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- PDB-6h6k: The structure of the FKR mutant of the archaeal translation initi... -

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Basic information

Entry
Database: PDB / ID: 6h6k
TitleThe structure of the FKR mutant of the archaeal translation initiation factor 2 gamma subunit in complex with GDPCP, obtained in the absence of magnesium salts in the crystallization solution.
ComponentsTranslation initiation factor 2 subunit gamma
KeywordsTRANSLATION / translation initiation / aIF2 / aIF2gamma / aIF2gamma switches / G-protein / GTP-binding domain / translation GTPases / GTP hydrolysis / conformational changes / magnesium ions
Function / homology
Function and homology information


selenocysteine metabolic process / selenocysteine incorporation / protein-synthesizing GTPase / selenocysteine insertion sequence binding / formation of translation preinitiation complex / translation elongation factor activity / translation initiation factor activity / tRNA binding / GTPase activity / GTP binding ...selenocysteine metabolic process / selenocysteine incorporation / protein-synthesizing GTPase / selenocysteine insertion sequence binding / formation of translation preinitiation complex / 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, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / 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 ...Translation initiation factor 2, gamma subunit / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / 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
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. / Kravchenko, O. / Nevskaya, N. / Stolboushkina, E. / Gabdulkhakov, A. / Garber, M. / Nikonov, S.
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: The third structural switch in the archaeal translation initiation factor 2 (aIF2) molecule and its possible role in the initiation of GTP hydrolysis and the removal of aIF2 from the ribosome.
Authors: Nikonov, O. / Kravchenko, O. / Nevskaya, N. / Stolboushkina, E. / Garber, M. / Nikonov, S.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2004
Title: Coot: model-building tools for molecular graphics.
Authors: Paul Emsley / Kevin Cowtan /
Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality ...CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2005
Title: Likelihood-enhanced fast translation functions.
Authors: McCoy, A.J. / Grosse-Kunstleve, R.W. / Storoni, L.C. / Read, R.J.
#3: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2010
Title: Integration, scaling, space-group assignment and post-refinement.
Authors: Kabsch, W.
#4: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2002
Title: PHENIX: building new software for automated crystallographic structure determination.
Authors: Adams, P.D. / Grosse-Kunstleve, R.W. / Hung, L.W. / Ioerger, T.R. / McCoy, A.J. / Moriarty, N.W. / Read, R.J. / Sacchettini, J.C. / Sauter, N.K. / Terwilliger, T.C.
History
DepositionJul 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 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.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_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,13720
Polymers228,1455
Non-polymers2,99215
Water14,970831
1
A: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2195
Polymers45,6291
Non-polymers5904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2195
Polymers45,6291
Non-polymers5904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3365
Polymers45,6291
Non-polymers7074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2123
Polymers45,6291
Non-polymers5832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1502
Polymers45,6291
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.710, 76.750, 146.790
Angle α, β, γ (deg.)101.463, 92.077, 95.974
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 45628.918 Da / Num. of mol.: 5 / Mutation: Phe221Ala, Lys225Ala, Arg280Ala
Source method: isolated from a genetically manipulated source
Details: mutations: Phe221Ala, Lys225Ala, Arg280Ala
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: eif2g, SSO0412 / Production host: Escherichia coli (E. coli) / References: UniProt: Q980A5
#2: Chemical
ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 831 / 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: 3.74 Å3/Da / Density % sol: 67.14 %
Crystal growTemperature: 301.15 K / Method: vapor diffusion, hanging drop
Details: Sodium chloride, 2-mercaptoethanol, Tris-HCl, sodium malonate, GDPCP, ethylene glycol.

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Data collection

DiffractionMean temperature: 193.15 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.91→20.03 Å / Num. obs: 235926 / % possible obs: 93.1 % / Redundancy: 1.84 % / Biso Wilson estimate: 43.02 Å2 / Net I/σ(I): 7.53
Reflection shellResolution: 1.91→2 Å / Redundancy: 1.17 % / Mean I/σ(I) obs: 0.66 / Num. unique obs: 20932 / % possible all: 62.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4rjl

4rjl


Resolution: 2→20.03 Å / SU ML: 0.2785 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.3853
RfactorNum. reflection% reflection
Rfree0.2478 10794 5.02 %
Rwork0.2157 --
obs0.2173 214954 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 61.25 Å2
Refinement stepCycle: LAST / Resolution: 2→20.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15789 0 182 831 16802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002316265
X-RAY DIFFRACTIONf_angle_d0.585222089
X-RAY DIFFRACTIONf_chiral_restr0.04812586
X-RAY DIFFRACTIONf_plane_restr0.00412763
X-RAY DIFFRACTIONf_dihedral_angle_d14.11049889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.35913560.35886343X-RAY DIFFRACTION90.42
2.02-2.050.37293610.34366686X-RAY DIFFRACTION97.05
2.05-2.070.35683680.33116856X-RAY DIFFRACTION97.27
2.07-2.10.32293650.31816715X-RAY DIFFRACTION97.31
2.1-2.130.37173720.31716793X-RAY DIFFRACTION97.51
2.13-2.150.30043300.29496788X-RAY DIFFRACTION97.29
2.15-2.190.30013840.28716800X-RAY DIFFRACTION97.6
2.19-2.220.32273700.28876725X-RAY DIFFRACTION97.5
2.22-2.250.29633730.27686833X-RAY DIFFRACTION97.68
2.25-2.290.30483430.27436772X-RAY DIFFRACTION97.72
2.29-2.330.32413490.27086934X-RAY DIFFRACTION97.89
2.33-2.370.28743290.25876747X-RAY DIFFRACTION97.75
2.37-2.420.28483450.25756808X-RAY DIFFRACTION97.96
2.42-2.470.32463820.26056794X-RAY DIFFRACTION98.06
2.47-2.520.29963300.2616846X-RAY DIFFRACTION98.05
2.52-2.580.2873620.25566889X-RAY DIFFRACTION98.2
2.58-2.640.30453690.25256903X-RAY DIFFRACTION98.31
2.64-2.710.28953890.25216777X-RAY DIFFRACTION98.26
2.71-2.790.3063520.23716826X-RAY DIFFRACTION98.37
2.79-2.880.27193480.23226864X-RAY DIFFRACTION98.38
2.88-2.990.2693930.22876815X-RAY DIFFRACTION98.59
2.99-3.10.25893850.22776846X-RAY DIFFRACTION98.66
3.1-3.250.25783970.21366859X-RAY DIFFRACTION98.65
3.25-3.420.24493490.21416879X-RAY DIFFRACTION98.7
3.42-3.630.23773490.20086897X-RAY DIFFRACTION98.83
3.63-3.910.21553440.18926918X-RAY DIFFRACTION98.84
3.91-4.30.21543480.17736909X-RAY DIFFRACTION99.03
4.3-4.910.20273530.1726907X-RAY DIFFRACTION99.07
4.91-6.160.19733840.18646888X-RAY DIFFRACTION99.32
6.16-20.030.21173150.19336543X-RAY DIFFRACTION93.41

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