PDB-2om7: Structural Basis for Interaction of the Ribosome with t...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 2om7
Title	Structural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors
Descriptor	RNA binding protein/RNA Complex
Keywords	RIBOSOME, RNA-Protein Complex
Authors	Connell, S.R., Wilson, D.N., Rost, M., Schueler, M., Giesebrecht, J., Dabrowski, M., Mielke, T., Fucini, P., Spahn, C.M.T.
Date	Deposition: 2007-01-21, Release: 2008-01-15
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-1315, Made by Jmol #3: Superimposing with EM 3D map: EMDB-1315, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1315 CiteFit PDB-1fnm PDB-1wdt PDB-1yl3 PDB-1yl4 PDB-2j00 PDB-2j01 Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram EMDB-1196 EMDB-2204 EMDB-2226 List of similar structure data about Omokage system

Article
Citation - primary
Article	Mol. Cell, Vol. 25, Issue 5, Page 751-64, Year 2007
Title	Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
Authors	Sean R Connell, Chie Takemoto, Daniel N Wilson, Hongfei Wang, Kazutaka Murayama, Takaho Terada, Mikako Shirouzu, Maximilian Rost, Martin Schüler, Jan Giesebrecht, Marylena Dabrowski, Thorsten Mielke, Paola Fucini, Shigeyuki Yokoyama, Christian M T Spahn Institut für Medizinische Physik und Biophysik, Charite-Universitätsmedizin Berlin, Ziegelstrasse 5-9, 10117 Berlin, Germany.
Keywords	Binding Sites, Cryoelectron Microscopy, Crystallography, X-Ray, Guanosine Triphosphate (metabolism, 86-01-1), Guanylyl Imidodiphosphate (metabolism, 34273-04-6), Models, Molecular, Peptide Elongation Factor G (chemistry), Protein Structure, Secondary, Protein Structure, Tertiary, Ribosomes (chemistry), Structure-Activity Relationship, Thermus thermophilus (metabolism)
Links	PII: S1097-2765(07)00050-0, DOI: 10.1016/j.molcel.2007.01.027, PubMed: 17349960

Components
ID 1 : Fragment of 16S rRNA (h14)
Image
Description	Fragment of 16S rRNA (h14)
Type	polymer
Formula weight	3827.362 Da
Number of molecules	1
Source	Method: Isolated from a natural source Details: 16S rRNA Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	Sequence view
ID 2 : Fragment of 16S rRNA (h15)
Image
Description	Fragment of 16S rRNA (h15)
Type	polymer
Formula weight	9048.513 Da
Number of molecules	1
Source	Method: Isolated from a natural source Details: 16S rRNA Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	Sequence view
ID 3 : Fragment of 16S rRNA (h44)
Image
Description	Fragment of 16S rRNA (h44)
Type	polymer
Formula weight	31208.826 Da
Number of molecules	1
Source	Method: Isolated from a natural source Details: 16S rRNA Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	GenBank: 118505352, Sequence view
ID 4 : 16S ribosomal RNA (H5)
Image
Description	16S ribosomal RNA (H5)
Type	polymer
Formula weight	98293.047 Da
Number of molecules	1
Source	Method: Isolated from a natural source Details: 16S rRNA Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	GenBank: 48256, Sequence view
ID 5 : Fragment of23S rRNA (H95)
Image
Description	Fragment of23S rRNA (H95)
Type	polymer
Formula weight	9378.706 Da
Number of molecules	1
Source	Method: Isolated from a natural source Details: 23S rRNA Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	Sequence view
ID 6 : Fragment of23S rRNA (H68)
Image
Description	Fragment of23S rRNA (H68)
Type	polymer
Formula weight	17631.746 Da
Number of molecules	1
Source	Method: Isolated from a natural source Details: 23S rRNA Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	GenBank: 37223182, Sequence view
ID 7 : Fragment of23S rRNA (H89)
Image
Description	Fragment of23S rRNA (H89)
Type	polymer
Formula weight	13540.153 Da
Number of molecules	1
Source	Method: Isolated from a natural source Details: 23S rRNA Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	Sequence view
ID 8 : Fragment of23S rRNA (H42-44)
Image
Description	Fragment of23S rRNA (H42-44)
Type	polymer
Formula weight	18710.258 Da
Number of molecules	1
Source	Method: Isolated from a natural source Details: 23S rRNA Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	GenBank: 37223182, Sequence view
ID 9 : Fragment of23S rRNA (H76)
Image
Description	Fragment of23S rRNA (H76)
Type	polymer
Formula weight	33148.875 Da
Number of molecules	1
Source	Method: Isolated from a natural source Details: 23S rRNA Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	GenBank: 37223182, Sequence view
ID 10 : p/E-tRNA
Image
Description	p/E-tRNA
Type	polymer
Formula weight	23728.281 Da
Number of molecules	1
Source	Method: Isolated from a natural source Details: tRNA Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	Sequence view
ID 11 : 30S ribosomal protein S12
Image
Description	30S ribosomal protein S12
Type	polymer
Formula weight	14920.887 Da
Number of molecules	1
Source	Method: Isolated from a natural source Details: Small ribosomal subunit protein S12 Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	UniProt: P17293, Sequence view
ID 12 : 50S ribosomal protein L1
Image
Description	50S ribosomal protein L1
Type	polymer
Formula weight	24872.914 Da
Number of molecules	1
Source	Method: Isolated from a natural source Details: Large ribosomal subunit protein L1 Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	UniProt: Q5SLP7, Sequence view
ID 13 : EF-G
Image
Description	Elongation factor G
Type	polymer
Formula weight	76977.914 Da
Number of molecules	1
Source	Method: Isolated from a genetically manipulated source Gene: Thermus, fusA, fus, ID:274, Thermus thermophilus Host: Escherichia, Escherichia coli , ID:469008, Escherichia coli BL21(DE3), BL21(DE3)
Links	UniProt: P13551, Sequence view
ID 14 : 30S ribosomal protein S2
Image
Description	30S ribosomal protein S2
Type	polymer
Formula weight	29317.918 Da
Number of molecules	1
Source	Method: Isolated from a natural source Details: Small ribosomal subunit protein S2 Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	UniProt: P80371, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	complex of Thermus thermophilus 70S ribosomes and EF-G-GMPPNP
Entity assembly
GO-ID	GO:0015935
InterPro-ID	IPR:005679
Name	30S ribosomal protein S12
Entity assembly
GO-ID	GO:0006412
InterPro-ID	IPR:002143
Name	50S ribosomal protein L1
Entity assembly
GO-ID	GO:0006414
InterPro-ID	IPR:004540
Name	Elongation factor G
Entity assembly
GO-ID	GO:0003735
InterPro-ID	IPR:001865
Name	30S ribosomal protein S2
Buffer
Name	0.3 mM GMPPNP, 10 mM Hepes-KOH (pH 7.8), 10 mM Mg acetate, 60 mM NH4Cl, and 6 mM B-mercaptoethanol
Sample preparation
pH	7.8
Vitrification
Cryogen name	ETHANE
Humidity	95
Instrument	Vitrobot
Temp	277 Kelvin

Electron Microscopy
Imaging
Microscope	model: FEI TECNAI F30
Electron gun
Electron source	FIELD EMISSION GUN
Accelerating voltage	300 kV
Electron dose	19 e/A**2
Illumination mode	FLOOD BEAM
Lens
Mode	BRIGHT FIELD
Magnification	nominal: 39000 X
Nominal defocus	max: 4000 nm, min: 800 nm
Specimen holder
Specimen holder	type: Eucentric
Detector
Type	Kodak SO163 film

Processing
2D projection selection
Software name	SPIDER
3D reconstruction
CTF correction method	defocus groups
Details	The geometry of linkages between some residues in chains J, M and L are distorted. They were not resolved based on the data used for solving this structure.
Resolution	7.3 A
3D fitting
Method	Rigid Body
Software name	Situs
Refine hist
Total atoms	19031
Nucleic acid atoms	9891
Protein atoms	9140
Software
Classification	refinement
Name	SPIDER