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Bacteriophage T7 prohead shell EM-derived atomic model

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

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#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 / IDPORTEIN DATA BANK (PDB) / 3izg
TitleBacteriophage T7 prohead shell EM-derived atomic model
DescriptorMajor capsid protein 10A
KeywordsVIRUS, bacteriophage, virus, capsid maturation, cryoelectron microscopy, morphogenetic intermediate, icosahedral
AuthorsIonel, A., Velazquez-Muriel, J.A., Agirrezabala, X., Luque, D., Cuervo, A., Caston, J.R., Valpuesta, J.M., Martin-Benito, J., Carrascosa, J.L.
DateDeposition: 2010-10-27, Release: 2010-11-17
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie 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 viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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List of similar structure data about Omokage system
Article
Citation - primary
ArticleJ. Biol. Chem., Vol. 286, Issue 1, Page 234-42, Year 2011
TitleMolecular rearrangements involved in the capsid shell maturation of bacteriophage T7.
AuthorsAlina 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.
KeywordsBacteriophage T7 (metabolism), Capsid (chemistry), Capsid Proteins (chemistry), Cryoelectron Microscopy, Models, Molecular, Protein Structure, Tertiary
LinksDOI: 10.1074/jbc.M110.187211, PubMed: 20962334, PMC: PMC3012979
Citation - 1
ArticleStructure, Vol. 15, Issue 4, Page 461-72, Year 2007
TitleQuasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold.
AuthorsXabier 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.
KeywordsAmino Acid Sequence, Bacteriophage T7 (chemistry), Biological Evolution, Capsid (chemistry), DNA (9007-49-2), Molecular Sequence Data, Protein Binding, Protein Folding, Protein Structure, Tertiary
LinksPII: S0969-2126(07)00111-6, DOI: 10.1016/j.str.2007.03.004, PubMed: 17437718
Components
ID 1 : Major capsid protein 10A
Image
DescriptionMajor capsid protein 10A
Typepolypeptide(L)
Formula weight36589.906 Da
Number of molecules7
ID1
SourceMethod: Isolated from a natural source
Common name: Bacteriophage T7
NCBI taxonomy: ID:10760
Organism scientific: Enterobacteria phage T7
LinksUniProt: P19726, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Namebacteriophage T7 prohead
Entity assembly
Assembly-ID1
Namegp10A
Virus entity
Virus host categoryBacteria
Virus host growth cellEscherichia coli
Virus host speciesEscherichia coli
Virus typeProhead virion
Buffer
Name50mM Tris-HCl pH:7.7 10mM MgCl2 100mM NaCl
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.7
Sample support
DetailsQuantifoil R2/2 carbon grids
Vitrification
Cryogen nameETHANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: Tecnai G2
Electron gun
Electron sourceField Emission Gun
Accelerating voltage200 kV
Electron dose10 e/A**2
Illumination modeSPOT SCAN
Lens
ModeBright field
MagnificationCalibrated: 51600 X, Nominal: 50000 X
CsNominal: 2.26 mm
Nominal defocusMax: 1000 nm, Min: 3000 nm
Specimen holder
Specimen holderModel: GATAN LIQUID NITROGEN
Tilt angleMin: 0 degrees, Max: 0 degrees
Detector
TypeKODAK SO163 FILM
Processing
Single particle entity
Symmetry typeICOSAHEDRAL
3D reconstruction
Actual pixel size2.72 A/pix
CTF correction methodWiener filter, defocus groups
MethodSpider
Resolution10.9 A
SoftwareSpider
3D fitting list
3D Fitting ID1
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms12831
Protein atoms12831
Download
PDB format
Allpdb3izg.ent.gz
pdb3izg.ent (uncompressed file)
Header onlypdb3izg.ent.gz
mmCIF format
mmCIF3izg.cif.gz
XML format
All3izg.xml.gz
No-atom3izg-noatom.xml.gz
Ext-atom3izg-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