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- PDB-5h7u: NMR structure of eIF3 36-163 -

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Basic information

Entry
Database: PDB / ID: 5h7u
TitleNMR structure of eIF3 36-163
ComponentsEukaryotic translation initiation factor 3 subunit C
KeywordsTRANSLATION / initiation factor / eukaryotic initiation factor
Function / homology
Function and homology information


eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor binding ...eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor binding / translation initiation factor activity / translational initiation / cytoplasmic stress granule / mRNA binding / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile.
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit C
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsNagata, T. / Obayashi, E.
Funding support Japan, 2items
OrganizationGrant numberCountry
KAKENHI15H01634 Japan
KAKENHI26440026 Japan
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
DepositionNov 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 3 subunit C


Theoretical massNumber of molelcules
Total (without water)14,5981
Polymers14,5981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 93 kDa subunit / eIF3 p93 / Nuclear transport ...eIF3c / Eukaryotic translation initiation factor 3 93 kDa subunit / eIF3 p93 / Nuclear transport protein NIP1 / Translation initiation factor eIF3 / p93 subunit


Mass: 14598.317 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 36-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NIP1, YMR309C, YM9924.01C, YM9952.11C / Production host: Escherichia coli (E. coli) / References: UniProt: P32497

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic23D HNCO
131isotropic23D HN(CA)CO
141isotropic23D CBCA(CO)NH
151isotropic23D HN(CA)CB
161isotropic23D C(CO)NH
171isotropic23D HBHA(CO)NH
181isotropic12D 1H-13C HSQC
191isotropic23D (H)CCH-TOCSY
1101isotropic23D (H)CCH-COSY
1111isotropic13D 1H-15N NOESY
1121isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.4 mM [U-100% 13C; U-100% 15N] eIF3c 36-163, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM DTT, 95% H2O/5% D2O
Label: 15N_13C_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMeIF3c 36-163[U-100% 13C; U-100% 15N]1
20 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
Sample conditionsIonic strength: 170 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / 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
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
KUJIRA0.98Naohiro Kobayashichemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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