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- PDB-8qzz: Crystal structure of human eIF2 alpha-gamma complexed with PPP1R1... -

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Basic information

Entry
Database: PDB / ID: 8qzz
TitleCrystal structure of human eIF2 alpha-gamma complexed with PPP1R15A_420-452
Components
  • Eukaryotic translation initiation factor 2 subunit 1
  • Eukaryotic translation initiation factor 2 subunit 3
  • Protein phosphatase 1 regulatory subunit 15A
KeywordsTRANSLATION / Eukaryotic Initiation Factor-2 / PP1 regulatory subunit / dephosphorylation / metabolism
Function / homology
Function and homology information


positive regulation of translational initiation in response to stress / positive regulation of endoplasmic reticulum stress-induced eIF2 alpha dephosphorylation / regulation of translational initiation by eIF2 alpha dephosphorylation / positive regulation of peptidyl-serine dephosphorylation / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / Cellular response to mitochondrial stress / protein phosphatase type 1 complex / glial limiting end-foot / response to kainic acid ...positive regulation of translational initiation in response to stress / positive regulation of endoplasmic reticulum stress-induced eIF2 alpha dephosphorylation / regulation of translational initiation by eIF2 alpha dephosphorylation / positive regulation of peptidyl-serine dephosphorylation / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / Cellular response to mitochondrial stress / protein phosphatase type 1 complex / glial limiting end-foot / response to kainic acid / negative regulation of protein dephosphorylation / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / methionyl-initiator methionine tRNA binding / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / PERK-mediated unfolded protein response / eukaryotic translation initiation factor 2 complex / PERK regulates gene expression / regulation of translational initiation in response to stress / protein localization to endoplasmic reticulum / protein-synthesizing GTPase / cytoplasmic translational initiation / translation factor activity, RNA binding / protein phosphatase 1 binding / protein phosphatase regulator activity / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / negative regulation of phosphoprotein phosphatase activity / negative regulation of PERK-mediated unfolded protein response / protein phosphatase activator activity / positive regulation of phosphoprotein phosphatase activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / stress granule assembly / translational initiation / translation initiation factor activity / cellular response to amino acid starvation / response to endoplasmic reticulum stress / Downregulation of TGF-beta receptor signaling / ABC-family proteins mediated transport / PKR-mediated signaling / cytoplasmic stress granule / cellular response to UV / ribosome binding / cellular response to oxidative stress / cellular response to heat / mitochondrial outer membrane / regulation of cell cycle / cadherin binding / GTPase activity / apoptotic process / synapse / DNA damage response / endoplasmic reticulum membrane / GTP binding / protein kinase binding / Golgi apparatus / endoplasmic reticulum / mitochondrion / RNA binding / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / Phosphatase-1 catalytic subunit binding region / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal ...Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / Phosphatase-1 catalytic subunit binding region / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha 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 / S1 domain profile. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Protein phosphatase 1 regulatory subunit 15A / Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsYan, Y. / Ron, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustSGAG/182 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Substrate recruitment via eIF2 gamma enhances catalytic efficiency of a holophosphatase that terminates the integrated stress response.
Authors: Yan, Y. / Shetty, M. / Harding, H.P. / George, G. / Zyryanova, A. / Labbe, K. / Mafi, A. / Hao, Q. / Sidrauski, C. / Ron, D.
History
DepositionOct 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 2 subunit 3
B: Eukaryotic translation initiation factor 2 subunit 1
C: Protein phosphatase 1 regulatory subunit 15A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5504
Polymers91,0273
Non-polymers5221
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-21 kcal/mol
Surface area25510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.594, 120.594, 158.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Eukaryotic translation initiation factor 2 subunit 3 / Eukaryotic translation initiation factor 2 subunit gamma X / eIF-2gX


Mass: 51178.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2S3, EIF2G / Production host: Escherichia coli (E. coli) / References: UniProt: P41091, protein-synthesizing GTPase
#2: Protein Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit alpha / eIF-2alpha


Mass: 36161.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2S1, EIF2A / Production host: Escherichia coli (E. coli) / References: UniProt: P05198
#3: Protein/peptide Protein phosphatase 1 regulatory subunit 15A / Growth arrest and DNA damage-inducible protein GADD34 / Myeloid differentiation primary response ...Growth arrest and DNA damage-inducible protein GADD34 / Myeloid differentiation primary response protein MyD116 homolog


Mass: 3687.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R15A, GADD34 / Production host: Escherichia coli (E. coli) / References: UniProt: O75807
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
Has ligand of interestN

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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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 11-12% PEG 6000, 0.1M Tris-HCl pH8.5 supplemented with amino acids

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 3.35→41.17 Å / Num. obs: 17421 / % possible obs: 99.9 % / Redundancy: 12.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.113 / Rrim(I) all: 0.28 / Net I/σ(I): 7.2
Reflection shellResolution: 3.35→3.62 Å / Rmerge(I) obs: 2.618 / Num. unique obs: 3497 / CC1/2: 0.521 / Rpim(I) all: 1.109 / Rrim(I) all: 2.714

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→41.15 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.895 / SU B: 33.973 / SU ML: 0.509 / Cross valid method: THROUGHOUT / ESU R Free: 0.515 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29915 859 4.9 %RANDOM
Rwork0.2407 ---
obs0.24368 16510 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 140.91 Å2
Baniso -1Baniso -2Baniso -3
1--5.41 Å20 Å2-0 Å2
2---5.41 Å20 Å2
3---10.82 Å2
Refinement stepCycle: 1 / Resolution: 3.35→41.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 0 0 4218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124284
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164209
X-RAY DIFFRACTIONr_angle_refined_deg1.9111.6525821
X-RAY DIFFRACTIONr_angle_other_deg0.6071.5699713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7295549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.324521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35610750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02845
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it22.44213.9972214
X-RAY DIFFRACTIONr_mcbond_other22.4413.9982214
X-RAY DIFFRACTIONr_mcangle_it31.5725.1822757
X-RAY DIFFRACTIONr_mcangle_other31.56725.1842758
X-RAY DIFFRACTIONr_scbond_it24.68614.9542070
X-RAY DIFFRACTIONr_scbond_other24.61714.9562070
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other35.41727.1163065
X-RAY DIFFRACTIONr_long_range_B_refined40.725168.9216833
X-RAY DIFFRACTIONr_long_range_B_other40.724168.9316834
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.35→3.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 52 -
Rwork0.379 1194 -
obs--100 %

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