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- PDB-2pmd: The structures of aIF2gamma subunit from the archaeon Sulfolobus ... -

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Basic information

Entry
Database: PDB / ID: 2pmd
TitleThe structures of aIF2gamma subunit from the archaeon Sulfolobus solfataricus in the GDP-bound form.
ComponentsTranslation initiation factor 2 gamma subunit
KeywordsTRANSLATION / aIF2 / Initiation factor 2 gamma subunit / Initiation of the translation / nucleotide binding / GDPNP / GDP / pyrophosphate
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
Similarity search - Function
Translation initiation factor 2, gamma subunit / 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 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 ...Translation initiation factor 2, gamma subunit / 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 / 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
GUANOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / PYROPHOSPHATE / Translation initiation factor 2 subunit gamma
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsNikonov, O.S. / Stolboushkina, E.A. / Nikulin, A.D. / Hasenohrl, D. / Blaesi, U. / Manstein, D.J. / Fedorov, R.V. / Garber, M.B. / Nikonov, S.V.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: New Insights into the Interactions of the Translation Initiation Factor 2 from Archaea with Guanine Nucleotides and Initiator tRNA.
Authors: Nikonov, O. / Stolboushkina, E. / Nikulin, A. / Hasenohrl, D. / Blasi, U. / Manstein, D.J. / Fedorov, R. / Garber, M. / Nikonov, S.
History
DepositionApr 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Aug 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 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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 gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,17511
Polymers91,6982
Non-polymers2,4769
Water2,882160
1
A: Translation initiation factor 2 gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3496
Polymers45,8491
Non-polymers1,4995
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Translation initiation factor 2 gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8265
Polymers45,8491
Non-polymers9774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.060, 95.060, 165.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 45849.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: eif2g / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q980A5
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H4O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 4.71 Å3/Da / Density % sol: 73.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: natrium malonate dihydrate, glycine,CdCl2, GDPNP., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→19.85 Å / Num. all: 48398 / Num. obs: 45642 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.076
Reflection shellResolution: 2.65→2.81 Å / Mean I/σ(I) obs: 2.58 / % possible all: 85.1

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Processing

Software
NameClassification
XDSdata scaling
MOLREPphasing
CNSrefinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: gamma subunit form the aIF2 alpha-gamma dimer. PDB ENTRY: 2AHO

2aho


Resolution: 2.65→19.85 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.275 2406 -
Rwork0.22 --
all0.22 48398 -
obs0.22 45642 89.3 %
Refinement stepCycle: LAST / Resolution: 2.65→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6424 0 142 160 6726

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