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- PDB-4m0l: Gamma subunit of the translation initiation factor 2 from Sulfolo... -

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Basic information

Entry
Database: PDB / ID: 4m0l
TitleGamma subunit of the translation initiation factor 2 from Sulfolobus solfataricus complexed with GDP
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


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 / PHOSPHATE ION / Translation initiation factor 2 subunit gamma
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNikonov, O.S. / Stolboushkina, E.A. / Arkhipova, V.I. / Gabdulkhakov, A.G. / Nikulin, A.D. / Lazopulo, A.M. / Lazopulo, S.M. / 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 1, 2013Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 28, 2013ID: 3P3M
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
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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_asym_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
Revision 1.4Oct 30, 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
B: Translation initiation factor 2 subunit gamma
C: Translation initiation factor 2 subunit gamma
D: Translation initiation factor 2 subunit gamma
E: Translation initiation factor 2 subunit gamma
F: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,02020
Polymers275,0956
Non-polymers2,92414
Water6,539363
1
A: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3173
Polymers45,8491
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3173
Polymers45,8491
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3414
Polymers45,8491
Non-polymers4923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3173
Polymers45,8491
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4124
Polymers45,8491
Non-polymers5623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3173
Polymers45,8491
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.050, 106.550, 156.300
Angle α, β, γ (deg.)90.00, 90.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 45849.230 Da / Num. of mol.: 6
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
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Tris-HCl, 50mM NaCl, 50mM KCl, 5mM MgCl2, 5mM 2-mercaptoethanol, 90mM KBr, 7.5% PEG 4000, 0.5mM GTP, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 18, 2012
RadiationMonochromator: Montel 200 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.6→19.811 Å / Num. all: 84101 / Num. obs: 84101 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.27 % / Biso Wilson estimate: 59.6 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.4437 / Mean I/σ(I) obs: 1.93 / Num. unique all: 8374 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QN6

2qn6


Resolution: 2.6→19.811 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 31.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2858 4213 5.02 %RANDOM
Rwork0.2338 ---
all0.2364 83988 --
obs0.2364 83988 96.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.31 Å2 / Biso mean: 54.6 Å2 / Biso min: 18.33 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18901 0 180 363 19444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00519440
X-RAY DIFFRACTIONf_angle_d0.96526356
X-RAY DIFFRACTIONf_chiral_restr0.0613086
X-RAY DIFFRACTIONf_plane_restr0.0063293
X-RAY DIFFRACTIONf_dihedral_angle_d15.7067311
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.62950.37581240.33762099222377
2.6295-2.66040.33581420.33572588273097
2.6604-2.69280.3911560.34362663281997
2.6928-2.72680.37521340.33422662279697
2.7268-2.76250.32851430.32842593273697
2.7625-2.80030.3991380.3252707284597
2.8003-2.84020.41671200.33222666278698
2.8402-2.88250.37661430.31612692283597
2.8825-2.92740.33231300.32562667279798
2.9274-2.97520.37691340.3072707284198
2.9752-3.02630.34181100.30472689279998
3.0263-3.08120.35491370.3052688282598
3.0812-3.14020.3531400.31342696283698
3.1402-3.2040.33451660.29682677284398
3.204-3.27340.3561490.28992662281198
3.2734-3.34920.31531440.28432705284998
3.3492-3.43250.2951390.2772730286998
3.4325-3.52480.31991520.27322658281099
3.5248-3.62790.40331240.36822584270894
3.6279-3.74430.38871480.34062534268293
3.7443-3.87720.33331400.27172607274796
3.8772-4.03110.27041560.23342716287298
4.0311-4.21290.27131410.20162691283299
4.2129-4.43270.19771350.17112735287099
4.4327-4.70690.21641290.16232726285599
4.7069-5.06470.18521440.15482745288999
5.0647-5.56420.24361510.1722694284599
5.5642-6.3460.25561370.19122733287099
6.346-7.90980.22921710.18322736290799
7.9098-19.8120.2191360.1342725286196

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