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- PDB-5dqs: Complex structure of human elongation factor 1B alpha and gamma G... -

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Basic information

Entry
Database: PDB / ID: 5dqs
TitleComplex structure of human elongation factor 1B alpha and gamma GST-like domains
Components
  • Elongation factor 1-beta
  • Elongation factor 1-gamma
KeywordsTRANSLATION / eEF1B / elongation factor
Function / homology
Function and homology information


Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / translational elongation / Signaling by ALK fusions and activated point mutants / translation elongation factor activity / guanyl-nucleotide exchange factor activity / response to virus / cadherin binding / extracellular exosome / membrane ...Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / translational elongation / Signaling by ALK fusions and activated point mutants / translation elongation factor activity / guanyl-nucleotide exchange factor activity / response to virus / cadherin binding / extracellular exosome / 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-beta / Elongation factor 1-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsChoi, Y.S. / Cho, H.Y. / Kang, B.S.
CitationJournal: To be published
Title: Complex structure of human elongation factor 1B alpha and gamma GST-like domains
Authors: Choi, Y.S. / Cho, H.Y. / Kang, B.S.
History
DepositionSep 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor 1-gamma
D: Elongation factor 1-beta


Theoretical massNumber of molelcules
Total (without water)34,5362
Polymers34,5362
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.788, 50.788, 187.439
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 24865.869 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-218
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 Elongation factor 1-beta / EF-1-beta


Mass: 9669.846 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-88
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EEF1B2, EEF1B, EF1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P24534
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.02 Å3/Da / Density % sol: 39.13 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: glycerol ethoxylate

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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: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→43.984 Å / Num. obs: 31057 / % possible obs: 98.56 % / Redundancy: 17.5 % / Net I/σ(I): 54.1

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data scaling
RefinementResolution: 2.1→43.984 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.94 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2416 3125 10.06 %
Rwork0.204 --
obs0.2079 31057 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→43.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 0 57 2331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042332
X-RAY DIFFRACTIONf_angle_d0.8023182
X-RAY DIFFRACTIONf_dihedral_angle_d14.02819
X-RAY DIFFRACTIONf_chiral_restr0.052354
X-RAY DIFFRACTIONf_plane_restr0.004413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1005-2.13330.40571320.30191277X-RAY DIFFRACTION98
2.1333-2.16830.31141340.28311183X-RAY DIFFRACTION98
2.1683-2.20570.32631590.2751322X-RAY DIFFRACTION97
2.2057-2.24580.25621260.25971231X-RAY DIFFRACTION99
2.2458-2.2890.28181500.25551258X-RAY DIFFRACTION98
2.289-2.33570.3441280.25631274X-RAY DIFFRACTION98
2.3357-2.38650.28551420.25731250X-RAY DIFFRACTION98
2.3865-2.4420.30921500.25471310X-RAY DIFFRACTION99
2.442-2.50310.3611440.24121234X-RAY DIFFRACTION98
2.5031-2.57070.3141470.23781301X-RAY DIFFRACTION100
2.5707-2.64640.3151430.23561260X-RAY DIFFRACTION99
2.6464-2.73180.3061410.23951293X-RAY DIFFRACTION100
2.7318-2.82940.28271450.241294X-RAY DIFFRACTION99
2.8294-2.94260.33911440.24891280X-RAY DIFFRACTION100
2.9426-3.07650.32821440.251254X-RAY DIFFRACTION100
3.0765-3.23870.3491390.23871315X-RAY DIFFRACTION100
3.2387-3.44150.20711460.22181295X-RAY DIFFRACTION100
3.4415-3.70710.2191420.19061262X-RAY DIFFRACTION100
3.7071-4.080.20981290.16581296X-RAY DIFFRACTION99
4.08-4.66980.17681540.16271284X-RAY DIFFRACTION99
4.6698-5.88120.19961390.16641270X-RAY DIFFRACTION99
5.8812-43.99330.20541470.18411189X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01240.06490.13810.05280.25570.33290.04460.2417-0.31810.0736-0.1294-0.12760.22290.712900.4792-0.0474-0.05840.56310.08960.52568.9799-16.83340.5995
20.14340.0547-0.13620.4330.24970.3054-0.28920.3431-0.3012-0.6029-0.0721-0.51630.1110.964400.594-0.14160.04590.73740.1030.718511.3385-14.4686-11.0046
30.5645-0.66650.44320.7088-0.44121.0526-0.16650.11470.12030.02-0.001-0.1001-0.06880.2579-0.00380.4769-0.1508-0.08940.39580.07270.50191.6459-8.13132.8981
41.5524-1.03610.55150.7823-0.64851.6636-0.2890.05660.39380.3097-0.0185-0.1939-0.48620.4887-0.1420.5482-0.2078-0.15410.43960.09440.52226.5374-5.9216.2835
50.07640.0579-0.0248-0.0601-0.01210.0075-0.2524-0.65410.39590.91410.0352-0.2364-1.1210.4677-0.00040.8867-0.021-0.05510.86110.1320.4822-0.9064-15.637938.327
60.52840.0161-0.6210.3517-0.5850.9135-0.1312-0.2363-0.36880.21830.0460.2442-0.07130.0308-0.07270.5577-0.06360.01450.54530.15810.4915-2.366-22.761729.3499
7-0.0153-0.00260.0417-0.0109-0.00350.02630.51140.05580.11541.0729-0.59071.3652-0.43460.5544-0.00381.2089-0.0608-0.05321.2080.42890.89199.8718-24.025242.7913
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 214 )
5X-RAY DIFFRACTION5chain 'D' and (resid 2 through 21 )
6X-RAY DIFFRACTION6chain 'D' and (resid 22 through 78 )
7X-RAY DIFFRACTION7chain 'D' and (resid 79 through 88 )

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