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- PDB-2qmu: Structure of an archaeal heterotrimeric initiation factor 2 revea... -

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Basic information

Entry
Database: PDB / ID: 2qmu
TitleStructure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states
Components(Translation initiation factor 2 ...Initiation factor) x 3
KeywordsTRANSLATION / initiation of translation / GTP-binding / Initiation factor / Nucleotide-binding / Protein biosynthesis / RNA-binding
Function / homology
Function and homology information


protein-synthesizing GTPase / formation of translation preinitiation complex / formation of cytoplasmic translation initiation complex / translation elongation factor activity / translational initiation / translation initiation factor activity / ribosome binding / tRNA binding / GTPase activity / GTP binding ...protein-synthesizing GTPase / formation of translation preinitiation complex / formation of cytoplasmic translation initiation complex / translation elongation factor activity / translational initiation / translation initiation factor activity / ribosome binding / tRNA binding / GTPase activity / GTP binding / RNA binding / metal ion binding
Similarity search - Function
Defensin A-like - #170 / EIF_2_alpha / Translation initiation factor 2, alpha subunit, archaeal / Translation initiation factor 2, beta subunit / Translation initiation factor 2, gamma subunit / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Domain found in IF2B/IF5 ...Defensin A-like - #170 / EIF_2_alpha / Translation initiation factor 2, alpha subunit, archaeal / Translation initiation factor 2, beta subunit / Translation initiation factor 2, gamma subunit / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, C terminal / Defensin A-like / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / S1 domain profile. / Elongation factor Tu domain 2 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Translation initiation factor 2 subunit beta / Translation initiation factor 2 subunit alpha / Translation initiation factor 2 subunit gamma
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsYatime, L. / Mechulam, Y. / Blanquet, S. / Schmitt, E.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states.
Authors: Yatime, L. / Mechulam, Y. / Blanquet, S. / Schmitt, E.
History
DepositionJul 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 alpha subunit
C: Translation initiation factor 2 beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5736
Polymers71,9703
Non-polymers6043
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
MethodPISA
2
A: Translation initiation factor 2 gamma subunit
B: Translation initiation factor 2 alpha subunit
C: Translation initiation factor 2 beta subunit
hetero molecules

A: Translation initiation factor 2 gamma subunit
B: Translation initiation factor 2 alpha subunit
C: Translation initiation factor 2 beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,14712
Polymers143,9396
Non-polymers1,2076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.323, 118.323, 161.449
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Translation initiation factor 2 ... , 3 types, 3 molecules ABC

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


Mass: 45718.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: eif2g / Plasmid: pET3alpa / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-De3 / References: UniProt: Q980A5
#2: Protein Translation initiation factor 2 alpha subunit / eIF-2-alpha / aIF2- alpha


Mass: 10440.162 Da / Num. of mol.: 1 / Fragment: aif2-alpha3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: eif2a / Plasmid: pET3alpa / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-De3 / References: UniProt: Q97Z79
#3: Protein Translation initiation factor 2 beta subunit / eIF-2-beta / aIF2-beta


Mass: 15811.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: eif2b / Plasmid: pET3alpa / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-De3 / References: UniProt: Q97W59

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Non-polymers , 4 types, 4 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.52 Å3/Da / Density % sol: 72.77 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6M ammonium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.007 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2006
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 21823 / Num. obs: 21823 / % possible obs: 98.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 66 Å2 / Rsym value: 0.111 / Net I/σ(I): 8.9
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 1900 / Rsym value: 0.338 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: chain A from 2AHO

2aho


Resolution: 3.2→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.314 1209 -random
Rwork0.254 ---
all0.254 22105 --
obs0.254 20674 93.5 %-
Displacement parametersBiso mean: 66.3 Å2
Baniso -1Baniso -2Baniso -3
1--9.772 Å2-27.048 Å20 Å2
2---9.772 Å20 Å2
3---19.545 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4989 0 34 1 5024
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008895
X-RAY DIFFRACTIONc_angle_d1.7088
LS refinement shellResolution: 3.2→3.25 Å /
RfactorNum. reflection
Rfree0.372 53
Rwork0.344 -
obs-735

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