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- PDB-2d74: Crystal structure of translation initiation factor aIF2betagamma ... -

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Basic information

Entry
Database: PDB / ID: 2d74
TitleCrystal structure of translation initiation factor aIF2betagamma heterodimer
Components
  • Translation initiation factor 2 beta subunit
  • Translation initiation factor 2 gamma subunit
KeywordsTRANSLATION / PROTEIN COMPLEX
Function / homology
Function and homology information


formation of translation preinitiation complex / protein-synthesizing GTPase / translation elongation factor activity / translation initiation factor activity / tRNA binding / GTPase activity / GTP binding / metal ion binding / cytosol
Similarity search - Function
Alpha-Beta Plaits - #3150 / Translation initiation factor 2, beta subunit / Translation initiation factor 2, gamma subunit / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / Initiation factor eIF2 gamma, C-terminal ...Alpha-Beta Plaits - #3150 / Translation initiation factor 2, beta subunit / Translation initiation factor 2, gamma subunit / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Translation elongation factor EFTu-like, domain 2 / 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 / Alpha-Beta Plaits / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Translation initiation factor 2 subunit gamma / Translation initiation factor 2 subunit beta
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSokabe, M. / Yao, M. / Sakai, N. / Toya, S. / Tanaka, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Structure of archaeal translational initiation factor 2 betagamma-GDP reveals significant conformational change of the beta-subunit and switch 1 region.
Authors: Sokabe, M. / Yao, M. / Sakai, N. / Toya, S. / Tanaka, I.
History
DepositionNov 16, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Translation initiation factor 2 gamma subunit
B: Translation initiation factor 2 beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6924
Polymers63,5622
Non-polymers1312
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-17 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.467, 76.177, 98.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Translation initiation factor 2 gamma subunit / eIF-2-gamma / aIF2-gamma


Mass: 46229.484 Da / Num. of mol.: 1 / Mutation: G236D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF1717 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-codonplus-RIL / References: UniProt: Q8U082
#2: Protein Translation initiation factor 2 beta subunit / eIF-2-beta / aIF2-beta


Mass: 17332.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF0481 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-codonplus-RIL / References: UniProt: Q8U3I5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.01 Å3/Da / Density % sol: 38.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 8000, 0.1M tris-HCl, 0.2M magnesium chloride, pH 8.5, 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: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 13070 / Num. obs: 12894 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0.2 / Redundancy: 5.3 % / Biso Wilson estimate: 62.02 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 16.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2 / Num. unique all: 1166 / % possible all: 91.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KK1

1kk1


Resolution: 2.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 966 7.5 %random
Rwork0.244 ---
all-12851 --
obs-12851 97.9 %-
Displacement parametersBiso mean: 61.94 Å2
Baniso -1Baniso -2Baniso -3
1-14.709 Å20 Å20 Å2
2--6.688 Å20 Å2
3----21.397 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4216 0 2 180 4398
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00679
X-RAY DIFFRACTIONc_angle_deg1.85
X-RAY DIFFRACTIONc_dihedral_angle_d26.93
X-RAY DIFFRACTIONc_improper_angle_d1.14
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.339 73 6.5 %
Rwork0.326 1055 -
obs-1073 87.5 %

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