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- PDB-2mvm: Solution structure of eEF1Bdelta CAR domain -

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Basic information

Entry
Database: PDB / ID: 2mvm
TitleSolution structure of eEF1Bdelta CAR domain
ComponentsElongation factor 1-delta
KeywordsTRANSLATION / guanine nucleotide exchange factor
Function / homology
Function and homology information


Eukaryotic Translation Elongation / cytoplasmic translational elongation / eukaryotic translation elongation factor 1 complex / translation factor activity, RNA binding / translational elongation / translation elongation factor activity / heat shock protein binding / guanyl-nucleotide exchange factor activity / cellular response to ionizing radiation / fibrillar center ...Eukaryotic Translation Elongation / cytoplasmic translational elongation / eukaryotic translation elongation factor 1 complex / translation factor activity, RNA binding / translational elongation / translation elongation factor activity / heat shock protein binding / guanyl-nucleotide exchange factor activity / cellular response to ionizing radiation / fibrillar center / cellular response to heat / DNA-binding transcription factor binding / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EF1B, beta/delta chains, conserved site / Elongation factor 1 beta central acidic region, eukaryote / : / Eukaryotic elongation factor 1 beta central acidic region / Elongation factor 1 beta/beta'/delta chain signature 1. / Elongation factor 1 beta/beta'/delta chain signature 2. / Eukaryotic elongation factor 1 beta central acidic region / Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange domain / Translation elongation factor eEF-1beta-like superfamily / EF-1 guanine nucleotide exchange domain ...Translation elongation factor EF1B, beta/delta chains, conserved site / Elongation factor 1 beta central acidic region, eukaryote / : / Eukaryotic elongation factor 1 beta central acidic region / Elongation factor 1 beta/beta'/delta chain signature 1. / Elongation factor 1 beta/beta'/delta chain signature 2. / Eukaryotic elongation factor 1 beta central acidic region / Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange domain / Translation elongation factor eEF-1beta-like superfamily / EF-1 guanine nucleotide exchange domain / EF-1 guanine nucleotide exchange domain / Translation elongation factor EF1B/ribosomal protein S6
Similarity search - Domain/homology
Elongation factor 1-delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics simulated annealing
Model detailslowest energy, model1
AuthorsWu, H. / Feng, Y.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Evolutionarily Conserved Binding of Translationally Controlled Tumor Protein to Eukaryotic Elongation Factor 1B.
Authors: Wu, H. / Gong, W. / Yao, X. / Wang, J. / Perrett, S. / Feng, Y.
History
DepositionOct 9, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor 1-delta


Theoretical massNumber of molelcules
Total (without water)5,0001
Polymers5,0001
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Elongation factor 1-delta / eEF1Bdelta / EF-1-delta / Antigen NY-CO-4


Mass: 5000.357 Da / Num. of mol.: 1 / Fragment: CAR domain (UNP residues 153-192)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EEF1D, EF1D / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P29692

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1613D HN(CA)CO
1713D HBHA(CO)NH
1813D HBHANH
1913D (H)CCH-TOCSY
11013D CCH-TOCSY
11113D CCH-COSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.2-0.8 mM [U-13C; U-15N] eEF1Bdelta, 20 mM Tris, 200 mM sodium chloride, 0.01% DSS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMeEF1Bdelta-1[U-13C; U-15N]0.2-0.81
20 mMTris-21
200 mMsodium chloride-31
0.01 %DSS-41
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
FelixAccelrys Software Inc.processing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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