[English] 日本語
Yorodumi
- PDB-1zy4: Crystal Structure of eIF2alpha Protein Kinase GCN2: R794G Hyperac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zy4
TitleCrystal Structure of eIF2alpha Protein Kinase GCN2: R794G Hyperactivating Mutant in Apo Form.
ComponentsSerine/threonine-protein kinase GCN2
KeywordsTRANSFERASE / TRANSLATION REGULATOR / PROTEIN KINASE / SIGNAL TRANSDUCTION / AMINO-ACID STARVATION / STARVATION STRESS RESPONSE / EIF2ALPHA KINASE
Function / homology
Function and homology information


cellular response to histidine / regulation of cytoplasmic translational initiation in response to stress / positive regulation of translational initiation in response to starvation / negative regulation of cytoplasmic translational initiation in response to stress / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / positive regulation of cellular response to amino acid starvation / regulation of translational initiation / protein kinase inhibitor activity / ribosomal large subunit binding ...cellular response to histidine / regulation of cytoplasmic translational initiation in response to stress / positive regulation of translational initiation in response to starvation / negative regulation of cytoplasmic translational initiation in response to stress / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / positive regulation of cellular response to amino acid starvation / regulation of translational initiation / protein kinase inhibitor activity / ribosomal large subunit binding / cytosolic ribosome / translation initiation factor binding / cellular response to amino acid starvation / DNA damage checkpoint signaling / large ribosomal subunit / : / double-stranded RNA binding / ribosome binding / small ribosomal subunit / protein autophosphorylation / tRNA binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / translation / protein phosphorylation / protein serine kinase activity / protein homodimerization activity / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
eIF-2-alpha kinase Gcn2 / Histidyl tRNA synthetase-related domain / Anticodon binding domain of tRNAs / RWD domain / RWD domain / RWD domain profile. / RWD / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain superfamily ...eIF-2-alpha kinase Gcn2 / Histidyl tRNA synthetase-related domain / Anticodon binding domain of tRNAs / RWD domain / RWD domain / RWD domain profile. / RWD / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain superfamily / Ubiquitin-conjugating enzyme/RWD-like / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
eIF-2-alpha kinase GCN2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPadyana, A.K. / Qiu, H. / Roll-Mecak, A. / Hinnebusch, A.G. / Burley, S.K.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Structural Basis for Autoinhibition and Mutational Activation of Eukaryotic Initiation Factor 2{alpha} Protein Kinase GCN2
Authors: Padyana, A.K. / Qiu, H. / Roll-Mecak, A. / Hinnebusch, A.G. / Burley, S.K.
#1: Journal: Genes Dev. / Year: 2002
Title: Mutations that Bypass tRNA Binding Activate the Intrinsically Defective Kinase Domain in GCN2.
Authors: Qiu, H. / Hu, C. / Dong, J. / Hinnebusch, A.G.
History
DepositionJun 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN GOL 997 is associated with protein chain A. GOL 998 is associated with protein chain B.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase GCN2
B: Serine/threonine-protein kinase GCN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2714
Polymers70,0872
Non-polymers1842
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-8 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.833, 79.257, 146.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly of GCN2 protein kinase is a dimer. The asymmetric unit of this crystal lattice contains one dimer assembled into one biological unit.

-
Components

#1: Protein Serine/threonine-protein kinase GCN2


Mass: 35043.336 Da / Num. of mol.: 2 / Mutation: R794G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GCN2, AAS1 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / References: UniProt: P15442, EC: 2.7.1.37
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: PEG 6000, CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 19, 2004
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 45568 / Num. obs: 45176 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 22.4
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.8 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
CNX2000.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZYC

1zyc


Resolution: 1.95→37.72 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1973272.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1407 3.1 %SHELLS
Rwork0.224 ---
all0.224 45568 --
obs0.224 45110 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.6746 Å2 / ksol: 0.359013 e/Å3
Displacement parametersBiso mean: 48.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.68 Å20 Å20 Å2
2---5.01 Å20 Å2
3---0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.95→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4293 0 12 234 4539
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.091.5
X-RAY DIFFRACTIONc_mcangle_it4.32
X-RAY DIFFRACTIONc_scbond_it4.452
X-RAY DIFFRACTIONc_scangle_it5.972.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 229 3.3 %
Rwork0.276 6816 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3water_rep.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4GOL_par.txtGOL_top.txt

+
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