PDB-1gw8: quasi-atomic resolution model of bacteriophage PRD1 sus...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 1gw8
Title	quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography.
Descriptor	MAJOR CAPSID PROTEIN
Keywords	VIRUS/VIRAL PROTEIN, TECTIVIRIDAE, BACTERIOPHAGE PRD1, CRYO- EM, IMAGE RECONSTRUCTION, ICOSAHEDRAL VIRUS, VIRUS-VIRAL PROTEIN complex
Authors	San Martin, C., Huiskonen, J.T., Bamford, J.K.H., Butcher, S.J., Fuller, S.D., Bamford, D.H., Burnett, R.M.
Date	Deposition: 2002-03-08, Release: 2002-03-15
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Compound details	BACTERIOPHAGE PRD1 SUS607 MUTANT LACKS THE VIRAL MEMBRANE AGGREGATION PROTEIN P11
Structure Visualization
Movies	Movie Page #1: Biological unit as complete icosahedral assembly, Made by Jmol #2: Biological unit as icosahedral pentamer, Made by Jmol #3: Biological unit as icosahedral 23 hexamer, Made by Jmol #4: Depositted structure unit, Made by Jmol #5: Superimposing with simplified surface model of EM map, EMDB-1012, Made by Jmol #6: Superimposing with EM 3D map: EMDB-1012, Made by UCSF CHIMERA #7: Superimposing with EM 3D map: EMDB-1012, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1012 CiteFit EMDB-1011 Cite PDB-1gw7 Cite PDB-1cjd PDB-1hb5 PDB-1hb7 PDB-1hqn PDB-1hx6 Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-1gw7 PDB-1hb9 PDB-1hb7 PDB-4an5 List of similar structure data about Omokage system

Article
Citation - primary
Article	Nat. Struct. Biol., Vol. 9, Issue 10, Page 756-63, Year 2002
Title	Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid.
Authors	Carmen San Martín, Juha T Huiskonen, Jaana K H Bamford, Sarah J Butcher, Stephen D Fuller, Dennis H Bamford, Roger M Burnett The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA.
Keywords	Bacteriophage PRD1 (genetics), Capsid (metabolism), Cloning, Molecular, Crystallography, X-Ray, Intracellular Membranes (metabolism), Models, Molecular
Links	PubMed: 12219080, DOI: 10.1038/nsb837
Citation - 1
Article	Acta Crystallogr. D Biol. Crystallogr., Vol. 58, Issue Pt 1, Page 39-59, Year 2002
Title	The X-ray crystal structure of P3, the major coat protein of the lipid-containing bacteriophage PRD1, at 1.65 A resolution.
Authors	Stacy D Benson, Jaana K H Bamford, Dennis H Bamford, Roger M Burnett The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.
Keywords	Bacteriophage PRD1 (chemistry), Capsid (chemistry), Crystallography, X-Ray, Lipids (chemistry), Models, Molecular, Molecular Structure, Virion (chemistry)
Links	PubMed: 11752778
Citation - 2
Article	Structure, Vol. 9, Issue 10, Page 917-30, Year 2001
Title	Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions.
Authors	C S Martín, R M Burnett, F de Haas, R Heinkel, T Rutten, S D Fuller, S J Butcher, D H Bamford The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.
Keywords	Adenoviruses, Human (chemistry), Bacteriophage PRD1 (chemistry), Capsid (chemistry), Computer Simulation, Cryoelectron Microscopy (methods), Crystallography, X-Ray (methods), DNA, Viral (chemistry), Image Enhancement (methods), Models, Molecular, Protein Conformation, Viral Envelope Proteins (chemistry), Virion (chemistry)
Links	PubMed: 11591347, PII: S0969212601006426
Citation - 3
Article	Cell, Vol. 98, Issue 6, Page 825-33, Year 1999
Title	Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures.
Authors	S D Benson, J K Bamford, D H Bamford, R M Burnett The Wistar Institute, Philadelphia, Pennsylvania 19104, USA.
Keywords	Adenoviruses, Human (chemistry), Amino Acid Sequence, Capsid (chemistry), Capsid Proteins, Crystallization, Crystallography, X-Ray, Evolution, Molecular, Models, Molecular, Molecular Sequence Data, Protein Conformation, Synchrotrons, Tectiviridae (chemistry), hexon capsid protein, Adenovirus, protein P3, bacteriophage PRD1
Links	PubMed: 10499799, PII: S0092-8674(00)81516-0

Components
ID 1 : PROTEIN P3
Image
Description	MAJOR CAPSID PROTEIN
Type	polymer
Formula weight	43346.695 Da
Number of molecules	12
Details	SUS607 MUTANT LACKS THE VIRAL MEMBRANE AGGREGATION PROTEIN P11
Source	Method: Isolated from a genetically manipulated source Gene: ID:10658, BACTERIOPHAGE PRD1 Host: ID:602, SALMONELLA TYPHIMURIUM, DS88 Plasmid name: PSN3
Links	UniProt: P22535, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	BACTERIOPHAGE PRD1 SUS607
Buffer
Name	TRIS
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7.2
Sample support
Details	HOLEY CARBON
Vitrification
Details	ETHANE

Electron Microscopy
Imaging
Microscope	model: FEI CM200 FEG
Date	2001-12-01
Electron gun
Electron source	FEG
Accelerating voltage	200 kV
Illumination mode	LOW DOSE
Lens
Magnification	calibrated: 45100 X, nominal: 50000 X
Cs	nominal: 2 mm
Nominal defocus	max: 4100 nm, min: 1300 nm
Specimen holder
Temperature	95 Kelvin
Detector
Type	KODAK SO-163 FILM
Image scans
Number digital images	21

Processing
2D projection selection
Number of particles	569
Software name	SPIDER, MRC_ICOS
Single particle entity
Symmetry type	ICOSAHEDRAL
3D reconstruction
Actual pixel size	3.32 A/pix
CTF correction method	PHASE RESTORATION BY CTF- MULTIPLICATION OF IMAGES; AMPLITUDE RESTORATION BY COMPARISON WITH QUASI- ATOMIC MODEL
Details	RIGID BODY REFINEMENT AGAINST CRYO-EM MAP XPLOR 3.851 (BRUNGER). DATA USED IN REFINEMENT. RESOLUTION RANGE HIGH INFINITY RESOLUTION RANGE LOW 15A DATA CUTOFF (SIGMA(F)) 0.0 NUMBER OF REFLECTIONS 1430672 FIT TO DATA USED IN
Magnification calibration	COMPARISON WITH X- RAY DATA
Method	POLAR FOURIER TRANSFORM, CROSS- COMMON LINES
Nominal pixel size	3.68 A/pix
Resolution	13.3 A
3D fitting
Method	RIGID BODY
Refinement Protocol	X-RAY
Refinement Space	RECIPROCAL
Target criteria	R-FACTOR
3D fitting list
PDB entry ID	1HX6 PDB-1hx6
Refine
Ls d res high	13.30 A
ID	1
Refine hist
D res high	13.30
Total atoms	34170
Protein atoms	34170

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mmCIF

1gw8.cif.gz

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1gw8.xml.gz

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1gw8-noatom.xml.gz

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Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.7 MB .webm (WebM/VP8 format), 5.3 MB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.2 MB .webm (WebM/VP8 format), 4.1 MB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.3 MB .webm (WebM/VP8 format), 4.1 MB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 2.9 MB .webm (WebM/VP8 format), 3.8 MB

movie #5

	.mp4 (H.264/MPEG-4 AVC format), 4 MB .webm (WebM/VP8 format), 6 MB

movie #6

	.mp4 (H.264/MPEG-4 AVC format), 1.9 MB .webm (WebM/VP8 format), 2.9 MB

movie #7

	.mp4 (H.264/MPEG-4 AVC format), 1.9 MB .webm (WebM/VP8 format), 2.9 MB