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tRNA tranlocation on the 70S ribosome: the pre-translocational translocation intermediate TI(PRE)

by single particle reconstruction, at 7.8 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1798, Image by Jmol

#3: With PDB-2xtg, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-1798 (with PDB-2xtg), Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2xsy
TitletRNA tranlocation on the 70S ribosome: the pre-translocational translocation intermediate TI(PRE)
DescriptorELONGATION FACTOR G/RNA Complex
FUSIDIC ACID
GUANOSINE-5'-DIPHOSPHATE
(30S ribosomal protein ...) x 20
KeywordsRIBOSOME, TRANSLATION, ELONGATION CYCLE
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: 2010-10-01, Release: 2010-12-08
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Sequence detailsMRNA WAS COPURIFIED, THEREFORE UNKNOWN SEQUENCE. TRNA WAS COPURIFIED, THEREFORE UNKNOWN SEQUENCE.
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1798, Image by Jmol

#3: With PDB-2xtg, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-1798 (with PDB-2xtg), Image by UCSF CHIMERA

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EMDB-1798

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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 : 16S RRNA
Image
Description16S RRNA
Typepolyribonucleotide
Formula weight493959.469 Da
Number of molecules1
ID1
SourceMethod: Obtained synthetically
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksGenBank: NC_006461, Sequence view
ID 2 : 30S RIBOSOMAL PROTEIN S2
Image
Description30S RIBOSOMAL PROTEIN S2
Typepolypeptide(L)
Formula weight29317.918 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P80371, Sequence view
ID 3 : 30S RIBOSOMAL PROTEIN S3
Image
Description30S RIBOSOMAL PROTEIN S3
Typepolypeptide(L)
Formula weight26751.309 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P80372, Sequence view
ID 4 : 30S RIBOSOMAL PROTEIN S4
Image
Description30S RIBOSOMAL PROTEIN S4
Typepolypeptide(L)
Formula weight24373.617 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P80373, Sequence view
ID 5 : 30S RIBOSOMAL PROTEIN S5
Image
Description30S RIBOSOMAL PROTEIN S5
Typepolypeptide(L)
Formula weight17583.568 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SHQ5, Sequence view
ID 6 : 30S RIBOSOMAL PROTEIN S6
Image
Description30S RIBOSOMAL PROTEIN S6
Typepolypeptide(L)
Formula weight11988.862 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SLP8, Sequence view
ID 7 : 30S RIBOSOMAL PROTEIN S7
Image
Description30S RIBOSOMAL PROTEIN S7
Typepolypeptide(L)
Formula weight18051.123 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P17291, Sequence view
ID 8 : 30S RIBOSOMAL PROTEIN S8
Image
Description30S RIBOSOMAL PROTEIN S8
Typepolypeptide(L)
Formula weight15868.703 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SHQ2, Sequence view
ID 9 : 30S RIBOSOMAL PROTEIN S9
Image
Description30S RIBOSOMAL PROTEIN S9
Typepolypeptide(L)
Formula weight14410.751 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P80374, Sequence view
ID 10 : 30S RIBOSOMAL PROTEIN S10
Image
Description30S RIBOSOMAL PROTEIN S10
Typepolypeptide(L)
Formula weight11955.081 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SHN7, Sequence view
ID 11 : 30S RIBOSOMAL PROTEIN S11
Image
Description30S RIBOSOMAL PROTEIN S11
Typepolypeptide(L)
Formula weight13737.984 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P80376, Sequence view
ID 12 : 30S RIBOSOMAL PROTEIN S12
Image
Description30S RIBOSOMAL PROTEIN S12
Typepolypeptide(L)
Formula weight14637.519 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SHN3, Sequence view
ID 13 : 30S RIBOSOMAL PROTEIN S13
Image
Description30S RIBOSOMAL PROTEIN S13
Typepolypeptide(L)
Formula weight14338.986 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P80377, Sequence view
ID 14 : 30S RIBOSOMAL PROTEIN S14 TYPE Z
Image
Description30S RIBOSOMAL PROTEIN S14 TYPE Z
Typepolypeptide(L)
Formula weight7158.776 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SHQ1, Sequence view
ID 15 : 30S RIBOSOMAL PROTEIN S15
Image
Description30S RIBOSOMAL PROTEIN S15
Typepolypeptide(L)
Formula weight10578.502 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SJ76, Sequence view
ID 16 : 30S RIBOSOMAL PROTEIN S16
Image
Description30S RIBOSOMAL PROTEIN S16
Typepolypeptide(L)
Formula weight10410.089 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SJH3, Sequence view
ID 17 : 30S RIBOSOMAL PROTEIN S17
Image
Description30S RIBOSOMAL PROTEIN S17
Typepolypeptide(L)
Formula weight12325.766 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SHP7, Sequence view
ID 18 : 30S RIBOSOMAL PROTEIN S18
Image
Description30S RIBOSOMAL PROTEIN S18
Typepolypeptide(L)
Formula weight10258.396 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SLQ0, Sequence view
ID 19 : 30S RIBOSOMAL PROTEIN S19
Image
Description30S RIBOSOMAL PROTEIN S19
Typepolypeptide(L)
Formula weight10605.562 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SHP2, Sequence view
ID 20 : 30S RIBOSOMAL PROTEIN S20
Image
Description30S RIBOSOMAL PROTEIN S20
Typepolypeptide(L)
Formula weight11736.246 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: P80380, Sequence view
ID 21 : 30S RIBOSOMAL PROTEIN THX
Image
Description30S RIBOSOMAL PROTEIN THX
Typepolypeptide(L)
Formula weight3350.058 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksUniProt: Q5SIH3, Sequence view
ID 22 : TRNA
Image
DescriptionTRNA
Typepolyribonucleotide
Formula weight24802.943 Da
Number of molecules1
ID22
DetailsTRNA WAS COPURIFIED WITH 70S RIBOSOMES
SourceMethod: Obtained synthetically
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksSequence view
ID 23 : MRNA
Image
DescriptionMRNA
Typepolyribonucleotide
Formula weight3476.150 Da
Number of molecules1
ID23
DetailsMRNA WAS COPURIFIED WITH 70S RIBOSOMES
SourceMethod: Obtained synthetically
NCBI taxonomy: ID:300852
Organism scientific: THERMUS THERMOPHILUS
Strain: HB8
LinksSequence view
ID 24 : ELONGATION FACTOR G
Image
DescriptionELONGATION FACTOR G
Typepolypeptide(L)
Formula weight76977.914 Da
Number of molecules1
ID24
SourceMethod: Isolated from a genetically manipulated source
Gene: HB8, 27634, ID:300852, THERMUS THERMOPHILUS
Host: ID:469008, ESCHERICHIA COLI

, BL21(DE3)
Plasmid name: PET-46 EK/LIC
LinksUniProt: Q5SHN5, Sequence view
ID 25 : FUSIDIC ACID
Image
DescriptionFUSIDIC ACID
Typenon-polymer
Formula weight516.717 Da
Number of molecules1
ID25
SourceMethod: Obtained synthetically
ID 26 : GUANOSINE-5'-DIPHOSPHATE
Image
DescriptionGUANOSINE-5'-DIPHOSPHATE
Typenon-polymer
Formula weight443.203 Da
Number of molecules1
ID26
SourceMethod: Obtained synthetically
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-1798.
MethodMULTIPARTICLE REFINEMENT
Nominal pixel size1.26 A/pix
Resolution7.8 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 high7.80 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high7.80
Total atoms58624
Ligand atoms65
Nucleic acid atoms34199
Protein atoms24360
Download
PDB format
Allpdb2xsy.ent.gz
pdb2xsy.ent (uncompressed file)
Header onlypdb2xsy.ent.gz
mmCIF format
mmCIF2xsy.cif.gz
XML format
All2xsy.xml.gz
No-atom2xsy-noatom.xml.gz
Ext-atom2xsy-extatom.xml.gz
Movie files
movie #1
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.webm (WebM/VP8 format), 3.8 MB
movie #2
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movie #3
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movie #4
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