PDB-2xux: tRNA translocation on the 70S ribosome: the post- trans...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 2xux
Title	tRNA translocation on the 70S ribosome: the post- translocational translocation intermediate TI(POST)
Descriptor	50S RIBOSOMAL PROTEIN L27 50S RIBOSOMAL PROTEIN L28 50S RIBOSOMAL PROTEIN L29 50S RIBOSOMAL PROTEIN L30 50S RIBOSOMAL PROTEIN L31 50S RIBOSOMAL PROTEIN L32 50S RIBOSOMAL PROTEIN L33 50S RIBOSOMAL PROTEIN L34 50S RIBOSOMAL PROTEIN L35 50S RIBOSOMAL PROTEIN L36 50S RIBOSOMAL PROTEIN L1 50S RIBOSOMAL PROTEIN L4 50S RIBOSOMAL PROTEIN L5 50S RIBOSOMAL PROTEIN L6 50S RIBOSOMAL PROTEIN L11 50S RIBOSOMAL PROTEIN L7/L12 50S RIBOSOMAL PROTEIN L13 50S RIBOSOMAL PROTEIN L14 50S RIBOSOMAL PROTEIN L15 50S RIBOSOMAL PROTEIN L16 50S RIBOSOMAL PROTEIN L17 50S RIBOSOMAL PROTEIN L18 50S RIBOSOMAL PROTEIN L19 50S RIBOSOMAL PROTEIN L20 50S RIBOSOMAL PROTEIN L21 50S RIBOSOMAL PROTEIN L22 50S RIBOSOMAL PROTEIN L23 50S RIBOSOMAL PROTEIN L24 50S RIBOSOMAL PROTEIN L25
Keywords	RIBOSOME, TRANSLATION, ELONGATION CYCLE, TRNA TRANSLOCATION
Authors	Ratje, A.H., Loerke, J., Mikolajka, A., Bruenner, M., Hildebrand, P.W., Starosta, A.L., Doenhoefer, A., Connell, S.R., Fucini, P., Mielke, T., Whitford, P.C., Onuchic, J.N., Yu, Y., Sanbonmatsu, K.Y., Hartmann, R.K., Penczek, P.A., Wilson, D.N., Spahn, C.M.T.
Date	Deposition: 2010-10-21, Release: 2010-12-08
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-1799, Made by Jmol #3: With PDB-2xuy, Made by Jmol
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1799 CiteFit PDB-2xuy CiteSplit EMDB-1798 Cite PDB-2xsy Cite PDB-2xtg Cite PDB-1ctf PDB-1gd8 PDB-1giy PDB-1rqs PDB-1rqt PDB-1rqu PDB-1rqv PDB-1v8q PDB-1wki PDB-1yl3 PDB-2b66 PDB-2b9n PDB-2b9p PDB-2bcw PDB-2j01 PDB-2j03 PDB-2jl6 PDB-2jl8 PDB-2v47 PDB-2v49 PDB-2wdi PDB-2wdj PDB-2wdl PDB-2wdn PDB-2wh2 PDB-2wh4 PDB-2wro PDB-2wrr PDB-2x9s PDB-2x9u PDB-2xg0 PDB-2xg2 PDB-2xqe Cite: data citing same article Fit: target map of fitting Split: split data constructing the same model
Similar strucutres (beta)	Diagram PDB-2xtg PDB-3izt PDB-3izu PDB-3e1d PDB-3fin PDB-3j11 List of similar structure data about Omokage system

Article
Citation - primary
Article	Nature, Vol. 468, Issue 7324, Page 713-6, Year 2010
Title	Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites.
Authors	Andreas H Ratje, Justus Loerke, Aleksandra Mikolajka, Matthias Brünner, Peter W Hildebrand, Agata L Starosta, Alexandra Dönhöfer, Sean R Connell, Paola Fucini, Thorsten Mielke, Paul C Whitford, José N Onuchic, Yanan Yu, Karissa Y Sanbonmatsu, Roland K Hartmann, Pawel A Penczek, Daniel N Wilson, 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 Diphosphate (chemistry, 146-91-8), Models, Molecular, Movement, Peptide Elongation Factor G (chemistry), Protein Biosynthesis, Protein Conformation, Protein Subunits (chemistry), RNA, Transfer (chemistry, 9014-25-9), Ribosome Subunits, Small, Bacterial (chemistry), Thermus thermophilus (chemistry)
Links	DOI: 10.1038/nature09547, PubMed: 21124459, PMC: PMC3272701

Components
ID 1 : 50S RIBOSOMAL PROTEIN L27
Image
Description	50S RIBOSOMAL PROTEIN L27
Type	polymer
Formula weight	9529.156 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: P60493, Sequence view
ID 2 : 50S RIBOSOMAL PROTEIN L28
Image
Description	50S RIBOSOMAL PROTEIN L28
Type	polymer
Formula weight	11004.259 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: P60494, Sequence view
ID 3 : TL5
Image
Description	50S RIBOSOMAL PROTEIN L29
Type	polymer
Formula weight	8670.339 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SHP6, Sequence view
ID 4 : 50S RIBOSOMAL PROTEIN L30
Image
Description	50S RIBOSOMAL PROTEIN L30
Type	polymer
Formula weight	6799.196 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SHQ6, Sequence view
ID 5 : 50S RIBOSOMAL PROTEIN L31
Image
Description	50S RIBOSOMAL PROTEIN L31
Type	polymer
Formula weight	8300.601 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SJE1, Sequence view
ID 6 : 50S RIBOSOMAL PROTEIN L32
Image
Description	50S RIBOSOMAL PROTEIN L32
Type	polymer
Formula weight	6722.098 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: P80339, Sequence view
ID 7 : 50S RIBOSOMAL PROTEIN L33
Image
Description	50S RIBOSOMAL PROTEIN L33
Type	polymer
Formula weight	6632.944 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: P35871, Sequence view
ID 8 : 50S RIBOSOMAL PROTEIN L34
Image
Description	50S RIBOSOMAL PROTEIN L34
Type	polymer
Formula weight	6132.502 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: P80340, Sequence view
ID 9 : 50S RIBOSOMAL PROTEIN L35
Image
Description	50S RIBOSOMAL PROTEIN L35
Type	polymer
Formula weight	7506.249 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SKU1, Sequence view
ID 10 : RIBOSOMAL PROTEIN B
Image
Description	50S RIBOSOMAL PROTEIN L36
Type	polymer
Formula weight	4435.438 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SHR2, Sequence view
ID 11 : 23S RIBOSOMAL RNA
Image
Description	23S RIBOSOMAL RNA
Type	polymer
Formula weight	947936.750 Da
Number of molecules	1
Details	CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4
Source	Method: Obtained synthetically
Links	GenBank: NC_006461, Sequence view
ID 12 : 5S RIBOSOMAL RNA
Image
Description	5S RIBOSOMAL RNA
Type	polymer
Formula weight	39540.836 Da
Number of molecules	1
Source	Method: Obtained synthetically
Links	GenBank: NC_006461, Sequence view
ID 13 : 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 Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SLP7, Sequence view
ID 14 : 50S RIBOSOMAL PROTEIN L2
Image
Description	50S RIBOSOMAL PROTEIN L2
Type	polymer
Formula weight	30532.797 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: P60405, Sequence view
ID 15 : 50S RIBOSOMAL PROTEIN L3
Image
Description	50S RIBOSOMAL PROTEIN L3
Type	polymer
Formula weight	22450.389 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SHN8, Sequence view
ID 16 : L1E
Image
Description	50S RIBOSOMAL PROTEIN L4
Type	polymer
Formula weight	23272.105 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SHN9, Sequence view
ID 17 : 50S RIBOSOMAL PROTEIN L5
Image
Description	50S RIBOSOMAL PROTEIN L5
Type	polymer
Formula weight	21061.762 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SHQ0, Sequence view
ID 18 : 50S RIBOSOMAL PROTEIN L6
Image
Description	50S RIBOSOMAL PROTEIN L6
Type	polymer
Formula weight	19569.104 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SHQ3, Sequence view
ID 19 : 50S RIBOSOMAL PROTEIN L11
Image
Description	50S RIBOSOMAL PROTEIN L11
Type	polymer
Formula weight	15526.242 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SLP6, Sequence view
ID 20 : 50S RIBOSOMAL PROTEIN L7/L12
Image
Description	50S RIBOSOMAL PROTEIN L7/L12
Type	polymer
Formula weight	12309.269 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:83333 Organism scientific: ESCHERICHIA COLI Strain: K-12
Links	UniProt: P0A7K2, Sequence view
ID 21 : 50S RIBOSOMAL PROTEIN L13
Image
Description	50S RIBOSOMAL PROTEIN L13
Type	polymer
Formula weight	15928.042 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: P60488, Sequence view
ID 22 : 50S RIBOSOMAL PROTEIN L14
Image
Description	50S RIBOSOMAL PROTEIN L14
Type	polymer
Formula weight	13323.730 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SHP8, Sequence view
ID 23 : 50S RIBOSOMAL PROTEIN L15
Image
Description	50S RIBOSOMAL PROTEIN L15
Type	polymer
Formula weight	16319.272 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SHQ7, Sequence view
ID 24 : 50S RIBOSOMAL PROTEIN L16
Image
Description	50S RIBOSOMAL PROTEIN L16
Type	polymer
Formula weight	15994.034 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: P60489, Sequence view
ID 25 : 50S RIBOSOMAL PROTEIN L17
Image
Description	50S RIBOSOMAL PROTEIN L17
Type	polymer
Formula weight	13750.277 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q9Z9H5, Sequence view
ID 26 : TL24
Image
Description	50S RIBOSOMAL PROTEIN L18
Type	polymer
Formula weight	12639.966 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SHQ4, Sequence view
ID 27 : 50S RIBOSOMAL PROTEIN L19
Image
Description	50S RIBOSOMAL PROTEIN L19
Type	polymer
Formula weight	17188.984 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: P60490, Sequence view
ID 28 : 50S RIBOSOMAL PROTEIN L20
Image
Description	50S RIBOSOMAL PROTEIN L20
Type	polymer
Formula weight	13779.406 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: P60491, Sequence view
ID 29 : 50S RIBOSOMAL PROTEIN L21
Image
Description	50S RIBOSOMAL PROTEIN L21
Type	polymer
Formula weight	11069.264 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: P60492, Sequence view
ID 30 : 50S RIBOSOMAL PROTEIN L22
Image
Description	50S RIBOSOMAL PROTEIN L22
Type	polymer
Formula weight	12808.169 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SHP3, Sequence view
ID 31 : 50S RIBOSOMAL PROTEIN L23
Image
Description	50S RIBOSOMAL PROTEIN L23
Type	polymer
Formula weight	10759.923 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SHP0, Sequence view
ID 32 : 50S RIBOSOMAL PROTEIN L24
Image
Description	50S RIBOSOMAL PROTEIN L24
Type	polymer
Formula weight	12085.713 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SHP9, Sequence view
ID 33 : TL5
Image
Description	50S RIBOSOMAL PROTEIN L25
Type	polymer
Formula weight	23238.764 Da
Number of molecules	1
Source	Method: Isolated from a natural source Atcc: 27634 NCBI taxonomy: ID:300852 Organism scientific: THERMUS THERMOPHILUS Strain: HB8 - MRC - MSAW1
Links	UniProt: Q5SHZ1, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	70S-EFG-GDP-FA COMPLEX
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE
Sample support
Details	HOLEY CARBON
Vitrification
Details	VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- VITROBOT (FEI)

Electron Microscopy
Imaging
Microscope	model: OTHER
Details	LOW-DOSE
Electron gun
Electron source	FIELD EMISSION GUN
Accelerating voltage	300 kV
Electron dose	20 e/A**2
Illumination mode	FLOOD BEAM
Lens
Mode	BRIGHT FIELD
Magnification	calibrated: 65520 X, nominal: 39000 X
Cs	nominal: 2.0 mm
Nominal defocus	max: 4000 nm, min: 2000 nm
Specimen holder
Temperature	77 Kelvin
Detector
Type	KODAK SO163 FILM
Image scans
Number digital images	677

Processing
2D projection selection
Software name	SPIDER
3D reconstruction
Actual pixel size	1.26 A/pix
CTF correction method	DEFOCUS GROUPS
Details	SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1799.(DEPOSITION ID: 7584).
Method	MULTIPARTICLE REFINEMENT
Nominal pixel size	1.26 A/pix
Resolution	7.6 A
3D fitting
Method	MDFIT
Refinement Protocol	X-RAY
Refinement Space	REAL
3D fitting list
PDB entry ID	2WRI,2WRJ PDB-2wri PDB-2wrj
Refine
Ls d res high	7.60 A
ID	1
Refine hist
D res high	7.60
Total atoms	94153
Nucleic acid atoms	65025
Protein atoms	29128