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- PDB-6r8s: Crystal structure of aIF2gamma subunit I181K from archaeon Sulfol... -

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Basic information

Entry
Database: PDB / ID: 6r8s
TitleCrystal structure of aIF2gamma subunit I181K from archaeon Sulfolobus solfataricus complexed with GDPCP
ComponentsTranslation initiation factor 2 subunit gamma
KeywordsTRANSLATION / INITIATION FACTOR 2 / GAMMA SUBUNIT / INITIATION OF THE TRANSLATION / NUCLEOTIDE BINDING / GDPCP / PROTEIN BIOSYNTHESIS
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
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
FORMIC ACID / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Translation initiation factor 2 subunit gamma / Translation initiation factor 2 subunit gamma
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsKravchenko, O. / Arkhipova, V. / Gabdulkhakov, A. / Stolboushkina, E. / Nikonov, O. / Garber, M. / Nikonov, S.
CitationJournal: To Be Published
Title: Crystal structure of aIF2gamma subunit I181K from archaeon Sulfolobus solfataricus complexed with GDPCP
Authors: Nikonov, O. / Kravchenko, O. / Stolboushkina, E. / Nevskaya, N. / Garber, M. / Nikonov, S.
History
DepositionApr 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)47,00916
Polymers45,8651
Non-polymers1,14415
Water8,629479
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-18 kcal/mol
Surface area19240 Å2
Unit cell
Length a, b, c (Å)186.858, 186.858, 186.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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


Mass: 45865.250 Da / Num. of mol.: 1 / Mutation: I181K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (archaea)
Gene: eif2g, SSOP1_0394, SULA_1435, SULB_1436, SULC_1434, SULG_07135, SULH_07135, SULI_07135, SULM_07135, SULN_07135, SULO_07145, SULZ_07375
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3JTX3, UniProt: Q980A5*PLUS
#2: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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

Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop
Details: 17 mM TRIS-HCL pH7,5, 17 mM NaCl, 3,4mM 2-mercaptoethanol, 1,22 M sodium formate, 33,9 mM sodium cacodylate pH 6.5, 0,33% MMEPEG 5000, 1,7mM GDPCP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.18→46.714 Å / Num. obs: 56432 / % possible obs: 100 % / Redundancy: 11.39 % / Net I/σ(I): 14.24

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NBS

4nbs


Resolution: 2.18→46.714 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.5
RfactorNum. reflection% reflection
Rfree0.1897 2683 4.75 %
Rwork0.1663 --
obs0.1675 56426 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.18→46.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 72 479 3765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083371
X-RAY DIFFRACTIONf_angle_d1.1364562
X-RAY DIFFRACTIONf_dihedral_angle_d18.6621280
X-RAY DIFFRACTIONf_chiral_restr0.088528
X-RAY DIFFRACTIONf_plane_restr0.005571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1801-2.21980.28591360.24752851X-RAY DIFFRACTION100
2.2198-2.26250.22881270.22142818X-RAY DIFFRACTION100
2.2625-2.30870.25691770.22552761X-RAY DIFFRACTION100
2.3087-2.35890.22851420.21322804X-RAY DIFFRACTION100
2.3589-2.41370.21851270.20292818X-RAY DIFFRACTION100
2.4137-2.47410.20791640.19032769X-RAY DIFFRACTION100
2.4741-2.5410.23021130.18882858X-RAY DIFFRACTION100
2.541-2.61570.23211350.19082796X-RAY DIFFRACTION100
2.6157-2.70020.21051120.18732864X-RAY DIFFRACTION100
2.7002-2.79670.19831410.18462797X-RAY DIFFRACTION100
2.7967-2.90860.21711460.17792810X-RAY DIFFRACTION100
2.9086-3.0410.21711440.17572820X-RAY DIFFRACTION100
3.041-3.20130.19741490.17082805X-RAY DIFFRACTION100
3.2013-3.40180.18581310.15862856X-RAY DIFFRACTION100
3.4018-3.66430.16751570.14692819X-RAY DIFFRACTION100
3.6643-4.03290.15191420.12942835X-RAY DIFFRACTION100
4.0329-4.6160.13581330.12412854X-RAY DIFFRACTION100
4.616-5.8140.16091810.14212846X-RAY DIFFRACTION100
5.814-46.72520.20421260.17262962X-RAY DIFFRACTION100

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