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Structure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy

by helical reconstruction, at 7 A resolution

Movie

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-2090, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-2090, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 4ard
TitleStructure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy
DescriptorCAPSID PROTEIN P27
KeywordsVIRAL PROTEIN, RETROVIRUS, GAG
AuthorsBharat, T.A.M., Davey, N.E., Ulbrich, P., Riches, J.D., Marco, A.D., Rumlova, M., Sachse, C., Ruml, T., Briggs, J.A.G.
DateDeposition: 2012-04-23, Release: 2012-05-30
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-2090, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-2090, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-2090

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Article
Citation - primary
ArticleNature, Vol. 487, Issue 7407, Page 385-9, Year 2012
TitleStructure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy.
AuthorsTanmay A M Bharat, Norman E Davey, Pavel Ulbrich, James D Riches, Alex de Marco, Michaela Rumlova, Carsten Sachse, Tomas Ruml, John A G Briggs
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
KeywordsCapsid (metabolism), Cryoelectron Microscopy, Mason-Pfizer monkey virus (ultrastructure), Models, Molecular, Protein Structure, Tertiary, Virus Assembly
LinksDOI: 10.1038/nature11169, PubMed: 22722831
Components
ID 1 : M-PMV DPRO CANC PROTEIN
Image
DescriptionCAPSID PROTEIN P27
Typepolypeptide(L)
FragmentM-PMV CA-NTD, RESIDUES 318-433
Formula weight12885.351 Da
Number of molecules2
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: ID:11855, MASON-PFIZER MONKEY VIRUS
Host: ID:562, ESCHERICHIA COLI

LinksUniProt: P07567, Sequence view
Sample
Assembly
Aggregation stateFILAMENT
NameM-PMV CANC GAG TUBES
Buffer
Name100MM NACL, 50MM TRIS-HCL, 1UM ZN
Experiment
Reconstruction methodHELICAL
Specimen typeVITREOUS ICE CRYOEM
Sample preparation
pH7.7
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsLIQUID ETHANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: OTHER
Date2011-07-05
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose0.2 e/A**2
Illumination modeLOW DOSE
Lens
ModeBRIGHT FIELD
MagnificationNominal: 47000 X
CsNominal: 2.7 mm
Nominal defocusMax: 4000 nm, Min: 1000 nm
Detector
TypeKODAK SO163 FILM
Image scans
Number digital images46
Processing
2D projection selection
Software nameSPIDER, AV3
3D reconstruction
Actual pixel size1.53 A/pix
CTF correction methodDIVISION BY 3D CTF SQ
DetailsHELICAL RECONSTRUCTION WITH 3D ASYMMETRIC UNIT AVERAGING SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2090. (DEPOSITION ID: 10768).
MethodHELICAL RECONSTRUCTION WITH 3D ASYMMETRIC UNIT AVERAGING
Nominal pixel size1.53 A/pix
Resolution7 A
3D fitting
MethodRIGID BODY
Refinement ProtocolNMR
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
PDB entry ID2KGF
Refine
Refine idELECTRON MICROSCOPY
Ls d res high7.00 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high7.00
Total atoms232
Protein atoms232
Download
PDB format
Allpdb4ard.ent.gz
pdb4ard.ent (uncompressed file)
Header onlypdb4ard.ent.gz
mmCIF format
mmCIF4ard.cif.gz
XML format
All4ard.xml.gz
No-atom4ard-noatom.xml.gz
Ext-atom4ard-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 3.7 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.6 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.1 MB