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- PDB-2rvh: NMR structure of eIF1 -

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Basic information

Entry
Database: PDB / ID: 2rvh
TitleNMR structure of eIF1
ComponentsEukaryotic translation initiation factor eIF-1
KeywordsTRANSLATION / translation initiation factor
Function / homology
Function and homology information


multi-eIF complex / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / ribosomal small subunit binding / regulation of translational fidelity / translation initiation factor binding / translation initiation factor activity / maintenance of translational fidelity / RNA binding
Similarity search - Function
SUI1-like domain / Translation Initiation Factor Eif1 / Eukaryotic translation initiation factor SUI1 / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor eIF-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsNagata, T. / Obayashi, E. / Asano, K.
CitationJournal: Cell Rep / Year: 2017
Title: Molecular Landscape of the Ribosome Pre-initiation Complex during mRNA Scanning: Structural Role for eIF3c and Its Control by eIF5
Authors: Obayashi, E. / Luna, R.E. / Nagata, T. / Martin-Marcos, P. / Hiraishi, H. / Singh, C.R. / Erzberger, J.P. / Zhang, F. / Arthanari, H. / Morris, J. / Pellarin, R. / Moore, C. / Harmon, I. / ...Authors: Obayashi, E. / Luna, R.E. / Nagata, T. / Martin-Marcos, P. / Hiraishi, H. / Singh, C.R. / Erzberger, J.P. / Zhang, F. / Arthanari, H. / Morris, J. / Pellarin, R. / Moore, C. / Harmon, I. / Papadopoulos, E. / Yoshida, H. / Nasr, M.L. / Unzai, S. / Thompson, B. / Aube, E. / Hustak, S. / Stengel, F. / Dagraca, E. / Ananbandam, A. / Gao, P. / Urano, T. / Hinnebusch, A.G. / Wagner, G. / Asano, K.
History
DepositionOct 16, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor eIF-1


Theoretical massNumber of molelcules
Total (without water)12,3301
Polymers12,3301
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Eukaryotic translation initiation factor eIF-1 / Protein translation factor SUI1


Mass: 12330.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: SUI1, RFR1, YNL244C, N0905 / Production host: Escherichia coli (E. coli) / References: UniProt: P32911

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D C(CO)NH
1713D HBHA(CO)NH
1812D 1H-13C HSQC
1913D (H)CCH-TOCSY
11013D (H)CCH-COSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.4 mM [U-100% 13C; U-100% 15N] entity-1, 20 mM sodium phosphate-2, 150 mM sodium chloride-3, 1 mM DTT-4, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMentity-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
150 mMsodium chloride-31
1 mMDTT-41
Sample conditionsIonic strength: 170 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA2.0.17Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.0.17Guntert, Mumenthaler and Wuthrichchemical shift assignment
KUJIRA0.984Naohira Kobayashichemical shift assignment
KUJIRA0.984Naohira Kobayashipeak picking
KUJIRA0.984Naohira Kobayashidata analysis
NMRViewJohnsondata analysis
NMRViewJohnsonpeak picking
NMRViewJohnsoncollection
NMRDrawDelaglioprocessing
NMRPipeDelaglioprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1560 / NOE intraresidue total count: 463 / NOE long range total count: 442 / NOE medium range total count: 261 / NOE sequential total count: 394
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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