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- PDB-1zo1: IF2, IF1, and tRNA fitted to cryo-EM data OF E. COLI 70S initiati... -

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Basic information

Entry
Database: PDB / ID: 1zo1
TitleIF2, IF1, and tRNA fitted to cryo-EM data OF E. COLI 70S initiation complex
Components
  • P/I-site tRNA
  • translation Initiation Factor 1Initiation factor
  • translation initiation factor 2Initiation factor
Keywordstranslation/RNA / E. COLI / RIBOSOME / INITIATION OF PROTEIN SYNTHESIS / INITIATION FACTOR / CRYO-ELETRON MICROSCOPY / translation-RNA COMPLEX
Function / homology
Function and homology information


guanosine tetraphosphate binding / ribosomal small subunit binding / chaperone-mediated protein folding / translational initiation / translation initiation factor activity / response to cold / ribosome binding / rRNA binding / GTPase activity / GTP binding ...guanosine tetraphosphate binding / ribosomal small subunit binding / chaperone-mediated protein folding / translational initiation / translation initiation factor activity / response to cold / ribosome binding / rRNA binding / GTPase activity / GTP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor IF-1 / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 ...Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor IF-1 / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Putative DNA-binding domain superfamily / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein S1-like RNA-binding domain / S1 domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / Translation initiation factor IF-2 / Translation initiation factor IF-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.8 Å
AuthorsAllen, G.S. / Zavialov, A. / Gursky, R. / Ehrenberg, M. / Frank, J.
CitationJournal: Cell / Year: 2005
Title: The cryo-EM structure of a translation initiation complex from Escherichia coli.
Authors: Gregory S Allen / Andrey Zavialov / Richard Gursky / Måns Ehrenberg / Joachim Frank /
Abstract: The 70S ribosome and its complement of factors required for initiation of translation in E. coli were purified separately and reassembled in vitro with GDPNP, producing a stable initiation complex ...The 70S ribosome and its complement of factors required for initiation of translation in E. coli were purified separately and reassembled in vitro with GDPNP, producing a stable initiation complex (IC) stalled after 70S assembly. We have obtained a cryo-EM reconstruction of the IC showing IF2*GDPNP at the intersubunit cleft of the 70S ribosome. IF2*GDPNP contacts the 30S and 50S subunits as well as fMet-tRNA(fMet). IF2 here adopts a conformation radically different from that seen in the recent crystal structure of IF2. The C-terminal domain of IF2 binds to the single-stranded portion of fMet-tRNA(fMet), thereby forcing the tRNA into a novel orientation at the P site. The GTP binding domain of IF2 binds to the GTPase-associated center of the 50S subunit in a manner similar to EF-G and EF-Tu. Additionally, we present evidence for the localization of IF1, IF3, one C-terminal domain of L7/L12, and the N-terminal domain of IF2 in the initiation complex.
History
DepositionMay 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 18, 2019Group: Data collection / Other / Category: atom_sites / cell / em_image_scans
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
F: P/I-site tRNA
I: translation initiation factor 2
W: translation Initiation Factor 1


Theoretical massNumber of molelcules
Total (without water)86,8453
Polymers86,8453
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain P/I-site tRNA


Mass: 24518.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#2: Protein translation initiation factor 2 / Initiation factor / IF2


Mass: 54209.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A705
#3: Protein translation Initiation Factor 1 / Initiation factor / IF1


Mass: 8116.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P69222

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 70S INITIATION COMPLEX / Type: RIBOSOME
Details: 70S E. coli ribosomes, IF1, IF2(GDPNP), IF3, mRNA, and fMet-tRNAfmet formed in vitro
Buffer solutionName: POLYMIX BUFFER / pH: 7.5 / Details: POLYMIX BUFFER
SpecimenConc.: 0.032 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Details: HOLEY CARBON GRID AT 20C FLASH FROZEN INTO LIQUID ETHAN

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jan 1, 2004 / Details: LOW DOSE MODE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 X / Nominal defocus max: -3930 nm / Nominal defocus min: -930 nm / Cs: 2 mm
Specimen holderTemperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: KODAK SO-163 FILM

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Processing

CTF correctionDetails: DEFOCUS GROUPS 0.93-3.93 UM
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MULTI-REFERENCE / Resolution: 13.8 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 20283 / Nominal pixel size: 2.82 Å / Actual pixel size: 2.82 Å
Details: resolution 13.8 ANGSTROMS (FSC=0.5) and 8.6 ANGSTROMS (3sigma)
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: BEST FIT USING RSREF
Details: METHOD--COORDINATE FILES WERE FITTED TO THE E. COLI TRANSLATION INITIATION COMPLEX MAP (EMBL-EMD 3525). REFINEMENT PROTOCOL--RIGID BODY FIT OF DOMAINS I-V OF IF2, RIGID BODY FIT OF IF1 AND FMET-TRNA
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11G7T

1g7t

11G7T1PDBexperimental model
21HRO

1hro

11HRO2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 1622 0 0 5992

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