTS OF A KINESIN-DECORATED REMARK 245 MICROTUBULE. THE EXPERIMENT DESCRIBES A MICROTUBULE-RELATED REMARK 245 PROCESS. REMARK 245 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 OTHER_DETAILS: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN REMARK 245 TEMPERATURES IN THE ELECTRON MICROSCOPE. REMARK 245
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 OLIGOMERIC STATE: HELICAL FILAMENTS; 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 OLIGOMERIC STATE: DIMER; 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 OLIGOMERIC STATE: DIMER; 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 OLIGOMERIC STATE: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