[English] 日本語
Yorodumi
- PDB-6r8s: Crystal structure of aIF2gamma subunit I181K from archaeon Sulfol... -

+
Open data


ID or keywords:

Loading...

-
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


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 elongation factor EFTu-like, domain 2 / 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, 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 elongation factor EFTu-like, domain 2 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more