PDB-3eq3: Model of tRNA(Trp)-EF-Tu in the ribosomal pre-accommoda...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3eq3
Title	Model of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM
Descriptor	Elongation factor Tu 30S ribosomal protein S12 50S ribosomal protein L11/RNA complex
Keywords	RIBOSOMAL 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
Authors	Frank, J., Li, W., Agirrezabala, X.
Date	Deposition: 2008-09-30, Release: 2008-12-16
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-1565, Made by Jmol #3: Superimposing with EM 3D map: EMDB-1565, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1565 CiteFit EMDB-1564 Cite PDB-3ep2 Cite PDB-3eq4 Cite PDB-1ob2 PDB-1qza PDB-2avy PDB-2aw4 Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-3ep2 PDB-3eq4 PDB-3j2k EMDB-1788 List of similar structure data about Omokage system

Article
Citation - primary
Article	EMBO J., Vol. 27, Issue 24, Page 3322-31, Year 2008
Title	Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM.
Authors	Wen 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.
Keywords	Cryoelectron 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
Links	DOI: 10.1038/emboj.2008.243, PubMed: 19020518, PMC: PMC2586802

Components
ID 1 : EF-Tu, P-43
Image
Description	Elongation factor Tu
Type	polymer
Formula weight	43239.738 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:83333 Organism scientific: Escherichia coli K12
Links	UniProt: P0A6N1, Sequence view
ID 2 : 30S ribosomal protein S12
Image
Description	30S ribosomal protein S12
Type	polymer
Formula weight	13637.070 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:83333 Organism scientific: Escherichia coli K12
Links	UniProt: P0A7S3, Sequence view
ID 3 : 50S ribosomal protein L11
Image
Description	50S ribosomal protein L11
Type	polymer
Formula weight	14763.286 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:83333 Organism scientific: Escherichia coli K12
Links	UniProt: P0A7J7, Sequence view
ID 4 : tRNA
Image
Description	tRNA
Type	polymer
Formula weight	23844.316 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:83333 Organism scientific: Escherichia coli K12
Links	Sequence view
ID 5 : Fragment h18 of the 16S rRNA
Image
Description	Fragment h18 of the 16S rRNA
Type	polymer
Formula weight	2871.787 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:83333 Organism scientific: Escherichia coli K12
Links	Sequence view
ID 6 : Fragment h44 of the 16S rRNA
Image
Description	Fragment h44 of the 16S rRNA
Type	polymer
Formula weight	3601.242 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:83333 Organism scientific: Escherichia coli K12
Links	Sequence view
ID 7 : Fragment H43-44 of the 23S rRNA
Image
Description	Fragment H43-44 of the 23S rRNA
Type	polymer
Formula weight	15504.381 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:83333 Organism scientific: Escherichia coli K12
Links	Sequence view
ID 8 : Fragment H95 of the 23S rRNA
Image
Description	Fragment H95 of the 23S rRNA
Type	polymer
Formula weight	9089.521 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:83333 Organism scientific: Escherichia coli K12
Links	Sequence view
ID 9 : Fragment H69 of the 23S rRNA
Image
Description	Fragment H69 of the 23S rRNA
Type	polymer
Formula weight	5427.324 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:83333 Organism scientific: Escherichia coli K12
Links	Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Composition	A/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

Electron Microscopy
Imaging
Date	2007-01-01
Detector
Type	AMT

Processing
2D projection selection
Software name	RSRef
3D reconstruction
Method	SINGLE PARTICLE
Resolution	9 A
3D fitting
Method	See Method in the citation
Refinement Protocol	auto
Refinement Space	REAL
Software name	RSRef
Target criteria	cross-correlation coefficient
3D fitting list
PDB entry ID	2AVY, 2AW4, 1QZA, 1OB2 PDB-2avy PDB-2aw4 PDB-1qza PDB-1ob2
Refine hist
Total atoms	844
Nucleic acid atoms	187
Protein atoms	657