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Basic information

Entry
Database: PDB / ID: 3wbk
Titlecrystal structure analysis of eukaryotic translation initiation factor 5B and 1A complex
Components
  • Eukaryotic translation initiation factor 1A
  • Eukaryotic translation initiation factor 5B
KeywordsBIOSYNTHETIC PROTEIN / flexible / eukaryotic translation initiation
Function / homology
Function and homology information


formation of translation initiation ternary complex / translation reinitiation / formation of cytoplasmic translation initiation complex / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation ...formation of translation initiation ternary complex / translation reinitiation / formation of cytoplasmic translation initiation complex / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit binding / 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 / double-stranded RNA binding / small ribosomal subunit rRNA binding / ribosome binding / cytosolic small ribosomal subunit / GTPase activity / GTP binding / protein kinase 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 1A (eIF-1A), conserved site / Translation initiation factor IF-2, domain 3 superfamily / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A ...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 1A (eIF-1A), conserved site / Translation initiation factor IF-2, domain 3 superfamily / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / 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 / Nucleic acid-binding, OB-fold / 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 1A / Eukaryotic translation initiation factor 5B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 1.3Nov 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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: Eukaryotic translation initiation factor 5B
C: Eukaryotic translation initiation factor 1A


Theoretical massNumber of molelcules
Total (without water)150,4883
Polymers150,4883
Non-polymers00
Water00
1
A: Eukaryotic translation initiation factor 5B
C: Eukaryotic translation initiation factor 1A


Theoretical massNumber of molelcules
Total (without water)82,7642
Polymers82,7642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-5 kcal/mol
Surface area31350 Å2
MethodPISA
2
B: Eukaryotic translation initiation factor 5B


Theoretical massNumber of molelcules
Total (without water)67,7241
Polymers67,7241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.939, 120.942, 132.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 2 - 602 / Label seq-ID: 6 - 606

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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.: 2 / 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 / Production host: Escherichia coli (E. coli) / Strain (production host): B834-CodonPlus(DE3)-RIL / References: UniProt: P39730
#2: Protein Eukaryotic translation initiation factor 1A / eIF-1A / Eukaryotic translation initiation factor 4C / eIF-4C


Mass: 15040.341 Da / Num. of mol.: 1 / Fragment: UNP residues 27-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: TIF11, YMR260C, YM8156.02C / Production host: Escherichia coli (E. coli) / Strain (production host): B834-CodonPlus(DE3)-RIL / References: UniProt: P38912

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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: 2.72 Å3/Da / Density % sol: 54.76 % / Mosaicity: 0.422 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 100mM Tris-HCl pH 8.2, 12.5%(w/v) PEG 3350, 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: 0.98 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 28, 2010
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 24875 / % possible obs: 98.5 % / Observed criterion σ(I): -1.15 / Redundancy: 9.4 % / Rmerge(I) obs: 0.071 / Χ2: 1.371 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.3-3.425.80.49223180.753192.9
3.42-3.557.20.4124410.787198.6
3.55-3.728.80.32524600.826199.8
3.72-3.919.80.24925150.8221100
3.91-4.16100.14624870.8691100
4.16-4.4810.30.08424960.9891100
4.48-4.9310.60.06325191.141100
4.93-5.6410.60.07325351.451100
5.64-7.110.60.06525591.8011100
7.1-509.70.03325453.689194.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3WBI

3wbi


Resolution: 3.3→40 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.3272 / WRfactor Rwork: 0.2706 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7357 / SU B: 36.687 / SU ML: 0.608 / SU Rfree: 0.6868 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.687 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3173 1769 7.1 %RANDOM
Rwork0.257 ---
obs0.2613 24828 98.23 %-
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: 349.8 Å2 / Biso mean: 159.3338 Å2 / Biso min: 47.82 Å2
Baniso -1Baniso -2Baniso -3
1--12.35 Å20 Å2-0 Å2
2--1.66 Å20 Å2
3---10.7 Å2
Refinement stepCycle: LAST / Resolution: 3.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9309 0 0 0 9309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199448
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.98512772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02651184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68924.988401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.218151780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7631555
X-RAY DIFFRACTIONr_chiral_restr0.0810.21510
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216882
X-RAY DIFFRACTIONr_mcbond_it10.38315.6724757
X-RAY DIFFRACTIONr_mcangle_it16.55523.495934
X-RAY DIFFRACTIONr_scbond_it11.41816.0854691
Refine LS restraints NCS

Ens-ID: 1 / Number: 626 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.23 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.304→3.389 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 146 -
Rwork0.354 1504 -
all-1650 -
obs--89.77 %

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