PDB-3deg: Complex of elongating Escherichia coli 70S ribosome and...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3deg
Title	Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP
Descriptor	RNA binding protein/RNA Complex
Keywords	RIBOSOME, ribosome, translation, LepA, EF4, GTP-binding, Membrane, Nucleotide-binding, Antibiotic resistance, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, tRNA-binding, Methylation
Authors	Connell, S.R., Topf, M., Qin, Y., Wilson, D.N., Mielke, T., Fucini, P., Nierhaus, K.H., Spahn, C.M.T.
Date	Deposition: 2008-06-10, Release: 2008-08-19
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-1524, Made by Jmol #3: Superimposing with EM 3D map: EMDB-1524, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1524 CiteFit Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram EMDB-2189 PDB-3j1n EMDB-1438 EMDB-2193 EMDB-2192 List of similar structure data about Omokage system

Article
Citation - primary
Article	Nat. Struct. Mol. Biol., Vol. 15, Issue 9, Page 910-5, Year 2008
Title	A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation.
Authors	Sean R Connell, Maya Topf, Yan Qin, Daniel N Wilson, Thorsten Mielke, Paola Fucini, Knud H Nierhaus, Christian M T Spahn Institut für Medizinische Physik und Biophysik, Charite-Universitätsmedizin Berlin, Ziegelstrasse 5-9, 10117-Berlin, Germany.
Keywords	Biological Transport, Active, Escherichia coli (metabolism), Escherichia coli Proteins (chemistry), Guanosine Triphosphate (metabolism, 86-01-1), Hydrolysis, LepA protein, E coli, Macromolecular Substances, Models, Molecular, RNA, Bacterial (chemistry), RNA, Transfer (chemistry, 9014-25-9), Ribosomes (chemistry), Transcriptional Elongation Factors (chemistry)
Links	PubMed: 19172743

Components
ID 1 : A/L-tRNA
Image
Description	A/L-tRNA
Type	polymer
Formula weight	24890.293 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 2 : P-tRNA
Image
Description	P-tRNA
Type	polymer
Formula weight	24816.971 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 3 : 30S RNA helix 8
Image
Description	30S RNA helix 8
Type	polymer
Formula weight	5161.180 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 4 : 30S RNA helix 14
Image
Description	30S RNA helix 14
Type	polymer
Formula weight	3827.362 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 5 : 50S RNA helix 42-44
Image
Description	50S RNA helix 42-44
Type	polymer
Formula weight	22580.658 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 6 : 50S RNA helix 95
Image
Description	50S RNA helix 95
Type	polymer
Formula weight	9394.705 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 7 : 50S RNA helix 71
Image
Description	50S RNA helix 71
Type	polymer
Formula weight	5765.491 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 8 : 50S RNA helix 92
Image
Description	50S RNA helix 92
Type	polymer
Formula weight	4745.866 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 9 : GTP-binding protein lepA
Image
Description	GTP-binding protein lepA
Type	polymer
Fragment	EF4
Formula weight	60477.324 Da
Number of molecules	1
Source	Method: Isolated from a genetically manipulated source Gene: K12, lepA, b2569, JW2553, ID:83333, Escherichia coli Host: ID:562, Escherichia coli, Bl21(DE3), plasmid Plasmid name: pET14b
Links	UniProt: P60785, Sequence view
ID 10 : 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 Strain: K12
Links	UniProt: P0A7S3, Sequence view
ID 11 : 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 Strain: K12
Links	UniProt: P0A7J7, Sequence view

Sample

Electron Microscopy
Detector
Type	KODAK SO163 FILM

Processing
2D projection selection
Software name	Situs, Mod-EM, Flex-EM
3D reconstruction
Resolution	10.9 A
3D fitting
Refinement Protocol	rigid body and flexible fitting
Software name	Situs, Mod-EM, Flex-EM
3D fitting list
PDB entry ID	2i2p, 2i2t, 3cb4, 1gix, 2j01 PDB-2i2p PDB-2i2t PDB-3cb4 PDB-1gix PDB-2j01
Refine hist
Total atoms	12950
Nucleic acid atoms	6721
Protein atoms	6229