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Basic information

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


formation of cytoplasmic translation initiation complex / protein-synthesizing GTPase / eukaryotic 48S preinitiation complex / regulation of translational initiation / GTP hydrolysis and joining of the 60S ribosomal subunit / translation initiation factor binding / translation initiation factor activity / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly ...formation of cytoplasmic translation initiation complex / protein-synthesizing GTPase / eukaryotic 48S preinitiation complex / regulation of translational initiation / GTP hydrolysis and joining of the 60S ribosomal subunit / translation initiation factor binding / translation initiation factor activity / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / translational initiation / cytoplasmic stress granule / small ribosomal subunit rRNA binding / ribosome binding / cytosolic small ribosomal subunit / GTPase activity / GTP binding / mitochondrion / metal ion binding / cytosol / cytoplasm
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 / SAD / Resolution: 2.35 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 22, 2017Group: Refinement description / Category: software
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 5B


Theoretical massNumber of molelcules
Total (without water)67,7241
Polymers67,7241
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.570, 129.570, 70.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-787-

HOH

21A-788-

HOH

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Components

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


Mass: 67724.023 Da / Num. of mol.: 1 / Fragment: UNP residues 401-1002
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.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M Tri-Sodium Citrate, 19% PEG 3350, HEPES pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2008
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→43.19 Å / Num. obs: 25590 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 54.799 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 22.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.35-2.490.5070.9973.1956684407139731.03497.6
2.49-2.660.3050.6385.0856136382738270.661100
2.66-2.870.1850.3898.1652366357335730.403100
2.87-3.140.0940.19415.4648206331233120.201100
3.14-3.510.0470.10226.9643301302230220.106100
3.51-4.050.0290.06539.2937107266626650.068100
4.05-4.950.0180.04553.1731027229722970.046100
4.95-6.950.0180.04452.523636181618160.046100
6.950.0110.03160.6613308112011050.03298.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
SHELXCDphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→40.97 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.2572 / WRfactor Rwork: 0.1997 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8154 / SU B: 8.552 / SU ML: 0.205 / SU R Cruickshank DPI: 0.4946 / SU Rfree: 0.2869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.495 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2677 1821 7.1 %RANDOM
Rwork0.2104 ---
obs0.2145 25589 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 167.45 Å2 / Biso mean: 53.8743 Å2 / Biso min: 18.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å2-0 Å2
2---0.09 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.35→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4614 0 0 93 4707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194683
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9866329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5695586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95325.025199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33715893
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7281527
X-RAY DIFFRACTIONr_chiral_restr0.070.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213406
X-RAY DIFFRACTIONr_mcbond_it3.1015.0562350
X-RAY DIFFRACTIONr_mcangle_it4.9247.5762934
X-RAY DIFFRACTIONr_scbond_it3.9385.6762329
LS refinement shellResolution: 2.346→2.407 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 130 -
Rwork0.272 1639 -
all-1769 -
obs--94.75 %

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