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- PDB-5jpo: Complex structure of human elongation factor 1B gamma GST-liked d... -

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Basic information

Entry
Database: PDB / ID: 5jpo
TitleComplex structure of human elongation factor 1B gamma GST-liked domain and delta N-terminal domain
Components
  • Elongation factor 1-delta
  • Elongation factor 1-gamma
KeywordsTRANSLATION / eEF1B / elongation factor 1B
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 / response to virus ...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 / response to virus / Signaling by ALK fusions and activated point mutants / 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 / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Elongation factor 1B gamma, C-terminal / Elongation factor EF1B gamma, C-terminal domain superfamily / Elongation factor 1 gamma, conserved domain / Elongation factor 1 (EF-1) gamma C-terminal domain profile. / Elongation factor 1 gamma, conserved 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 1B gamma, C-terminal / Elongation factor EF1B gamma, C-terminal domain superfamily / Elongation factor 1 gamma, conserved domain / Elongation factor 1 (EF-1) gamma C-terminal domain profile. / Elongation factor 1 gamma, conserved 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 / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Elongation factor 1-gamma / Elongation factor 1-delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.998 Å
AuthorsChoi, Y.S. / Kang, B.S.
CitationJournal: To Be Published
Title: Complex structure of human elongation factor 1B gamma GST-liked domain and delta N-terminal domain
Authors: Choi, Y.S. / Kang, B.S.
History
DepositionMay 4, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor 1-gamma
B: Elongation factor 1-gamma
C: Elongation factor 1-gamma
D: Elongation factor 1-gamma
E: Elongation factor 1-delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,34110
Polymers102,8805
Non-polymers4605
Water9,350519
1
A: Elongation factor 1-gamma
B: Elongation factor 1-gamma
C: Elongation factor 1-gamma
D: Elongation factor 1-gamma
E: Elongation factor 1-delta
hetero molecules

A: Elongation factor 1-gamma
B: Elongation factor 1-gamma
C: Elongation factor 1-gamma
D: Elongation factor 1-gamma
E: Elongation factor 1-delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,68120
Polymers205,76010
Non-polymers92110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area25940 Å2
ΔGint-161 kcal/mol
Surface area68720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.499, 101.054, 93.732
Angle α, β, γ (deg.)90.000, 98.750, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Elongation factor 1-gamma / EF-1-gamma / eEF-1B gamma


Mass: 24725.184 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EEF1G, EF1G, PRO1608 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26641
#2: Protein/peptide Elongation factor 1-delta / EF-1-delta / Antigen NY-CO-4


Mass: 3979.455 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EEF1D, EF1D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29692
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: SOKALAN CP7, KCl, HEPES

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Data collection

DiffractionMean temperature: 293.15 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.998→50 Å / Num. obs: 71801 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.105 / Net I/av σ(I): 24.739 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.076.50.708199.2
2.07-2.157.60.5441100
2.15-2.257.60.411100
2.25-2.377.60.3231100
2.37-2.527.60.2331100
2.52-2.717.60.1751100
2.71-2.997.60.1221100
2.99-3.427.60.0851100
3.42-4.317.40.0761100
4.31-507.30.054199.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
RefinementResolution: 1.998→44.358 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.86
RfactorNum. reflection% reflection
Rfree0.2026 1894 2.78 %
Rwork0.1683 --
obs0.1693 68025 94.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.48 Å2 / Biso mean: 33.6031 Å2 / Biso min: 15.43 Å2
Refinement stepCycle: final / Resolution: 1.998→44.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7039 0 30 519 7588
Biso mean--40.64 37.12 -
Num. residues----886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077274
X-RAY DIFFRACTIONf_angle_d1.0579896
X-RAY DIFFRACTIONf_chiral_restr0.0411082
X-RAY DIFFRACTIONf_plane_restr0.0061273
X-RAY DIFFRACTIONf_dihedral_angle_d15.2842601
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9979-2.04780.29561200.23654007412780
2.0478-2.10320.23131270.21384415454289
2.1032-2.16510.27811260.1954507463391
2.1651-2.2350.24411310.20034382451388
2.235-2.31480.26471300.21254564469491
2.3148-2.40750.21041340.18124721485595
2.4075-2.51710.25181310.17954749488096
2.5171-2.64980.21731360.18074912504897
2.6498-2.81580.22741420.18214858500098
2.8158-3.03310.2381420.18164932507499
3.0331-3.33830.21351430.17584999514299
3.3383-3.82110.16641430.15334983512699
3.8211-4.81320.1551450.134450155160100
4.8132-44.36920.17441440.148850875231100

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