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- PDB-6r8t: Crystal structure of aIF2gamma subunit I181T from archaeon Sulfol... -

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Basic information

Entry
Database: PDB / ID: 6r8t
TitleCrystal structure of aIF2gamma subunit I181T 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


protein-synthesizing GTPase / formation of translation preinitiation complex / 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 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain ...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 / Elongation factor Tu domain 2 / 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 nucleoside triphosphate hydrolase
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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 I181T 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_symmetry
Revision 1.2Oct 23, 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 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,51029
Polymers45,8371
Non-polymers1,67328
Water11,548641
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-38 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.585, 186.585, 186.585
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: 45837.176 Da / Num. of mol.: 1 / Mutation: I181T
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

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Non-polymers , 5 types, 669 molecules

#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.: 23 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 15,4 mM TRIS-HCL pH7,5, 30.8mM NaCl, 3.1mM 2-mercaptoethanol, 1,1 M sodium formate, 30.8mM sodium cacodylate pH 6.5, 1,15% MMEPEG 5000, 1,4mM GDPCP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Oct 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.1→26.39 Å / Num. obs: 62755 / % possible obs: 99.9 % / Redundancy: 3.41 % / Rmerge(I) obs: 0.3428 / Net I/σ(I): 8.02
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.1074

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RJL

4rjl


Resolution: 2.1→26.387 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.67
RfactorNum. reflection% reflection
Rfree0.2055 3184 5.08 %
Rwork0.1816 --
obs0.1828 62736 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→26.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 105 641 3958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053372
X-RAY DIFFRACTIONf_angle_d1.1024542
X-RAY DIFFRACTIONf_dihedral_angle_d18.6611268
X-RAY DIFFRACTIONf_chiral_restr0.076525
X-RAY DIFFRACTIONf_plane_restr0.004567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13140.25061350.23212593X-RAY DIFFRACTION100
2.1314-2.16470.2671420.23142596X-RAY DIFFRACTION100
2.1647-2.20010.25561200.23172537X-RAY DIFFRACTION100
2.2001-2.23810.25141460.22712569X-RAY DIFFRACTION100
2.2381-2.27870.23361400.21942578X-RAY DIFFRACTION100
2.2787-2.32250.23981500.22082532X-RAY DIFFRACTION100
2.3225-2.36990.24641390.22372592X-RAY DIFFRACTION100
2.3699-2.42140.26571400.21122601X-RAY DIFFRACTION100
2.4214-2.47770.24711330.19862546X-RAY DIFFRACTION100
2.4777-2.53960.22481500.2042577X-RAY DIFFRACTION100
2.5396-2.60820.25691480.20462570X-RAY DIFFRACTION100
2.6082-2.68490.24951370.20732557X-RAY DIFFRACTION100
2.6849-2.77150.22011250.19962606X-RAY DIFFRACTION100
2.7715-2.87040.23341220.19492640X-RAY DIFFRACTION100
2.8704-2.98520.21651320.18942539X-RAY DIFFRACTION100
2.9852-3.12080.21011280.18712598X-RAY DIFFRACTION100
3.1208-3.28510.20231670.17622586X-RAY DIFFRACTION100
3.2851-3.49050.17891290.1612590X-RAY DIFFRACTION100
3.4905-3.75930.20811460.15542604X-RAY DIFFRACTION100
3.7593-4.13630.16311410.14252594X-RAY DIFFRACTION100
4.1363-4.73180.13251350.12752610X-RAY DIFFRACTION100
4.7318-5.95030.14791340.14542651X-RAY DIFFRACTION100
5.9503-26.38920.17971450.16792686X-RAY DIFFRACTION99

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