PDB-2ob7: Structure of tmRNA-(SmpB)2 complex as inferred from cryo-EM

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 2ob7
Title	Structure of tmRNA-(SmpB)2 complex as inferred from cryo-EM
Descriptor	SsrA-binding protein/RNA Complex
Keywords	RNA BINDING PROTEIN/RNA, tmRNA, SmpB, RNA BINDING PROTEIN-RNA COMPLEX
Authors	Frank, J., Felden, B., Gillet, R., Li, W.
Date	Deposition: 2006-12-18, Release: 2007-01-23
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-1310, Made by Jmol #3: Superimposing with EM 3D map: EMDB-1310, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1310 CiteFit EMDB-1312 Cite EMDB-1311 PDB-1n34 PDB-1pv6 PDB-1q2b Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram EMDB-1211 EMDB-1092 EMDB-1318 PDB-3ize List of similar structure data about Omokage system

Article
Citation - primary
Article	J. Biol. Chem., Vol. 282, Issue 9, Page 6356-63, Year 2007
Title	Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1.
Authors	Reynald Gillet, Sukhjit Kaur, Wen Li, Marc Hallier, Brice Felden, Joachim Frank Université de Rennes I, IFR 140, UPRES JE 2311, INSERM U835 Biochimie Pharmaceutique, 2 Avenue du Professeur Léon Bernard, 35043 Rennes, France.
Keywords	Cryoelectron Microscopy, Macromolecular Substances (metabolism), Protein Binding, Protein Biosynthesis, RNA, Transfer (metabolism, 9014-25-9), RNA-Binding Proteins (metabolism), Ribosomal Proteins (metabolism), Thermus thermophilus (genetics), ribosomal protein S1, small protein B
Links	DOI: 10.1074/jbc.M609658200, PubMed: 17179154, PMC: PMC3230075
Citation - 1
Article	Proc.Natl.Acad.Sci.USA, Vol. 103, Page: 16484 - 16489, Year: 2006,
Title	Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome
Authors	Kaur, S., Gillet, R., Li, W., Gursky, R., Frank, J.
Citation - 2
Article	Science, Vol. 300, Page: 127 - 130, Year: 2003,
Title	Visualizing tmRNA entry into a stalled ribosome
Authors	Valle, M., Gillet, R., Kaur, K., Henne, A., Ramakrishnan, V., Frank, J.

Components
ID 1 : transfer-messenger RNA
Image
Description	transfer-messenger RNA
Type	polymer
Formula weight	105729.453 Da
Number of molecules	1
Source	Method: Isolated from a natural source Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	Sequence view
ID 2 : 16S ribosomal RNA
Image
Description	16S ribosomal RNA
Type	polymer
Formula weight	27987.885 Da
Number of molecules	1
Details	helix 44 of 30S ribosomal subunit
Source	Method: Isolated from a natural source Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	Sequence view
ID 3 : SsrA-binding protein
Image
Description	SsrA-binding protein
Type	polymer
Formula weight	18440.992 Da
Number of molecules	2
Source	Method: Isolated from a natural source Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Details	see Experimental Procedures in Kaur et al. (PNAS). [Deposition refers to structure of tmRNA-(SmpB)2 complex derived by fitting of EM map from Kaur et al. Fitting was modified in Gillet et al.]
Name	Binding of transfer messenger RNA with two SmpBs
Entity assembly
Name	Pre-accommodated ribosomal trans-translation complex: T. thermophilus 70S-mRNA-(P-site tRNA)-tmRNA-(SmpB)2-(EF-Tu)-GDP-kirromycin
Buffer
Name	polimix
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7.5
Sample concentration	32 mg/ml
Sample support
Details	This grid plus sample was kept at -80 degree C for several days before use.
Vitrification
Details	Blot for 5 seconds before plunging. Rapid plunge freezing in liquid ethane.

Processing
2D projection selection
Software name	O
Single particle entity
Symmetry type	ASYMMETRIC
3D reconstruction
CTF correction method	CTF correction of each defocus group reconstruction, by Wiener filtering
Method	single particle reconstruction
Nominal pixel size	2.82 A/pix
Resolution	13.6 A
3D fitting
Method	manual fitting using stereo visualization
Refinement Protocol	Manual
Refinement Space	REAL
Software name	O
Refine hist
Total atoms	651
Nucleic acid atoms	414
Protein atoms	237