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PSEUDO-ATOMIC MODEL OF BACTERIOPHAGE HK97 PROCAPSID (PROHEAD II)

by single particle (icosahedral) reconstruction, at 12 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

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 1if0
TitlePSEUDO-ATOMIC MODEL OF BACTERIOPHAGE HK97 PROCAPSID (PROHEAD II)
DescriptorMAJOR CAPSID PROTEIN GP5
KeywordsVirus, Bacteriophage, Capsid, cryoEM, Pseudo-atomic model., Icosahedral virus
AuthorsConway, J.F., Wikoff, W.R., Cheng, N., Duda, R.L., Hendrix, R.W., Johnson, J.E., Steven, A.C.
DateDeposition: 2001-04-11, Release: 2001-05-02
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

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
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Cite: data citing same article

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List of similar structure data about Omokage system
Article
Citation - primary
ArticleScience, Vol. 292, Issue 5517, Page 744-8, Year 2001
TitleVirus maturation involving large subunit rotations and local refolding.
AuthorsJ F Conway, W R Wikoff, N Cheng, R L Duda, R W Hendrix, J E Johnson, A C Steven
Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD 20892, USA.
KeywordsAmino Acid Motifs, Capsid (chemistry), Cryoelectron Microscopy, Crystallography, X-Ray, DNA, Viral (metabolism), Image Processing, Computer-Assisted, Models, Molecular, Protein Conformation, Protein Folding, Protein Precursors (chemistry), Protein Structure, Tertiary, Protein Subunits, Siphoviridae (chemistry), Surface Properties, Virus Assembly
LinksPubMed: 11326105, DOI: 10.1126/science.1058069
Citation - 1
ArticleScience, Vol. 289, Page: 2129 - 2133, Year: 2000,
TitleTopologically Linked Protein Rings in the Bacteriophage HK97 Capsid
AuthorsWikoff, W.R., Liljas, L., Duda, R.L., Tsuruta, H., Hendrix, R.W., Johnson, J.E.
LinksDOI: 10.1126/science.289.5487.2129
Citation - 2
ArticleScience, Vol. 253, Page: 86 - 99, Year: 1995,
TitleProteolytic and Conformational Control of Virus Capsid Maturation: The Bacteriophage HK97 System
AuthorsConway, J.F., Duda, R.L., Cheng, N., Hendrix, R.W., Steven, A.C.
LinksDOI: 10.1006/jmbi.1995.0538
Components
ID 1 : BACTERIOPHAGE HK97 CAPSID PROTEIN
Image
DescriptionPROTEIN (MAJOR CAPSID PROTEIN GP5)
Typepolypeptide(L)
Formula weight28279.945 Da
Number of molecules7
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: Lambda-like viruses, ID:37554, Enterobacteria phage HK97
Host: Escherichia, ID:562, Escherichia coli

, PT7-HD2.9B, PLASMID
Plasmid name: PT7-5
LinksUniProt: P49861, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI/PHILLIPS CM200FEG
Processing
2D projection selection
Number of particles981
Single particle entity
Symmetry typeICOSAHEDRAL
3D reconstruction
DetailsIMAGE RECONSTRUCTION INCLUDING CONTRAST TRANSFER CORRECTION, WAS DONE AS DESCRIBED IN T.S.Baker & R.H.Cheng, J.Struct.Biol. 116, 120-130 (1996) and J.F.Conway & A.C.Steven, J.Struct.Biol. 128, 106 (1999). Nine focal pairs were analyzed, yielding 2939 particles, of which 981 were included in the final map. This map was calculated to 12 Angstroms, its resolution as assessed by Fourier Ring Correlation (cutoff 2 sigma), as calculated between reprojections of two maps from half data sets.
Resolution12. A
3D fitting
Refinement SpaceREAL
Refine
Refine idELECTRON MICROSCOPY
Ls d res high12 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high12
Total atoms1792
Protein atoms1792
Download
PDB format
Allpdb1if0.ent.gz
pdb1if0.ent (uncompressed file)
Header onlypdb1if0.ent.gz
mmCIF format
mmCIF1if0.cif.gz
XML format
All1if0.xml.gz
No-atom1if0-noatom.xml.gz
Ext-atom1if0-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), 3.9 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), 2.8 MB
.webm (WebM/VP8 format), 3.6 MB