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- PDB-5sv7: The Crystal structure of a chaperone -

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Basic information

Entry
Database: PDB / ID: 5sv7
TitleThe Crystal structure of a chaperone
ComponentsEukaryotic translation initiation factor 2-alpha kinase 3
KeywordsTRANSLATION / chaperone
Function / homology
Function and homology information


regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of translational initiation by eIF2 alpha phosphorylation / eiF2alpha phosphorylation in response to endoplasmic reticulum stress / chondrocyte development / response to manganese-induced endoplasmic reticulum stress / negative regulation of translation in response to stress / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response / negative regulation of myelination ...regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of translational initiation by eIF2 alpha phosphorylation / eiF2alpha phosphorylation in response to endoplasmic reticulum stress / chondrocyte development / response to manganese-induced endoplasmic reticulum stress / negative regulation of translation in response to stress / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response / negative regulation of myelination / PERK regulates gene expression / mitochondria-associated endoplasmic reticulum membrane contact site / endocrine pancreas development / misfolded protein binding / ALK mutants bind TKIs / endoplasmic reticulum organization / regulation of translational initiation / cellular response to cold / ER overload response / bone mineralization / positive regulation of transcription by RNA polymerase I / positive regulation of vascular endothelial growth factor production / cellular response to glucose starvation / endoplasmic reticulum unfolded protein response / negative regulation of translational initiation / response to endoplasmic reticulum stress / ossification / cellular response to amino acid starvation / insulin-like growth factor receptor signaling pathway / : / skeletal system development / Hsp90 protein binding / non-specific protein-tyrosine kinase / calcium-mediated signaling / positive regulation of protein localization to nucleus / KEAP1-NFE2L2 pathway / Signaling by ALK fusions and activated point mutants / peptidyl-serine phosphorylation / protein tyrosine kinase activity / protein autophosphorylation / protein phosphatase binding / angiogenesis / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of translation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / endoplasmic reticulum membrane / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / ATP binding / identical protein binding / nucleus / membrane / cytosol / 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 / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...: / Quinoprotein alcohol dehydrogenase-like superfamily / 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, ATP binding site / Protein kinases ATP-binding region signature. / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.209 Å
AuthorsWang, P. / Li, J. / Sha, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM080261 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: The ER stress sensor PERK luminal domain functions as a molecular chaperone to interact with misfolded proteins.
Authors: Wang, P. / Li, J. / Sha, B.
History
DepositionAug 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 13, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 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
B: Eukaryotic translation initiation factor 2-alpha kinase 3
C: Eukaryotic translation initiation factor 2-alpha kinase 3
D: Eukaryotic translation initiation factor 2-alpha kinase 3


Theoretical massNumber of molelcules
Total (without water)146,0994
Polymers146,0994
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-60 kcal/mol
Surface area41070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.913, 163.913, 63.076
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 36524.777 Da / Num. of mol.: 4 / Fragment: UNP residues 95-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2AK3, PEK, PERK / Production host: Bacteria (eubacteria) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS
References: UniProt: Q9NZJ5, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES 0.1M, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→37.851 Å / Num. obs: 30419 / % possible obs: 99 % / Redundancy: 9.4 % / Net I/σ(I): 40.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YZS

4yzs


Resolution: 3.209→37.851 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.08
RfactorNum. reflection% reflection
Rfree0.3218 1572 5.17 %
Rwork0.2705 --
obs0.2732 30419 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.209→37.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6573 0 0 29 6602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126688
X-RAY DIFFRACTIONf_angle_d1.6999029
X-RAY DIFFRACTIONf_dihedral_angle_d15.0253956
X-RAY DIFFRACTIONf_chiral_restr0.0851029
X-RAY DIFFRACTIONf_plane_restr0.0091113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2085-3.3120.33691320.2552308X-RAY DIFFRACTION85
3.312-3.43030.2921580.23932627X-RAY DIFFRACTION100
3.4303-3.56760.28551390.21962644X-RAY DIFFRACTION99
3.5676-3.72980.30881360.22862704X-RAY DIFFRACTION100
3.7298-3.92630.2911500.23992657X-RAY DIFFRACTION100
3.9263-4.1720.33161480.26262661X-RAY DIFFRACTION100
4.172-4.49360.33991750.25272655X-RAY DIFFRACTION100
4.4936-4.94490.27821370.26652628X-RAY DIFFRACTION100
4.9449-5.65840.35031430.31712695X-RAY DIFFRACTION100
5.6584-7.12130.33551520.342664X-RAY DIFFRACTION100
7.1213-37.85360.38971020.33212604X-RAY DIFFRACTION96
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)
11.2933-0.1329-0.23341.5058-0.43840.1851-0.0013-0.2948-0.01050.0723-0.0794-0.22360.080.10160.03130.2197-0.0385-0.11530.48770.09160.3273-5.4844-40.636322.1937
20.8526-0.04310.12811.1089-0.26051.10530.08490.1449-0.0977-0.15150.0781-0.11410.02510.1128-0.0350.3527-0.2118-0.06980.61010.06330.3727-14.6424-32.3783-1.4894
30.52510.18460.48720.36890.39060.90390.0745-0.089-0.20360.0933-0.0383-0.21460.0851-0.0425-0.11410.2384-0.1695-0.10580.59890.05340.2457-22.7299-46.358310.2312
40.43750.02910.51620.41090.45161.4274-0.0272-0.06590.1081-0.05950.0706-0.1721-0.01230.0703-0.04480.1995-0.2233-0.06590.51540.01640.2969-16.5081-40.11365.4496
50.37490.22140.08380.3486-0.26270.71790.0703-0.06930.16960.01180.08580.09620.0219-0.0219-0.10560.24910.0480.00350.5321-0.01950.2515-7.624-32.085520.2868
62.22720.90530.10793.51291.42721.8901-0.0246-0.0565-0.0120.22710.0228-0.26430.05060.0423-0.02280.3459-0.2662-0.04030.4882-0.04480.3609-13.2152-15.60719.4551
72.12551.25080.97042.6126-0.35312.7325-0.1110.039-0.1180.0117-0.0687-0.21880.13670.20810.02050.2213-0.13980.00260.4988-0.0650.2775-9.4645-32.36842.7113
81.03870.21770.57380.29410.09070.52660.04970.1375-0.2407-0.01460.1071-0.14820.32870.2913-0.15050.4035-0.1671-0.05790.3206-0.03230.3828-42.0693-62.4415-9.386
90.69760.120.13980.76740.0761.01050.03320.1117-0.1220.0626-0.07180.0247-0.00740.04190.07520.2686-0.11570.01130.3499-0.03120.2224-37.0761-50.04354.3159
100.79740.213-0.12680.2775-0.06260.9362-0.0253-0.2104-0.07550.0459-0.0526-0.0140.0420.0156-0.11160.2359-0.26020.07260.5689-0.1060.2681-34.2364-51.68236.1193
110.93790.07810.69630.7584-0.13090.65530.0242-0.17770.01210.0871-0.0096-0.0099-0.0307-0.113-0.06820.2292-0.14840.00470.3437-0.12950.3348-51.4065-57.1155-10.8426
120.90580.6450.30510.82280.44450.4287-0.05630.07570.0263-0.17890.0450.13260.0411-0.05040.00880.2389-0.1442-0.18930.17130.00010.4045-53.8529-60.7326-12.4525
130.44440.1399-0.07050.61620.08390.4959-0.0018-0.0380.0628-0.0548-0.03560.0896-0.0158-0.09120.09240.3655-0.27320.06310.395-0.12120.3209-54.3497-49.2374-2.8119
140.62050.05380.11520.63310.18230.42820.07830.02640.1661-0.0622-0.0162-0.1056-0.088-0.0264-0.01340.245-0.19190.04260.17440.09850.3488-31.4144-0.9755-8.9205
151.2837-0.6034-0.08851.8696-1.35521.77390.007-0.1085-0.0230.15030.0189-0.0325-0.07870.0093-0.01940.2663-0.1059-0.04750.41310.18570.1631-25.8739-14.549913.06
160.5655-0.3766-0.29470.30280.11280.29240.0327-0.1391-0.01330.146-0.0943-0.1320.00320.12290.0330.3675-0.2063-0.17790.36470.07310.356-26.7479-20.235115.3323
170.28340.2268-0.11830.33980.00120.1578-0.0410.22630.1609-0.32080.07640.0269-0.1062-0.04930.11680.007-0.34160.00560.1080.05130.0902-43.3761-9.5253-4.6042
180.6637-0.0816-0.12990.5613-0.00320.25560.0386-0.00940.1694-0.1536-0.1049-0.1052-0.00130.019-0.03930.1882-0.18050.06160.20350.01530.05-27.7239-7.245-4.0634
192.8756-1.7274-0.57192.32520.6631.36420.10770.02940.0783-0.04220.0047-0.2877-0.140.0976-0.05440.2233-0.12-0.05750.264-0.0340.2972-17.7617-13.03633.1633
200.7003-0.1809-0.60130.60210.08891.1196-0.05840.3568-0.0248-0.1928-0.1080.2510.0502-0.18130.03190.11670.0204-0.01430.4644-0.03530.1616-58.731-27.16425.2411
210.84750.04450.06020.6899-0.16011.7358-0.2205-0.04410.29690.1121-0.1050.1008-0.1661-0.0860.02680.0935-0.0705-0.01880.3159-0.05990.2109-52.2978-16.12959.73
220.4467-0.05430.23450.77420.43290.756-0.0092-0.2179-0.20080.0095-0.12660.24730.0648-0.18310.13990.1795-0.11980.03130.2952-0.01490.1926-63.2994-35.118613.9646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 104 through 128 )
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 173 )
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 236 )
4X-RAY DIFFRACTION4chain 'A' and (resid 237 through 318 )
5X-RAY DIFFRACTION5chain 'A' and (resid 319 through 376 )
6X-RAY DIFFRACTION6chain 'A' and (resid 377 through 386 )
7X-RAY DIFFRACTION7chain 'A' and (resid 387 through 400 )
8X-RAY DIFFRACTION8chain 'B' and (resid 104 through 140 )
9X-RAY DIFFRACTION9chain 'B' and (resid 141 through 235 )
10X-RAY DIFFRACTION10chain 'B' and (resid 236 through 268 )
11X-RAY DIFFRACTION11chain 'B' and (resid 269 through 317 )
12X-RAY DIFFRACTION12chain 'B' and (resid 318 through 344 )
13X-RAY DIFFRACTION13chain 'B' and (resid 345 through 400 )
14X-RAY DIFFRACTION14chain 'C' and (resid 104 through 140 )
15X-RAY DIFFRACTION15chain 'C' and (resid 141 through 164 )
16X-RAY DIFFRACTION16chain 'C' and (resid 165 through 192 )
17X-RAY DIFFRACTION17chain 'C' and (resid 193 through 248 )
18X-RAY DIFFRACTION18chain 'C' and (resid 249 through 374 )
19X-RAY DIFFRACTION19chain 'C' and (resid 375 through 401 )
20X-RAY DIFFRACTION20chain 'D' and (resid 104 through 192 )
21X-RAY DIFFRACTION21chain 'D' and (resid 193 through 268 )
22X-RAY DIFFRACTION22chain 'D' and (resid 269 through 400 )

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