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- PDB-2e9h: Solution structure of the eIF-5_eIF-2B domain from human Eukaryot... -

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Basic information

Entry
Database: PDB / ID: 2e9h
TitleSolution structure of the eIF-5_eIF-2B domain from human Eukaryotic translation initiation factor 5
ComponentsEukaryotic translation initiation factor 5
KeywordsTRANSLATION / zinc binding / C4 type zinc finger / translation initiation factor / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


eukaryotic initiation factor eIF2 binding / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / GDP-dissociation inhibitor activity / regulation of translational initiation / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosome assembly / translation initiation factor activity / GTPase activator activity ...eukaryotic initiation factor eIF2 binding / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / GDP-dissociation inhibitor activity / regulation of translational initiation / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosome assembly / translation initiation factor activity / GTPase activator activity / cadherin binding / synapse / GTP binding / RNA binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
N-terminal domain of TfIIb - #350 / Defensin A-like - #170 / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 ...N-terminal domain of TfIIb - #350 / Defensin A-like - #170 / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Defensin A-like / N-terminal domain of TfIIb / Single Sheet / Armadillo-type fold / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsTomizawa, T. / Tochio, N. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the eIF-5_eIF-2B domain from human Eukaryotic translation initiation factor 5
Authors: Tomizawa, T. / Tochio, N. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S.
History
DepositionJan 25, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5522
Polymers17,4871
Non-polymers651
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 / 100structures with the least restraint violations,structures with the lowest energy,target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Eukaryotic translation initiation factor 5 / eIF-5


Mass: 17486.994 Da / Num. of mol.: 1 / Fragment: eIF-5_eIF-2B domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: EIF5 / Plasmid: P060411-05 / References: UniProt: P55010
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.32mM eIF-5_eIF-2B domain U-15N,13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20060524Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9747Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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