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Model of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM

by single particle reconstruction, at 9 A resolution

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#1: Depositted structure unit, Made by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1565, Made by Jmol

#3: Superimposing with EM 3D map: EMDB-1565, Made by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3eq3
TitleModel of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM
DescriptorElongation factor Tu
30S ribosomal protein S12
50S ribosomal protein L11/RNA complex
KeywordsRIBOSOMAL PROTEIN/RNA, protein translation, ternary complex, A/T-tRNA, automated data collection, Antibiotic resistance, Elongation factor, GTP-binding, Membrane, Methylation, Nucleotide-binding, Phosphoprotein, Protein biosynthesis, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, tRNA-binding, RIBOSOMAL PROTEIN-RNA COMPLEX
AuthorsFrank, J., Li, W., Agirrezabala, X.
DateDeposition: 2008-09-30, Release: 2008-12-16
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, Made by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1565, Made by Jmol

#3: Superimposing with EM 3D map: EMDB-1565, Made by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-1565

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Cite: data citing same article

Fit: target map of fitting

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - primary
ArticleEMBO J., Vol. 27, Issue 24, Page 3322-31, Year 2008
TitleRecognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM.
AuthorsWen Li, Xabier Agirrezabala, Jianlin Lei, Lamine Bouakaz, Julie L Brunelle, Rodrigo F Ortiz-Meoz, Rachel Green, Suparna Sanyal, Måns Ehrenberg, Joachim Frank
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
KeywordsCryoelectron Microscopy, Models, Molecular, Nucleic Acid Conformation, Peptide Elongation Factor Tu (chemistry, 3.6.1.-), Protein Structure, Quaternary, Protein Synthesis Inhibitors (pharmacology), Pyridones (pharmacology), RNA, Transfer (chemistry, 9014-25-9), Ribosomes (chemistry), mocimycin
LinksDOI: 10.1038/emboj.2008.243, PubMed: 19020518, PMC: PMC2586802
Components
ID 1 : EF-Tu, P-43
Image
DescriptionElongation factor Tu
Typepolypeptide(L)
Formula weight43239.738 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:83333
Organism scientific: Escherichia coli K12
LinksUniProt: P0A6N1, Sequence view
ID 2 : 30S ribosomal protein S12
Image
Description30S ribosomal protein S12
Typepolypeptide(L)
Formula weight13637.070 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:83333
Organism scientific: Escherichia coli K12
LinksUniProt: P0A7S3, Sequence view
ID 3 : 50S ribosomal protein L11
Image
Description50S ribosomal protein L11
Typepolypeptide(L)
Formula weight14763.286 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:83333
Organism scientific: Escherichia coli K12
LinksUniProt: P0A7J7, Sequence view
ID 4 : tRNA
Image
DescriptiontRNA
Typepolyribonucleotide
Formula weight23844.316 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:83333
Organism scientific: Escherichia coli K12
LinksSequence view
ID 5 : Fragment h18 of the 16S rRNA
Image
DescriptionFragment h18 of the 16S rRNA
Typepolyribonucleotide
Formula weight2871.787 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:83333
Organism scientific: Escherichia coli K12
LinksSequence view
ID 6 : Fragment h44 of the 16S rRNA
Image
DescriptionFragment h44 of the 16S rRNA
Typepolyribonucleotide
Formula weight3601.242 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:83333
Organism scientific: Escherichia coli K12
LinksSequence view
ID 7 : Fragment H43-44 of the 23S rRNA
Image
DescriptionFragment H43-44 of the 23S rRNA
Typepolyribonucleotide
Formula weight15504.381 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:83333
Organism scientific: Escherichia coli K12
LinksSequence view
ID 8 : Fragment H95 of the 23S rRNA
Image
DescriptionFragment H95 of the 23S rRNA
Typepolyribonucleotide
Formula weight9089.521 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:83333
Organism scientific: Escherichia coli K12
LinksSequence view
ID 9 : Fragment H69 of the 23S rRNA
Image
DescriptionFragment H69 of the 23S rRNA
Typepolyribonucleotide
Formula weight5427.324 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:83333
Organism scientific: Escherichia coli K12
LinksSequence view
Sample
Assembly
Aggregation statePARTICLE
CompositionA/T-tRNA(Trp), EF-Tu, L11, S12, fragments h44 and h18 from the 16S rRNA, fragments H43-H44, H69, and H95 from the 23S rRNA
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
Date2007-01-01
Detector
TypeAMT
Processing
2D projection selection
Software nameRSRef
3D reconstruction
MethodSINGLE PARTICLE
Resolution9 A
3D fitting
MethodSee Method in the citation
Refinement Protocolauto
Refinement SpaceREAL
Software nameRSRef
Target criteriacross-correlation coefficient
3D fitting list
3D Fitting ID1
PDB entry ID2AVY, 2AW4, 1QZA, 1OB2
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms844
Nucleic acid atoms187
Protein atoms657
Download
PDB format
Allpdb3eq3.ent.gz
pdb3eq3.ent (uncompressed file)
Header onlypdb3eq3.ent.gz
mmCIF format
mmCIF3eq3.cif.gz
XML format
All3eq3.xml.gz
No-atom3eq3-noatom.xml.gz
Ext-atom3eq3-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.4 MB
.webm (WebM/VP8 format), 3.3 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.2 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.2 MB