PDB-3izg: Bacteriophage T7 prohead shell EM-derived atomic model - EM Navigator

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Bacteriophage T7 prohead shell EM-derived atomic model

by single particle (icosahedral) reconstruction, at 10.9 A resolution

Movie

Orientation:

#1: Biological unit as complete icosahedral assembly, Made by Jmol

#2: Biological unit as icosahedral pentamer, Made by Jmol

#3: Biological unit as icosahedral 23 hexamer, Made by Jmol

#4: Depositted structure unit, Made by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-1321, Made by Jmol

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3izg
Title	Bacteriophage T7 prohead shell EM-derived atomic model
Descriptor	Major capsid protein 10A
Keywords	VIRUS, bacteriophage, virus, capsid maturation, cryoelectron microscopy, morphogenetic intermediate, icosahedral
Authors	Ionel, A., Velazquez-Muriel, J.A., Agirrezabala, X., Luque, D., Cuervo, A., Caston, J.R., Valpuesta, J.M., Martin-Benito, J., Carrascosa, J.L.
Date	Deposition: 2010-10-27, Release: 2010-11-17
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: Biological unit as complete icosahedral assembly, Made by Jmol #2: Biological unit as icosahedral pentamer, Made by Jmol #3: Biological unit as icosahedral 23 hexamer, Made by Jmol #4: Depositted structure unit, Made by Jmol #5: Superimposing with simplified surface model of EM map, EMDB-1321, Made by Jmol
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1321 Fit EMDB-1810 Cite PDB-2xvr Cite Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-1if0 PDB-1yxn PDB-2xyy PDB-3j0d List of similar structure data about Omokage system

Article
Citation - primary
Article	J. Biol. Chem., Vol. 286, Issue 1, Page 234-42, Year 2011
Title	Molecular rearrangements involved in the capsid shell maturation of bacteriophage T7.
Authors	Alina Ionel, Javier A Velázquez-Muriel, Daniel Luque, Ana Cuervo, José R Castón, José M Valpuesta, Jaime Martín-Benito, José L Carrascosa Department of Macromolecular Structure, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
Keywords	Bacteriophage T7 (metabolism), Capsid (chemistry), Capsid Proteins (chemistry), Cryoelectron Microscopy, Models, Molecular, Protein Structure, Tertiary
Links	DOI: 10.1074/jbc.M110.187211, PubMed: 20962334, PMC: PMC3012979
Citation - 1
Article	Structure, Vol. 15, Issue 4, Page 461-72, Year 2007
Title	Quasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold.
Authors	Xabier Agirrezabala, Javier A Velázquez-Muriel, Paulino Gómez-Puertas, Sjors H W Scheres, José M Carazo, José L Carrascosa Department of Structure of Macromolecules, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, Cantoblanco, 28049 Madrid, Spain.
Keywords	Amino Acid Sequence, Bacteriophage T7 (chemistry), Biological Evolution, Capsid (chemistry), DNA (9007-49-2), Molecular Sequence Data, Protein Binding, Protein Folding, Protein Structure, Tertiary
Links	PII: S0969-2126(07)00111-6, DOI: 10.1016/j.str.2007.03.004, PubMed: 17437718

Components
ID 1 : Major capsid protein 10A
Image
Description	Major capsid protein 10A
Type	polymer
Formula weight	36589.906 Da
Number of molecules	7
Source	Method: Isolated from a natural source Common name: Bacteriophage T7 NCBI taxonomy: ID:10760 Organism scientific: Enterobacteria phage T7
Links	UniProt: P19726, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	bacteriophage T7 prohead
Entity assembly
Name	gp10A
Virus entity
Virus host category	Bacteria
Virus host growth cell	Escherichia coli
Virus host species	Escherichia coli
Virus type	Prohead virion
Buffer
Name	50mM Tris-HCl pH:7.7 10mM MgCl2 100mM NaCl
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7.7
Sample support
Details	Quantifoil R2/2 carbon grids
Vitrification
Cryogen name	ETHANE

Electron Microscopy
Imaging
Microscope	model: Tecnai G2
Electron gun
Electron source	Field Emission Gun
Accelerating voltage	200 kV
Electron dose	10 e/A**2
Illumination mode	SPOT SCAN
Lens
Mode	Bright field
Magnification	calibrated: 51600 X, nominal: 50000 X
Cs	nominal: 2.26 mm
Nominal defocus	max: 1000 nm, min: 3000 nm
Specimen holder
Specimen holder	model: GATAN LIQUID NITROGEN
Tilt angle	min: 0 degrees, max: 0 degrees
Detector
Type	KODAK SO163 FILM

Processing
Single particle entity
Symmetry type	ICOSAHEDRAL
3D reconstruction
Actual pixel size	2.72 A/pix
CTF correction method	Wiener filter, defocus groups
Method	Spider
Resolution	10.9 A
Software	Spider
Refine hist
Total atoms	12831
Protein atoms	12831

PDB format

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pdb3izg.ent (uncompressed file)

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mmCIF format

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XML format

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No-atom

3izg-noatom.xml.gz

Ext-atom

3izg-extatom.xml.gz

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5 MB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 2.9 MB .webm (WebM/VP8 format), 3.7 MB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 2.8 MB .webm (WebM/VP8 format), 3.8 MB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 2.6 MB .webm (WebM/VP8 format), 3.5 MB

movie #5

	.mp4 (H.264/MPEG-4 AVC format), 3.8 MB .webm (WebM/VP8 format), 5.6 MB