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- PDB-4m53: Gamma subunit of the translation initiation factor 2 from Sulfolo... -

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Basic information

Entry
Database: PDB / ID: 4m53
TitleGamma subunit of the translation initiation factor 2 from Sulfolobus solfataricus in complex with GDPCP
ComponentsTranslation initiation factor 2 subunit gamma
KeywordsTRANSLATION / aIF2 / aIF2 gamma subunit / G-protein / translation initiation / protein biosynthesis / RNA-binding / GTP-binding / nucleotide-binding
Function / homology
Function and homology information


protein-synthesizing GTPase / formation of translation preinitiation complex / translation elongation factor activity / membrane scission GTPase motor activity / translation initiation factor activity / tRNA binding / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / FORMIC ACID / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Translation initiation factor 2 subunit gamma
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNikonov, O.S. / Stolboushkina, E.A. / Arkhipova, V.I. / Lazopulo, A.M. / Lazopulo, S.M. / Gabdulkhakov, A.G. / Nikulin, A.D. / Garber, M.B. / Nikonov, S.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Conformational transitions in the gamma subunit of the archaeal translation initiation factor 2.
Authors: Nikonov, O. / Stolboushkina, E. / Arkhipova, V. / Kravchenko, O. / Nikonov, S. / Garber, M.
History
DepositionAug 7, 2013Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 28, 2013ID: 3SJY
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,97437
Polymers44,5641
Non-polymers2,41036
Water11,782654
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)186.891, 186.891, 186.891
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 44563.738 Da / Num. of mol.: 1 / Mutation: 37-47 Deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: eif2g / Production host: Escherichia coli (E. coli) / References: UniProt: Q980A5

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Non-polymers , 6 types, 690 molecules

#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 6.103 Å3/Da / Density % sol: 79.847 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25mM Tris-HCl, 400mM NaCl, 10mM 2-mercaptoethanol, 2M sodium formate, 50 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2010
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→19.7 Å / Num. all: 72719 / Num. obs: 72719 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.01 % / Biso Wilson estimate: 26.961 Å2 / Rmerge(I) obs: 0.1076 / Net I/σ(I): 12.77
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.4907 / Mean I/σ(I) obs: 2.73 / Num. unique all: 9781 / % possible all: 98.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AHO

2aho


Resolution: 2→19.7 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.18 / σ(F): 2 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1845 3630 5.06 %RANDOM
Rwork0.16 ---
all0.1627 72715 --
obs0.1612 71771 98.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.52 Å2 / Biso mean: 25.4363 Å2 / Biso min: 7.02 Å2
Refinement stepCycle: LAST / Resolution: 2→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 0 147 654 3925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063413
X-RAY DIFFRACTIONf_angle_d1.1434624
X-RAY DIFFRACTIONf_chiral_restr0.075538
X-RAY DIFFRACTIONf_plane_restr0.004574
X-RAY DIFFRACTIONf_dihedral_angle_d15.5531284
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9998-2.02610.29331440.25092469261393
2.0261-2.05380.24511450.22772548269398
2.0538-2.08310.24561650.21852566273198
2.0831-2.11420.24171410.21572574271599
2.1142-2.14720.26671350.20892601273698
2.1472-2.18230.2271590.20962580273999
2.1823-2.21990.25781350.20682622275798
2.2199-2.26020.21911410.18922599274098
2.2602-2.30360.20531360.1892609274599
2.3036-2.35060.2061300.18292621275198
2.3506-2.40160.22281190.1792632275199
2.4016-2.45730.1861410.17342593273499
2.4573-2.51870.18641470.17242645279299
2.5187-2.58660.211110.17182615272699
2.5866-2.66260.22651520.1762620277299
2.6626-2.74830.18521110.17622672278399
2.7483-2.84620.21541370.16892604274198
2.8462-2.95980.18371360.17332609274599
2.9598-3.09410.18211410.16462670281199
3.0941-3.25650.18521410.15482630277199
3.2565-3.45950.17921550.14122624277999
3.4595-3.7250.15911400.13442658279899
3.725-4.09680.13221380.12332667280599
4.0968-4.68260.121560.10912660281699
4.6826-5.87360.13951390.12282695283499
5.8736-19.7010.15791350.13332758289399

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