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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 12.0 A resolution

Movie

Orientation:

#1: Depositted structure unit, Made by Jmol

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

#3: With PDB-1pdf, PDB-1pdi, PDB-1pdj, PDB-1pdl, PDB-1pdm, PDB-1pdp, PDB-2fl8, Made 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), Made by UCSF CHIMERA

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3h3w
Title	Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 dome-shaped baseplate
Descriptor	Baseplate structural protein Gp6
Keywords	VIRAL PROTEIN, viral structural protein, Virion
Authors	Aksyuk, A.A., Leiman, P.G., Shneider, M.M., Mesyanzhinov, V.V., Rossmann, M.G.
Date	Deposition: 2009-04-17, Release: 2009-05-19
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 simplified surface model of EM map, EMDB-1048, Made by Jmol #3: With PDB-1pdf, PDB-1pdi, PDB-1pdj, PDB-1pdl, PDB-1pdm, PDB-1pdp, PDB-2fl8, Made 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), Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1048 Fit PDB-3h2t Cite PDB-3h3y Cite Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-3h3y EMDB-1603 PDB-3foh List of similar structure data about Omokage system

Article
Citation - primary
Article	Structure, Vol. 17, Issue 6, Page 800-8, Year 2009
Title	The structure of gene product 6 of bacteriophage T4, the hinge-pin of the baseplate.
Authors	Anastasia 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.
Keywords	Amino 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)
Links	PII: S0969-2126(09)00185-3, DOI: 10.1016/j.str.2009.04.005, PubMed: 19523898

Components
ID 1 : Baseplate wedge protein 6
Image
Description	Baseplate structural protein Gp6
Type	polymer
Fragment	gene product 6 deletion fragment
Mutation	residues 334-660
Formula weight	38304.887 Da
Number of molecules	12
Source	Method: Isolated from a genetically manipulated source Gene: Bacteriophage T4, 6, ID:10665, Enterobacteria phage T4 Host: Escherichia coli , BL21(DE3)
Links	UniProt: P19060, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Entity assembly
Details	assembly of gp6 in the dome-shaped baseplate of bacteriophage T4
Name	ring of 12 molecules of gene product 6
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7
Sample concentration	5 mg/ml

Electron Microscopy
Imaging
Microscope	model: FEI/PHILIPS CM300FEG/T
Date	2001-01-30
Electron gun
Electron source	FIELD EMISSION GUN
Electron dose	25 e/A**2
Illumination mode	FLOOD BEAM
Lens
Magnification	calibrated: 47000 X, nominal: 45000 X
Nominal defocus	max: 5000 nm, min: 1200 nm
Specimen holder
Specimen holder	model: GATAN LIQUID NITROGEN, type: 626 Single Tilt Cryotransfer System

Processing
Reflection
D resolution high	12.0
Entry id	3H3W
ID	1
2D projection selection
Software name	COLORES from the SITUS program package was used for the fitting
Single particle entity
Symmetry type	CYCLIC
3D fitting
Refinement Space	REAL
Software name	COLORES from the SITUS program package was used for the fitting
Refine
Ls d res high	12.0 A
ID	1
Refine hist
D res high	12.0
Total atoms	31380
Protein atoms	31380

PDB format

All

pdb3h3w.ent (uncompressed file)

Header only

mmCIF format

mmCIF

XML format

All

No-atom

3h3w-noatom.xml.gz

Ext-atom

3h3w-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