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- PDB-3qd2: Crystal structure of mouse PERK kinase domain -

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Basic information

Entry
Database: PDB / ID: 3qd2
TitleCrystal structure of mouse PERK kinase domain
ComponentsEukaryotic translation initiation factor 2-alpha kinase 3
KeywordsGENE REGULATION / eIF2a Kinase / Phosphoryalation
Function / homology
Function and homology information


eiF2alpha phosphorylation in response to endoplasmic reticulum stress / regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / PERK regulates gene expression / regulation of translational initiation by eIF2 alpha phosphorylation / positive regulation of glutathione biosynthetic process / negative regulation of translation in response to endoplasmic reticulum stress / regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of translation initiation in response to endoplasmic reticulum stress / chondrocyte development / eukaryotic initiation factor eIF2 binding ...eiF2alpha phosphorylation in response to endoplasmic reticulum stress / regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / PERK regulates gene expression / regulation of translational initiation by eIF2 alpha phosphorylation / positive regulation of glutathione biosynthetic process / negative regulation of translation in response to endoplasmic reticulum stress / regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of translation initiation in response to endoplasmic reticulum stress / chondrocyte development / eukaryotic initiation factor eIF2 binding / eukaryotic translation initiation factor 2alpha kinase activity / negative regulation of translation in response to stress / positive regulation of signal transduction / SREBP signaling pathway / PERK-mediated unfolded protein response / negative regulation of myelination / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum quality control compartment / mitochondria-associated endoplasmic reticulum membrane contact site / endocrine pancreas development / mitochondrial respirasome assembly / regulation of fatty acid metabolic process / regulation of translational initiation in response to stress / misfolded protein binding / endoplasmic reticulum organization / pancreas development / regulation of translational initiation / ER overload response / cellular response to cold / bone mineralization / positive regulation of transcription by RNA polymerase I / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of vascular endothelial growth factor production / fat cell differentiation / cellular response to glucose starvation / endoplasmic reticulum unfolded protein response / lactation / ERAD pathway / translation regulator activity / insulin-like growth factor receptor signaling pathway / ossification / response to endoplasmic reticulum stress / cellular response to amino acid starvation / non-membrane spanning protein tyrosine kinase activity / skeletal system development / non-specific protein-tyrosine kinase / calcium-mediated signaling / translational initiation / Hsp90 protein binding / positive regulation of protein localization to nucleus / protein autophosphorylation / response to oxidative stress / protein tyrosine kinase activity / angiogenesis / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of translation / translation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / Quinoprotein alcohol dehydrogenase-like superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...: / Quinoprotein alcohol dehydrogenase-like superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / 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
Eukaryotic translation initiation factor 2-alpha kinase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsWenjun, C. / Jingzhi, L. / David, R. / Bingdong, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: The structure of the PERK kinase domain suggests the mechanism for its activation.
Authors: Cui, W. / Li, J. / Ron, D. / Sha, B.
History
DepositionJan 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Jan 16, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,6701
Polymers38,6701
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.891, 97.891, 116.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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: 38670.223 Da / Num. of mol.: 1 / Fragment: UNP Q9Z2B5 residues 582-701 and 867-1078
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eif2ak3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus
References: UniProt: Q9Z2B5, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 702-866 WERE DELETED FROM UNP Q9Z2B5

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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: 3.62 Å3/Da / Density % sol: 66.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.1M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.998 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 3, 2009
RadiationMonochromator: insertion device / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.998 Å / Relative weight: 1
ReflectionResolution: 2.8→44.63 Å / Num. all: 13680 / Num. obs: 13283 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→44.63 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 1 / SU B: 41.669 / SU ML: 0.356 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3323 709 5.1 %RANDOM
Rwork0.2698 ---
obs0.2729 13283 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 171.11 Å2 / Biso mean: 93.8811 Å2 / Biso min: 59.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.81→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 0 21 2267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222293
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9623088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2895267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14524.017117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.56115425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4441517
X-RAY DIFFRACTIONr_chiral_restr0.0910.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021718
X-RAY DIFFRACTIONr_nbd_refined0.1950.21094
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21557
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.24
X-RAY DIFFRACTIONr_mcbond_it0.5221.51394
X-RAY DIFFRACTIONr_mcangle_it0.84522201
X-RAY DIFFRACTIONr_scbond_it0.85931000
X-RAY DIFFRACTIONr_scangle_it1.2824.5887
LS refinement shellResolution: 2.808→2.881 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 39 -
Rwork0.387 791 -
all-830 -
obs--78.52 %

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