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tRNA translocation on the 70S ribosome: the post- translocational translocation intermediate TI(POST)

by single particle reconstruction, at 7.6 A resolution

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Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2xux
TitletRNA translocation on the 70S ribosome: the post- translocational translocation intermediate TI(POST)
Descriptor(50S ribosomal protein ...) x 29
KeywordsRIBOSOME, TRANSLATION, ELONGATION CYCLE, TRNA TRANSLOCATION
AuthorsRatje, 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.
DateDeposition: 2010-10-21, Release: 2010-12-08
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
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#2: Superimposing with simplified surface model of EM map, EMDB-1799, Image by Jmol

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Article
Citation - primary
ArticleNature, Vol. 468, Issue 7324, Page 713-6, Year 2010
TitleHead swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites.
AuthorsAndreas 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.
KeywordsBinding 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)
LinksDOI: 10.1038/nature09547, PubMed: 21124459, PMC: PMC3272701
Components
ID 1 : 50S RIBOSOMAL PROTEIN L27
Image
Description50S RIBOSOMAL PROTEIN L27
Typepolypeptide(L)
Formula weight9529.156 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60493, Sequence view
ID 2 : 50S RIBOSOMAL PROTEIN L28
Image
Description50S RIBOSOMAL PROTEIN L28
Typepolypeptide(L)
Formula weight11004.259 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60494, Sequence view
ID 3 : TL5
Image
Description50S RIBOSOMAL PROTEIN L29
Typepolypeptide(L)
Formula weight8670.339 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHP6, Sequence view
ID 4 : 50S RIBOSOMAL PROTEIN L30
Image
Description50S RIBOSOMAL PROTEIN L30
Typepolypeptide(L)
Formula weight6799.196 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHQ6, Sequence view
ID 5 : 50S RIBOSOMAL PROTEIN L31
Image
Description50S RIBOSOMAL PROTEIN L31
Typepolypeptide(L)
Formula weight8300.601 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SJE1, Sequence view
ID 6 : 50S RIBOSOMAL PROTEIN L32
Image
Description50S RIBOSOMAL PROTEIN L32
Typepolypeptide(L)
Formula weight6722.098 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P80339, Sequence view
ID 7 : 50S RIBOSOMAL PROTEIN L33
Image
Description50S RIBOSOMAL PROTEIN L33
Typepolypeptide(L)
Formula weight6632.944 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P35871, Sequence view
ID 8 : 50S RIBOSOMAL PROTEIN L34
Image
Description50S RIBOSOMAL PROTEIN L34
Typepolypeptide(L)
Formula weight6132.502 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P80340, Sequence view
ID 9 : 50S RIBOSOMAL PROTEIN L35
Image
Description50S RIBOSOMAL PROTEIN L35
Typepolypeptide(L)
Formula weight7506.249 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SKU1, Sequence view
ID 10 : RIBOSOMAL PROTEIN B
Image
Description50S RIBOSOMAL PROTEIN L36
Typepolypeptide(L)
Formula weight4435.438 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHR2, Sequence view
ID 11 : 23S RIBOSOMAL RNA
Image
Description23S RIBOSOMAL RNA
Typepolyribonucleotide
Formula weight947936.750 Da
Number of molecules1
ID11
DetailsCHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4
SourceMethod: Obtained synthetically
LinksGenBank: NC_006461, Sequence view
ID 12 : 5S RIBOSOMAL RNA
Image
Description5S RIBOSOMAL RNA
Typepolyribonucleotide
Formula weight39540.836 Da
Number of molecules1
ID12
SourceMethod: Obtained synthetically
LinksGenBank: NC_006461, Sequence view
ID 13 : 50S RIBOSOMAL PROTEIN L1
Image
Description50S RIBOSOMAL PROTEIN L1
Typepolypeptide(L)
Formula weight24872.914 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SLP7, Sequence view
ID 14 : 50S RIBOSOMAL PROTEIN L2
Image
Description50S RIBOSOMAL PROTEIN L2
Typepolypeptide(L)
Formula weight30532.797 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60405, Sequence view
ID 15 : 50S RIBOSOMAL PROTEIN L3
Image
Description50S RIBOSOMAL PROTEIN L3
Typepolypeptide(L)
Formula weight22450.389 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHN8, Sequence view
ID 16 : L1E
Image
Description50S RIBOSOMAL PROTEIN L4
Typepolypeptide(L)
Formula weight23272.105 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHN9, Sequence view
ID 17 : 50S RIBOSOMAL PROTEIN L5
Image
Description50S RIBOSOMAL PROTEIN L5
Typepolypeptide(L)
Formula weight21061.762 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHQ0, Sequence view
ID 18 : 50S RIBOSOMAL PROTEIN L6
Image
Description50S RIBOSOMAL PROTEIN L6
Typepolypeptide(L)
Formula weight19569.104 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHQ3, Sequence view
ID 19 : 50S RIBOSOMAL PROTEIN L11
Image
Description50S RIBOSOMAL PROTEIN L11
Typepolypeptide(L)
Formula weight15526.242 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SLP6, Sequence view
ID 20 : 50S RIBOSOMAL PROTEIN L7/L12
Image
Description50S RIBOSOMAL PROTEIN L7/L12
Typepolypeptide(L)
Formula weight12309.269 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:83333
Organism scientific: ESCHERICHIA COLI


Strain: K-12
LinksUniProt: P0A7K2, Sequence view
ID 21 : 50S RIBOSOMAL PROTEIN L13
Image
Description50S RIBOSOMAL PROTEIN L13
Typepolypeptide(L)
Formula weight15928.042 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60488, Sequence view
ID 22 : 50S RIBOSOMAL PROTEIN L14
Image
Description50S RIBOSOMAL PROTEIN L14
Typepolypeptide(L)
Formula weight13323.730 Da
Number of molecules1
ID22
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHP8, Sequence view
ID 23 : 50S RIBOSOMAL PROTEIN L15
Image
Description50S RIBOSOMAL PROTEIN L15
Typepolypeptide(L)
Formula weight16319.272 Da
Number of molecules1
ID23
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHQ7, Sequence view
ID 24 : 50S RIBOSOMAL PROTEIN L16
Image
Description50S RIBOSOMAL PROTEIN L16
Typepolypeptide(L)
Formula weight15994.034 Da
Number of molecules1
ID24
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60489, Sequence view
ID 25 : 50S RIBOSOMAL PROTEIN L17
Image
Description50S RIBOSOMAL PROTEIN L17
Typepolypeptide(L)
Formula weight13750.277 Da
Number of molecules1
ID25
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q9Z9H5, Sequence view
ID 26 : TL24
Image
Description50S RIBOSOMAL PROTEIN L18
Typepolypeptide(L)
Formula weight12639.966 Da
Number of molecules1
ID26
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHQ4, Sequence view
ID 27 : 50S RIBOSOMAL PROTEIN L19
Image
Description50S RIBOSOMAL PROTEIN L19
Typepolypeptide(L)
Formula weight17188.984 Da
Number of molecules1
ID27
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60490, Sequence view
ID 28 : 50S RIBOSOMAL PROTEIN L20
Image
Description50S RIBOSOMAL PROTEIN L20
Typepolypeptide(L)
Formula weight13779.406 Da
Number of molecules1
ID28
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60491, Sequence view
ID 29 : 50S RIBOSOMAL PROTEIN L21
Image
Description50S RIBOSOMAL PROTEIN L21
Typepolypeptide(L)
Formula weight11069.264 Da
Number of molecules1
ID29
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: P60492, Sequence view
ID 30 : 50S RIBOSOMAL PROTEIN L22
Image
Description50S RIBOSOMAL PROTEIN L22
Typepolypeptide(L)
Formula weight12808.169 Da
Number of molecules1
ID30
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHP3, Sequence view
ID 31 : 50S RIBOSOMAL PROTEIN L23
Image
Description50S RIBOSOMAL PROTEIN L23
Typepolypeptide(L)
Formula weight10759.923 Da
Number of molecules1
ID31
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHP0, Sequence view
ID 32 : 50S RIBOSOMAL PROTEIN L24
Image
Description50S RIBOSOMAL PROTEIN L24
Typepolypeptide(L)
Formula weight12085.713 Da
Number of molecules1
ID32
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHP9, Sequence view
ID 33 : TL5
Image
Description50S RIBOSOMAL PROTEIN L25
Typepolypeptide(L)
Formula weight23238.764 Da
Number of molecules1
ID33
SourceMethod: Isolated from a natural source
Atcc: 27634
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8 - MRC - MSAW1
LinksUniProt: Q5SHZ1, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Name70S-EFG-GDP-FA COMPLEX
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsVITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- VITROBOT (FEI)
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: OTHER
DetailsLOW-DOSE
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose20 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 65520 X, Nominal: 39000 X
CsNominal: 2.0 mm
Nominal defocusMax: 4000 nm, Min: 2000 nm
Specimen holder
Temperature77 Kelvin
Detector
TypeKODAK SO163 FILM
Image scans
Number digital images677
Processing
2D projection selection
Software nameSPIDER
3D reconstruction
Actual pixel size1.26 A/pix
CTF correction methodDEFOCUS GROUPS
DetailsSUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1799.(DEPOSITION ID: 7584).
MethodMULTIPARTICLE REFINEMENT
Nominal pixel size1.26 A/pix
Resolution7.6 A
3D fitting
MethodMDFIT
Refinement ProtocolX-RAY
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
PDB entry ID2WRI,2WRJ
Refine
Refine idELECTRON MICROSCOPY
Ls d res high7.60 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high7.60
Total atoms94153
Nucleic acid atoms65025
Protein atoms29128
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movie #2
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movie #3
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