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Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 star-shaped baseplate

by single particle reconstruction, at 16 A resolution

Movie

Orientation:

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1086, Image by Jmol

#3: With PDB-1tja, PDB-2fl9, PDB-3foi, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-1086 (with PDB-1tja, PDB-2fl9, PDB-3foi), Image by UCSF CHIMERA

#5: Superimposing with EM 3D map: EMDB-1089 (with PDB-1tja, PDB-2fl9, PDB-3foi), Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3h3y
TitleFitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 star-shaped baseplate
DescriptorBaseplate structural protein Gp6
KeywordsVIRAL PROTEIN, viral structural protein, Virion
AuthorsAksyuk, A.A., Leiman, P.G., Shneider, M.M., Mesyanzhinov, V.V., Rossmann, M.G.
DateDeposition: 2009-04-17, Release: 2009-05-19
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-1086, Image by Jmol

#3: With PDB-1tja, PDB-2fl9, PDB-3foi, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-1086 (with PDB-1tja, PDB-2fl9, PDB-3foi), Image by UCSF CHIMERA

#5: Superimposing with EM 3D map: EMDB-1089 (with PDB-1tja, PDB-2fl9, PDB-3foi), Image by UCSF CHIMERA

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Fit: target map of fitting

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List of similar structure data about Omokage system
Article
Citation - primary
ArticleStructure, Vol. 17, Issue 6, Page 800-8, Year 2009
TitleThe structure of gene product 6 of bacteriophage T4, the hinge-pin of the baseplate.
AuthorsAnastasia A Aksyuk, Petr G Leiman, Mikhail M Shneider, Vadim V Mesyanzhinov, Michael G Rossmann
Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.
KeywordsAmino Acid Sequence, Bacteriophage T4 (genetics), Cryoelectron Microscopy, Crystallization, Dimerization, Genes, Viral, Glycoproteins (genetics), Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Viral Proteins (genetics)
LinksPII: S0969-2126(09)00185-3, DOI: 10.1016/j.str.2009.04.005, PubMed: 19523898
Components
ID 1 : Baseplate wedge protein 6
Image
DescriptionBaseplate structural protein Gp6
Typepolypeptide(L)
Fragmentgene product 6 fragment
Mutationresidues 334 to 660
Formula weight38304.887 Da
Number of molecules12
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: 6, bacteriophage T4
Host: ID:562, Escherichia coli

LinksUniProt: P19060, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Experimental Mass220
Mass-estimation MethodEstimate
Theoretical Mass220
NameT4 phages treated with 3 M urea
Num components1
Entity assembly
Assembly-ID1
NameA ring of six gp6 dimers in the star-shaped baseplate of bacteriophage T4
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Vitrification
Cryogen nameETHANE
Temp100 Kelvin
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
Date2002-01-06
Electron gun
Accelerating voltage300 kV
Electron dose20 e/A**2
Illumination modeSPOT SCAN
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 47000 X, Nominal: 45000 X
Detector distance0.0
Nominal defocusMax: 3400 nm, Min: 500 nm
Energy filterFEI
Specimen holder
Specimen holderModel: GATAN LIQUID NITROGEN, Type: Side entry liquid nitrogen-cooled cryo specimen holder
Tilt angleMin: -9999.0 degrees, Max: -9999.0 degrees
Temperature100 Kelvin
Detector
TypeKodak SO163 film
Image scans
Number digital images100
Quant bit size8
Sampling size3.93285
Scanner modelZEISS SCAI
Processing
2D projection selection
Number of particles1965
Software nameCOLORES from the SITUS program package
Single particle entity
Symmetry typeCYCLIC
3D reconstruction
CTF correction methodEach particle
Euler angles detailstheta 45 degrees, phi 180 degrees
Methodback-projection
Number of particles1965
Resolution16 A
Resolution methodFSC at 0.5 cut-off
SoftwareSpider
3D fitting
Software nameCOLORES from the SITUS program package
3D fitting list
3D Fitting ID1
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms31380
Protein atoms31380
Download
PDB format
Allpdb3h3y.ent.gz
pdb3h3y.ent (uncompressed file)
Header onlypdb3h3y.ent.gz
mmCIF format
mmCIF3h3y.cif.gz
XML format
All3h3y.xml.gz
No-atom3h3y-noatom.xml.gz
Ext-atom3h3y-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), 3.7 MB
.webm (WebM/VP8 format), 5.4 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 3.5 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.7 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.9 MB