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De Novo model of Bacteriophage P22 virion coat protein

by single particle reconstruction, at 4 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: Depositted structure unit, Image by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-1826, Image by Jmol

#6: Superimposing with EM 3D map: EMDB-1826, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2xyz
TitleDe Novo model of Bacteriophage P22 virion coat protein
DescriptorCOAT PROTEIN
KeywordsVIRUS, MATURATION, DSDNA VIRUS
AuthorsChen, D.-H., Baker, M.L., Hryc, C.F., DiMaio, F., Jakana, J., Wu, W., Dougherty, M., Haase-Pettingell, C., Schmid, M.F., Jiang, W., Baker, D., King, J.A., Chiu, W.
DateDeposition: 2010-11-19, Release: 2011-02-02
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
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: Depositted structure unit, Image by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-1826, Image by Jmol

#6: Superimposing with EM 3D map: EMDB-1826, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
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EMDB-1826

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Article
Citation - primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 108, Issue 4, Page 1355-60, Year 2011
TitleStructural basis for scaffolding-mediated assembly and maturation of a dsDNA virus.
AuthorsDong-Hua Chen, Matthew L Baker, Corey F Hryc, Frank DiMaio, Joanita Jakana, Weimin Wu, Matthew Dougherty, Cameron Haase-Pettingell, Michael F Schmid, Wen Jiang, David Baker, Jonathan A King, Wah Chiu
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
KeywordsBacteriophage P22 (genetics), Binding Sites, Capsid (chemistry), Capsid Proteins (chemistry), Cryoelectron Microscopy, DNA Viruses (genetics), Models, Molecular, Protein Binding, Protein Conformation, Protein Structure, Tertiary, VP3 protein, Bluetongue virus, Viral Core Proteins, Viral Proteins (chemistry), Virion (genetics), Virus Assembly
LinksDOI: 10.1073/pnas.1015739108, PubMed: 21220301, PMC: PMC3029737
Components
ID 1 : P22, PROTEIN GP5
Image
DescriptionCOAT PROTEIN
Typepolypeptide(L)
Formula weight46796.133 Da
Number of molecules7
ID1
SourceMethod: Isolated from a natural source
Atcc: 97540
NCBI taxonomy: ID:10754
Organism scientific: ENTEROBACTERIA PHAGE P22
LinksUniProt: A8CGC7, Sequence view
Sample
Assembly
Aggregation statePARTICLE
DetailsBAD MICROGRAPHS WERE EXCLUDED VISUALLY
NameBACTERIOPHAGE P22 VIRION
Buffer
Name50 MM TRIS PH 7.6, 25 MM NACL
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE
Sample preparation
pH7.6
Sample concentration1.0 mg/ml
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsVITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, TEMPERATURE- 4.2, INSTRUMENT- VITROBOT, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING,
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: JEOL KYOTO-3000SFF
Date2005-12-06
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose36 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 60000 X, Nominal: 60000 X
CsNominal: 1.6 mm
Nominal defocusMax: 2300 nm, Min: 300 nm
Specimen holder
Temperature4.2 Kelvin
Detector
TypeKODAK SO163 FILM
Image scans
Number digital images1262
Processing
2D projection selection
Number of particles18300
Software nameEMAN
3D reconstruction
Actual pixel size1.06 A/pix
CTF correction methodEACH PARTICLE
DetailsMAKE3D IN EMAN. C-TERMINAL 5 RESIDUES WERE NOT MODELE MODELED SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1826.
MethodFOURIER METHODS
Nominal pixel size1.06 A/pix
Resolution4.0 A
3D fitting
Refinement ProtocolEM
Refinement SpaceREAL
Target criteriaFSC
Refine
Refine idELECTRON MICROSCOPY
Ls d res high4.00 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high4.00
Total atoms2975
Protein atoms2975
Download
PDB format
Allpdb2xyz.ent.gz
pdb2xyz.ent (uncompressed file)
Header onlypdb2xyz.ent.gz
mmCIF format
mmCIF2xyz.cif.gz
XML format
All2xyz.xml.gz
No-atom2xyz-noatom.xml.gz
Ext-atom2xyz-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.9 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 3.7 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 3.7 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), 3.8 MB
.webm (WebM/VP8 format), 5.6 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.3 MB