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Mammalian mitochondrial translation initiation factor 2

by single particle reconstruction, at 10.8 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1855, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3izy
TitleMammalian mitochondrial translation initiation factor 2
DescriptorProtein/RNA complex
KeywordsRNA, RIBOSOMAL PROTEIN, translation initiation factor 2, IF2, E coli
AuthorsYassin, A.S., Haque, E, Datta, P.P, Elmore, K, Banavali, N.K., Spremulli, L.L., Agrawal, R.K.
DateDeposition: 2011-01-19, Release: 2011-03-23
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-1855, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-1855

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Article
Citation - primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 108, Issue 10, Page 3918-23, Year 2011
TitleInsertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1.
AuthorsAymen S Yassin, Md Emdadul Haque, Partha P Datta, Kevin Elmore, Nilesh K Banavali, Linda L Spremulli, Rajendra K Agrawal
Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA.
KeywordsAmino Acids (chemistry), Animals, Cattle, Cryoelectron Microscopy, Eubacterium (metabolism), Eukaryotic Initiation Factor-1 (chemistry), Eukaryotic Initiation Factor-2 (chemistry), Models, Molecular, Oxidative Phosphorylation, Ribosomes (metabolism)
LinksDOI: 10.1073/pnas.1017425108, PubMed: 21368145, PMC: PMC3053986
Components
ID 1 : tRNA-Phe
Image
DescriptiontRNA-Phe
Typepolyribonucleotide
Formula weight24518.730 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Common name: cow
NCBI taxonomy: ID:9913
Organism scientific: Bos taurus

LinksSequence view
ID 2 : IF-2(Mt), IF-2Mt, IF2(mt)
Image
DescriptionTranslation initiation factor IF-2, mitochondrial
Typepolypeptide(L)
Formula weight59602.836 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Common name: cow
NCBI taxonomy: ID:9913
Organism scientific: Bos taurus
LinksUniProt: P46198, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameMammalian mitochondrial translation initiation factor 2 interaction with tRNA
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: Tecnai F20
Electron gun
Electron sourceFEG
Accelerating voltage200 kV
Lens
MagnificationCalibrated: 50760 X, Nominal: 50000 X
Detector
TypeKodak S0163
Processing
Single particle entity
Symmetry typeASYMMETRIC
3D reconstruction
Actual pixel size2.76 A/pix
CTF correction methodEvery Micrograph
MethodBack Projection
Number of particles121742
Resolution10.8 A
SoftwareSpider
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms5802
Nucleic acid atoms1622
Protein atoms4180
Download
PDB format
Allpdb3izy.ent.gz
pdb3izy.ent (uncompressed file)
Header onlypdb3izy.ent.gz
mmCIF format
mmCIF3izy.cif.gz
XML format
All3izy.xml.gz
No-atom3izy-noatom.xml.gz
Ext-atom3izy-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.4 MB
.webm (WebM/VP8 format), 3.4 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.3 MB