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

by electron microscopy, at 34 A resolution

Movie

Orientation:

#1: Depositted structure unit, Made by Jmol

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

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3ezk
Title	Bacteriophage T4 gp17 motor assembly based on crystal structures and cryo-EM reconstructions
Descriptor	DNA packaging protein Gp17
Keywords	HYDROLASE, pentameric motor, DNA packaging, Alternative initiation, ATP-binding, DNA-binding, Hydrolase, Nuclease, Nucleotide-binding
Authors	Sun, S., Rossmann, M.G.
Date	Deposition: 2008-10-23, Release: 2009-01-13
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with EM 3D map: EMDB-1572, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1572 CiteFit EMDB-1573 Cite PDB-3c6a Cite PDB-3c6h Cite PDB-3cpe Cite Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-3izz EMDB-2040 PDB-3lu0 List of similar structure data about Omokage system

Article
Citation - primary
Article	Cell, Vol. 135, Issue 7, Page 1251-62, Year 2008
Title	The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces.
Authors	Siyang 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.
Keywords	Bacteriophage T4 (metabolism), Crystallography, X-Ray, DNA Packaging, Models, Molecular, Static Electricity, Viral Proteins (chemistry), Virus Assembly, gp17 protein, Enterobacteria phage T4
Links	PII: S0092-8674(08)01447-5, DOI: 10.1016/j.cell.2008.11.015, PubMed: 19109896

Components
ID 1 : Terminase
Image
Description	DNA packaging protein Gp17
Type	polymer
Fragment	Residues 1-577
Formula weight	66204.734 Da
Number of molecules	5
Source	Method: Isolated from a genetically manipulated source Gene: D, 17, ID:10665, Bacteriophage T4 Host: ID:562, Escherichia coli , BL21(DE3), Plasmid Plasmid name: pET
Links	UniProt: P17312, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	T4 procapsid with gp17 bound
Buffer
Name	50mM Tris-HCl, 100mM NaCl, 5mM MgCl2, 3mM beta-Mercaptoethanol
Sample preparation
pH	7.4
Vitrification
Details	flash-frozen on holey grids in liquid ethane

Electron Microscopy

Processing
2D projection selection
Software name	EMFIT
3D reconstruction
Actual pixel size	6.48 A/pix
CTF correction method	phase flipping of each micrograph
Method	Spider
Nominal pixel size	6.48 A/pix
Resolution	34.0 A
3D fitting
Method	N- and C-terminal domains were separately fitted into their corresponding cryoEM densities
Refinement Protocol	Rigid body
Refinement Space	REAL
Software name	EMFIT
Target criteria	Sumf
Refine hist
Total atoms	2765
Protein atoms	2765

PDB format

All

pdb3ezk.ent (uncompressed file)

Header only

mmCIF format

mmCIF

XML format

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No-atom

3ezk-noatom.xml.gz

Ext-atom

3ezk-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