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Capsid structure of the infectious Prochlorococcus Cyanophage P-SSP7

by single particle reconstruction, at 4.6 A resolution

Movie

Orientation:

#1: Biological unit as complete icosahedral assembly, Image by Jmol

#2: Biological unit as icosahedral pentamer, Image by Jmol

#3: Biological unit as icosahedral 23 hexamer, Image by Jmol

#4: Deposited structure unit, Image by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-1713, Image by Jmol

#6: Superimposing with EM 3D map: EMDB-1713, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2xd8
TitleCapsid structure of the infectious Prochlorococcus Cyanophage P-SSP7
DescriptorT7-LIKE CAPSID PROTEIN
KeywordsVIRUS, MARINE PODOVIRUS, T7-LIKE VIRUS
AuthorsLiu, X., Zhang, Q., Murata, K., Baker, M.L., Sullivan, M.B., Fu, C., Dougherty, M., Schmid, M.F., Osburne, M.S., Chisholm, S.W., Chiu, W.
DateDeposition: 2010-04-30, Release: 2010-06-16
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Biological unit as complete icosahedral assembly, Image by Jmol

#2: Biological unit as icosahedral pentamer, Image by Jmol

#3: Biological unit as icosahedral 23 hexamer, Image by Jmol

#4: Deposited structure unit, Image by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-1713, Image by Jmol

#6: Superimposing with EM 3D map: EMDB-1713, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-1713

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Article
Citation - primary
ArticleNat. Struct. Mol. Biol., Vol. 17, Issue 7, Page 830-6, Year 2010
TitleStructural changes in a marine podovirus associated with release of its genome into Prochlorococcus.
AuthorsXiangan Liu, Qinfen Zhang, Kazuyoshi Murata, Matthew L Baker, Matthew B Sullivan, Caroline Fu, Matthew T Dougherty, Michael F Schmid, Marcia S Osburne, Sallie W Chisholm, Wah Chiu
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.
KeywordsCapsid (chemistry), Genome, Viral, Models, Molecular, Podoviridae (chemistry), Prochlorococcus (virology), Viral Proteins (chemistry), Virion (chemistry)
LinksDOI: 10.1038/nsmb.1823, PubMed: 20543830, PMC: PMC2924429
Components
ID 1 : GP10
Image
DescriptionT7-LIKE CAPSID PROTEIN
Typepolypeptide(L)
Formula weight39494.582 Da
Number of molecules7
ID1
SourceMethod: Isolated from a genetically manipulated source
Description: P-SSP7 WERE PROPAGATED ON PROCHLOROCOCCUS MED4.
Gene: ID:268748, PROCHLOROCOCCUS PHAGE P-SSP7
Host: ID:1220, PROCHLOROCOCCUS MED4
LinksUniProt: Q58N30, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameCYANOPHAGE P-SSP7
Buffer
Name100 MM TRIS-HCL, 100 MM MGSO4, AND 30 MM NACL
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE
Sample preparation
pH7.5
Sample concentration5.0 mg/ml
Sample support
DetailsHOLEY CARBON
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: OTHER
Date2007-08-31
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose20 e/A**2
Illumination modeLOW DOSE
Lens
ModeBRIGHT FIELD
MagnificationNominal: 60000 X
CsNominal: 4.1 mm
Nominal defocusMax: 3000 nm, Min: 600 nm
Specimen holder
Temperature101 Kelvin
Detector
TypeKODAK SO163 FILM
Image scans
Number digital images1059
Processing
2D projection selection
Number of particles36000
Software nameMPSA
3D reconstruction
Actual pixel size1.17 A/pix
CTF correction methodINDIVIDUAL MICROGRAPH
DetailsSUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1713.
Magnification calibration2D CRYSTAL
MethodCROSS-COMMON LINES
Nominal pixel size1.27 A/pix
Resolution4.6 A
3D fitting list
3D Fitting ID1
PDB entry ID1IJG, 2JES
Refine
Refine idELECTRON MICROSCOPY
Ls d res high4.60 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high4.60
Total atoms2541
Protein atoms2541
Download
PDB format
Allpdb2xd8.ent.gz
pdb2xd8.ent (uncompressed file)
Header onlypdb2xd8.ent.gz
mmCIF format
mmCIF2xd8.cif.gz
XML format
All2xd8.xml.gz
No-atom2xd8-noatom.xml.gz
Ext-atom2xd8-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.8 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.8 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 2.6 MB
.webm (WebM/VP8 format), 3.5 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 2.6 MB
.webm (WebM/VP8 format), 3.5 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.1 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.2 MB