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

by single particle reconstruction, at 12 A resolution

Movie

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1048, Image by Jmol

#3: With PDB-1pdf, PDB-1pdi, PDB-1pdj, PDB-1pdl, PDB-1pdm, PDB-1pdp, PDB-2fl8, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-1048 (with PDB-1pdf, PDB-1pdi, PDB-1pdj, PDB-1pdl, PDB-1pdm, PDB-1pdp, PDB-2fl8), Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3h3w
TitleFitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 dome-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-1048, Image by Jmol

#3: With PDB-1pdf, PDB-1pdi, PDB-1pdj, PDB-1pdl, PDB-1pdm, PDB-1pdp, PDB-2fl8, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-1048 (with PDB-1pdf, PDB-1pdi, PDB-1pdj, PDB-1pdl, PDB-1pdm, PDB-1pdp, PDB-2fl8), Image by UCSF CHIMERA

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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 deletion fragment
Mutationresidues 334-660
Formula weight38304.887 Da
Number of molecules12
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: Bacteriophage T4, 6, ID:10665, Enterobacteria phage T4
Host: Escherichia coli

, BL21(DE3)
LinksUniProt: P19060, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Entity assembly
Assembly-ID1
Detailsassembly of gp6 in the dome-shaped baseplate of bacteriophage T4
Namering of 12 molecules of gene product 6
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7
Sample concentration5 mg/ml
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI/PHILIPS CM300FEG/T
Date2001-01-30
Electron gun
Electron sourceFIELD EMISSION GUN
Electron dose25 e/A**2
Illumination modeFLOOD BEAM
Lens
MagnificationCalibrated: 47000 X, Nominal: 45000 X
Nominal defocusMax: 5000 nm, Min: 1200 nm
Specimen holder
Specimen holderModel: GATAN LIQUID NITROGEN, Type: 626 Single Tilt Cryotransfer System
Processing
Reflection
Ordinal1
D resolution high12.0
2D projection selection
Software nameCOLORES from the SITUS program package was used for the fitting
Single particle entity
Symmetry typeCYCLIC
3D fitting
Refinement SpaceREAL
Software nameCOLORES from the SITUS program package was used for the fitting
3D fitting list
3D Fitting ID1
Refine
Refine idELECTRON MICROSCOPY
Ls d res high12.0 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high12.0
Total atoms31380
Protein atoms31380
Download
PDB format
Allpdb3h3w.ent.gz
pdb3h3w.ent (uncompressed file)
Header onlypdb3h3w.ent.gz
mmCIF format
mmCIF3h3w.cif.gz
XML format
All3h3w.xml.gz
No-atom3h3w-noatom.xml.gz
Ext-atom3h3w-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), 3.5 MB
.webm (WebM/VP8 format), 5 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 3.7 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.1 MB