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Basic information

Entry
Database: PDB / ID: 3wbj
TitleCrystal structure analysis of eukaryotic translation initiation factor 5B structure II
ComponentsEukaryotic translation initiation factor 5B
KeywordsBIOSYNTHETIC PROTEIN / flexible / eukaryotic translation initiation / eIF1A
Function / homology
Function and homology information


protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / GTP hydrolysis and joining of the 60S ribosomal subunit / translation initiation factor binding / translational initiation / translation initiation factor activity / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / GTP hydrolysis and joining of the 60S ribosomal subunit / translation initiation factor binding / translational initiation / translation initiation factor activity / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / cytoplasmic stress granule / ribosome binding / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / GTPase activity / GTP binding / mitochondrion / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Translation initiation factor IF- 2, domain 3 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Translation factors / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 ...Translation initiation factor IF- 2, domain 3 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Translation factors / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 5B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.495 Å
AuthorsZheng, A. / Yamamoto, R. / Ose, T. / Yu, J. / Tanaka, I. / Yao, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: X-ray structures of eIF5B and the eIF5B-eIF1A complex: the conformational flexibility of eIF5B is restricted on the ribosome by interaction with eIF1A
Authors: Zheng, A. / Yu, J. / Yamamoto, R. / Ose, T. / Tanaka, I. / Yao, M.
History
DepositionMay 20, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 5B


Theoretical massNumber of molelcules
Total (without water)51,2561
Polymers51,2561
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.690, 120.690, 168.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-586-

HOH

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Components

#1: Protein Eukaryotic translation initiation factor 5B / eIF-5B / Translation initiation factor IF-2


Mass: 51255.902 Da / Num. of mol.: 1 / Fragment: UNP residues 401-855
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: FUN12, YAL035W / Plasmid: pDBHT2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834-CodonPlus(DE3)-RIL / References: UniProt: P39730
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.45 Å3/Da / Density % sol: 64.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.1M Tris-HCl pH 8.0, 40% PEG 400, 0.2M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.979 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 6, 2011
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.49→44.393 Å / Num. obs: 47589 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 23.33 % / Biso Wilson estimate: 42.45 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 35.07
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.49-2.650.527.26198
2.65-2.830.3710.241100
2.83-3.050.21716.951100
3.05-3.340.13226.571100
3.34-3.730.07842.281100
3.73-4.310.05460.111100
4.31-5.260.04275.061100
5.26-7.390.04173.471100
7.390.02994.16199

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3WBI
Resolution: 2.495→44.393 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.26 / σ(F): 2.03 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2558 1851 7.18 %
Rwork0.2146 --
obs0.2175 25766 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.0001 Å2
Refinement stepCycle: LAST / Resolution: 2.495→44.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 0 112 3589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053527
X-RAY DIFFRACTIONf_angle_d0.9384758
X-RAY DIFFRACTIONf_dihedral_angle_d14.4721336
X-RAY DIFFRACTIONf_chiral_restr0.032558
X-RAY DIFFRACTIONf_plane_restr0.004607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4954-2.56290.30771320.23851755X-RAY DIFFRACTION97
2.5629-2.63830.27661420.23971790X-RAY DIFFRACTION100
2.6383-2.72340.29531580.24171782X-RAY DIFFRACTION100
2.7234-2.82070.25521330.23241819X-RAY DIFFRACTION100
2.8207-2.93360.2721220.22781833X-RAY DIFFRACTION100
2.9336-3.06710.3021550.24011796X-RAY DIFFRACTION100
3.0671-3.22880.29161280.23151835X-RAY DIFFRACTION100
3.2288-3.4310.24071460.22171831X-RAY DIFFRACTION100
3.431-3.69580.22631520.21291820X-RAY DIFFRACTION100
3.6958-4.06750.27761510.20381858X-RAY DIFFRACTION100
4.0675-4.65550.19381360.17891867X-RAY DIFFRACTION100
4.6555-5.86330.24561350.20241908X-RAY DIFFRACTION100
5.8633-44.39960.26681610.22132021X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.07160.3955-0.15221.56920.27121.99150.0002-0.14060.03280.18570.07080.0858-0.3245-0.3063-0.04750.31920.06840.01290.24310.01740.248950.5119-19.16933.6174
20.9694-0.2055-0.15561.9563-0.27471.035-0.0288-0.08320.13360.0790.0259-0.2369-0.14380.04440.02470.28240.0296-0.02740.1563-0.01470.250461.8731-17.009-2.1971
31.84130.19990.46652.59930.25412.7292-0.065-0.1698-0.04560.38030.1130.1538-0.26-0.4468-0.05240.43350.11410.08080.32390.02750.282750.4278-22.073628.3731
41.47650.3909-0.00543.1388-0.13812.45910.2492-0.35880.22841.0546-0.1262-0.3033-0.6460.0035-0.0750.9021-0.028-0.09470.2981-0.02460.411169.6832-4.160729.4324
55.18262.41021.34531.8850.41031.1756-0.21150.2928-0.0152-0.03860.0713-0.2827-0.52910.91870.11950.6963-0.1861-0.13520.4546-0.01180.548581.38362.493322.5339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:95)
2X-RAY DIFFRACTION2chain 'A' and (resseq 96:239)
3X-RAY DIFFRACTION3chain 'A' and (resseq 240:354)
4X-RAY DIFFRACTION4chain 'A' and (resseq 355:435)
5X-RAY DIFFRACTION5chain 'A' and (resseq 436:455)

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