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De Novo model of Bacteriophage P22 procapsid coat protein

by single particle reconstruction, at 3.8 A resolution

Movie

Orientation:

#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-1824, Made by Jmol

#6: Superimposing with EM 3D map: EMDB-1824, Made by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2xyy
TitleDe Novo model of Bacteriophage P22 procapsid coat protein
DescriptorCOAT PROTEIN
KeywordsVIRUS, ICOSAHEDRAL RECONSTRUCTION
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, 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-1824, Made by Jmol

#6: Superimposing with EM 3D map: EMDB-1824, Made by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-1824

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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
Image
DescriptionCOAT PROTEIN
Typepolypeptide(L)
Formula weight46796.133 Da
Number of molecules7
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: 97540, ID:10754, ENTEROBACTERIA PHAGE P22
Host: ID:90371, SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM, DB7136, 13AMH101
LinksUniProt: A8CGC7, Sequence view
Sample
Assembly
Aggregation statePARTICLE
DetailsBAD MICROGRAPHS WERE EXCLUDED VISUALLY
NameBACTERIOPHAGE P22 PROCAPSID
Buffer
Name50 MM TRIS PH 7.6, 25 MM NACL, 2MM EDTA
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
Date2008-03-07
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: 2800 nm, Min: 500 nm
Specimen holder
Temperature4.2 Kelvin
Detector
TypeKODAK SO163 FILM
Image scans
Number digital images921
Processing
2D projection selection
Number of particles23400
Software nameEMAN
3D reconstruction
Actual pixel size1.06 A/pix
CTF correction methodEACH PARTICLE
DetailsMAKE3D IN EMAN.N-TERMINAL 9 RESIDUES AND C-TERMINAL 5 RESIDUES WERE NOT MODELED.SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1824.
MethodFOURIER METHODS
Nominal pixel size1.06 A/pix
Resolution3.8 A
3D fitting
Refinement ProtocolEM
Refinement SpaceREAL
Target criteriaFSC
Refine
Refine idELECTRON MICROSCOPY
Ls d res high3.80 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high3.80
Total atoms2912
Protein atoms2912
Download
PDB format
Allpdb2xyy.ent.gz
pdb2xyy.ent (uncompressed file)
Header onlypdb2xyy.ent.gz
mmCIF format
mmCIF2xyy.cif.gz
XML format
All2xyy.xml.gz
No-atom2xyy-noatom.xml.gz
Ext-atom2xyy-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.1 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), 2.8 MB
.webm (WebM/VP8 format), 3.7 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 2.7 MB
.webm (WebM/VP8 format), 3.6 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.7 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.7 MB