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- PDB-4yzy: Crystal structures reveal transient PERK luminal domain tetrameri... -

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Basic information

Entry
Database: PDB / ID: 4yzy
TitleCrystal structures reveal transient PERK luminal domain tetramerization in ER stress signaling
ComponentsEukaryotic translation initiation factor 2-alpha kinase 3
KeywordsSIGNALING PROTEIN / UPR / ER stress sensing / proteostasis / PERK / dimer
Function / homology
Function and homology information


PERK regulates gene expression / negative regulation of translation in response to endoplasmic reticulum stress / regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / positive regulation of glutathione biosynthetic process / negative regulation of translation in response to stress / regulation of translational initiation by eIF2 alpha phosphorylation / eiF2alpha phosphorylation in response to endoplasmic reticulum stress / eukaryotic initiation factor eIF2 binding / chondrocyte development / eukaryotic translation initiation factor 2alpha kinase activity ...PERK regulates gene expression / negative regulation of translation in response to endoplasmic reticulum stress / regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / positive regulation of glutathione biosynthetic process / negative regulation of translation in response to stress / regulation of translational initiation by eIF2 alpha phosphorylation / eiF2alpha phosphorylation in response to endoplasmic reticulum stress / eukaryotic initiation factor eIF2 binding / chondrocyte development / eukaryotic translation initiation factor 2alpha kinase activity / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of signal transduction / positive regulation of ERAD pathway / SREBP signaling pathway / PERK-mediated unfolded protein response / endoplasmic reticulum quality control compartment / endocrine pancreas development / negative regulation of myelination / regulation of fatty acid metabolic process / endoplasmic reticulum organization / pancreas development / regulation of translational initiation / cellular response to cold / positive regulation of transcription by RNA polymerase I / bone mineralization / ER overload response / fat cell differentiation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of vascular endothelial growth factor production / cellular response to glucose starvation / endoplasmic reticulum unfolded protein response / ERAD pathway / lactation / response to endoplasmic reticulum stress / cellular response to amino acid starvation / ossification / insulin-like growth factor receptor signaling pathway / skeletal system development / calcium-mediated signaling / Hsp90 protein binding / positive regulation of protein localization to nucleus / peptidyl-serine phosphorylation / protein autophosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / translation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / Quinoprotein alcohol dehydrogenase-like superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / WD40/YVTN repeat-like-containing domain superfamily / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Eukaryotic translation initiation factor 2-alpha kinase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsCarrara, M. / Prischi, F. / Ali, M.M.U.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC33269/A11161 United Kingdom
Medical Research Council (United Kingdom)MR/L007436/1 United Kingdom
CitationJournal: Embo J. / Year: 2015
Title: Crystal structures reveal transient PERK luminal domain tetramerization in endoplasmic reticulum stress signaling.
Authors: Carrara, M. / Prischi, F. / Nowak, P.R. / Ali, M.M.
History
DepositionMar 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 2-alpha kinase 3


Theoretical massNumber of molelcules
Total (without water)33,5101
Polymers33,5101
Non-polymers00
Water00
1
A: Eukaryotic translation initiation factor 2-alpha kinase 3

A: Eukaryotic translation initiation factor 2-alpha kinase 3


Theoretical massNumber of molelcules
Total (without water)67,0192
Polymers67,0192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2020 Å2
ΔGint-10 kcal/mol
Surface area17390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.770, 90.770, 75.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Eukaryotic translation initiation factor 2-alpha kinase 3 / PRKR-like endoplasmic reticulum kinase / Pancreatic eIF2-alpha kinase


Mass: 33509.504 Da / Num. of mol.: 1 / Fragment: UNP residues 100-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eif2ak3, Pek, Perk / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Z2B5, non-specific serine/threonine protein kinase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES/imidazole (pH 6.5), 0.09 sodium phosphate salts (NPS) mix (containing 0.03 M of each NaN03, Na2HPO4, (NH4)2SO4), 12.5% w/v PEG1000, 12.5% w/v PEG3350, 20% v/v MPD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→54.347 Å / Num. obs: 11682 / % possible obs: 99.7 % / Redundancy: 5.2 % / Rsym value: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.819 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIXdev_1448refinement
PHASERphasing
SCALAdata scaling
Cootmodel building
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YZS

4yzs


Resolution: 3.2→54.347 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 36.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.305 514 4.79 %
Rwork0.2903 --
obs0.291 10723 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→54.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 0 0 1187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041254
X-RAY DIFFRACTIONf_angle_d1.0651707
X-RAY DIFFRACTIONf_dihedral_angle_d15.695413
X-RAY DIFFRACTIONf_chiral_restr0.032204
X-RAY DIFFRACTIONf_plane_restr0.003211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2004-3.52240.46251330.40242372X-RAY DIFFRACTION88
3.5224-4.0320.3671230.34832520X-RAY DIFFRACTION92
4.032-5.07930.28121220.26642635X-RAY DIFFRACTION96
5.0793-54.3550.27511360.27072682X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9453-0.24222.38456.07560.63614.52131.1512-0.6625-1.2111-1.2329-0.50370.2424-0.73450.57070.09991.04330.277-0.11661.36210.21671.0127-4.47941.6586-6.2
28.2099-1.77870.3753.44171.16863.6799-0.5198-0.1177-0.40270.33570.55640.1792-0.1037-0.1276-0.1690.8681-0.0111-0.08680.98070.04481.1399.531333.314-1.9795
36.383-3.57522.11184.32560.12682.92020.7729-0.6082-0.37-0.2821-0.64151.3171-1.1764-0.31770.16861.0296-0.0093-0.15381.31130.10931.6781-13.465537.6901-10.3577
41.9526-2.17022.64534.6106-5.28466.09020.0056-1.8476-1.26562.6395-1.7506-0.1491-0.0536-0.92580.23932.3715-0.9530.57961.9103-0.00661.8896-12.495432.6362-0.3367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 103 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 268 )
3X-RAY DIFFRACTION3chain 'A' and (resid 269 through 345 )
4X-RAY DIFFRACTION4chain 'A' and (resid 346 through 355 )

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