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Bacteriophage T4 gp17 motor assembly based on crystal structures and cryo-EM reconstructions

by single particle reconstruction, at 34 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1572, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3ezk
TitleBacteriophage T4 gp17 motor assembly based on crystal structures and cryo-EM reconstructions
DescriptorDNA packaging protein Gp17
KeywordsHYDROLASE, pentameric motor, DNA packaging, Alternative initiation, ATP-binding, DNA-binding, Hydrolase, Nuclease, Nucleotide-binding
AuthorsSun, S., Rossmann, M.G.
DateDeposition: 2008-10-23, Release: 2009-01-13
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 EM 3D map: EMDB-1572, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
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EMDB-1572

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List of similar structure data about Omokage system
Article
Citation - primary
ArticleCell, Vol. 135, Issue 7, Page 1251-62, Year 2008
TitleThe structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces.
AuthorsSiyang Sun, Kiran Kondabagil, Bonnie Draper, Tanfis I Alam, Valorie D Bowman, Zhihong Zhang, Shylaja Hegde, Andrei Fokine, Michael G Rossmann, Venigalla B Rao
Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.
KeywordsBacteriophage T4 (metabolism), Crystallography, X-Ray, DNA Packaging, Models, Molecular, Static Electricity, Viral Proteins (chemistry), Virus Assembly, gp17 protein, Enterobacteria phage T4
LinksPII: S0092-8674(08)01447-5, DOI: 10.1016/j.cell.2008.11.015, PubMed: 19109896
Components
ID 1 : Terminase
Image
DescriptionDNA packaging protein Gp17
Typepolypeptide(L)
FragmentResidues 1-577
Formula weight66204.734 Da
Number of molecules5
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: D, 17, ID:10665, Bacteriophage T4
Host: ID:562, Escherichia coli

, BL21(DE3), Plasmid
Plasmid name: pET
LinksUniProt: P17312, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameT4 procapsid with gp17 bound
Buffer
Name50mM Tris-HCl, 100mM NaCl, 5mM MgCl2, 3mM beta-Mercaptoethanol
Sample preparation
pH7.4
Vitrification
Detailsflash-frozen on holey grids in liquid ethane
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Processing
2D projection selection
Software nameEMFIT
3D reconstruction
Actual pixel size6.48 A/pix
CTF correction methodphase flipping of each micrograph
MethodSpider
Nominal pixel size6.48 A/pix
Resolution34.0 A
3D fitting
MethodN- and C-terminal domains were separately fitted into their corresponding cryoEM densities
Refinement ProtocolRigid body
Refinement SpaceREAL
Software nameEMFIT
Target criteriaSumf
3D fitting list
3D Fitting ID1
PDB entry ID3CPE
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms2765
Protein atoms2765
Download
PDB format
Allpdb3ezk.ent.gz
pdb3ezk.ent (uncompressed file)
Header onlypdb3ezk.ent.gz
mmCIF format
mmCIF3ezk.cif.gz
XML format
All3ezk.xml.gz
No-atom3ezk-noatom.xml.gz
Ext-atom3ezk-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 3.8 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5 MB