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

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Basic information

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


regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / negative regulation of translation in response to stress / 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 / eukaryotic translation initiation factor 2alpha kinase activity / response to manganese-induced endoplasmic reticulum stress / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response ...regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / negative regulation of translation in response to stress / 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 / eukaryotic translation initiation factor 2alpha kinase activity / response to manganese-induced endoplasmic reticulum stress / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response / PERK regulates gene expression / negative regulation of myelination / endocrine pancreas development / ALK mutants bind TKIs / endoplasmic reticulum organization / cellular response to cold / positive regulation of transcription by RNA polymerase I / ER overload response / bone mineralization / positive regulation of vascular endothelial growth factor production / cellular response to glucose starvation / endoplasmic reticulum unfolded protein response / negative regulation of translational initiation / cellular response to amino acid starvation / response to endoplasmic reticulum stress / ossification / insulin-like growth factor receptor signaling pathway / skeletal system development / calcium-mediated signaling / Hsp90 protein binding / positive regulation of protein localization to nucleus / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / Signaling by ALK fusions and activated point mutants / peptidyl-serine phosphorylation / protein phosphatase binding / angiogenesis / protein autophosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / 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 / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Quinoprotein alcohol dehydrogenase-like superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40/YVTN repeat-like-containing domain superfamily / 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
Similarity search - Domain/homology
: / Eukaryotic translation initiation factor 2-alpha kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.14 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

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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-alpha kinase 3
B: Eukaryotic translation initiation factor 2-alpha kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6004
Polymers68,2322
Non-polymers3682
Water00
1
A: Eukaryotic translation initiation factor 2-alpha kinase 3
B: Eukaryotic translation initiation factor 2-alpha kinase 3
hetero molecules

A: Eukaryotic translation initiation factor 2-alpha kinase 3
B: Eukaryotic translation initiation factor 2-alpha kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,2008
Polymers136,4654
Non-polymers7354
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area9370 Å2
ΔGint-57 kcal/mol
Surface area41100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.900, 83.900, 186.240
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-alpha kinase 3 / PRKR-like endoplasmic reticulum kinase / Pancreatic eIF2-alpha kinase / HsPEK


Mass: 34116.215 Da / Num. of mol.: 2 / Fragment: UNP residues 104-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2AK3, PEK, PERK / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NZJ5, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: W

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris (pH 8.5), 0.2 M MgCl2, 25% w/v PEG3350, 7% glycerol
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.2148, 1.2152, 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.21481
21.21521
30.97951
ReflectionResolution: 3.1→75.6 Å / Num. obs: 22114 / % possible obs: 99.9 % / Redundancy: 10.4 % / Rsym value: 0.048 / Net I/σ(I): 32.3
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 11 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.657 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1448)refinement
SCALAdata scaling
SHELXDEphasing
Cootmodel building
iMOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 3.14→75.6 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 30.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2874 1046 4.73 %
Rwork0.2396 --
obs0.2419 22114 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.14→75.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 4 0 6564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043339
X-RAY DIFFRACTIONf_angle_d1.0294523
X-RAY DIFFRACTIONf_dihedral_angle_d16.6441157
X-RAY DIFFRACTIONf_chiral_restr0.037526
X-RAY DIFFRACTIONf_plane_restr0.004560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1401-3.30560.32331490.28453020X-RAY DIFFRACTION100
3.3056-3.51270.32221360.25063024X-RAY DIFFRACTION100
3.5127-3.7840.32291430.24963022X-RAY DIFFRACTION100
3.784-4.16470.3011700.2342992X-RAY DIFFRACTION100
4.1647-4.76730.24651710.19532981X-RAY DIFFRACTION100
4.7673-6.00590.26771370.23373033X-RAY DIFFRACTION100
6.0059-76.51870.29871400.2592996X-RAY DIFFRACTION99
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)
13.05270.0878-4.41984.0475-3.93939.80330.48330.37550.1584-0.03910.3135-0.65210.3765-0.1983-0.55890.6955-0.141-0.16381.3841-0.09151.086672.861842.890748.2554
23.0659-1.7532-1.14247.7072-1.96381.3733-0.2498-0.21510.1567-0.86470.04870.61410.7832-0.02970.25020.7771-0.0356-0.2131.0384-0.13640.688855.512536.21857.1154
33.2885-2.81560.07565.63431.44792.7133-0.23790.53111.7639-0.84540.5568-2.5629-1.14080.6749-0.07330.8994-0.26030.12451.3260.02471.57466.681555.952445.3383
43.4722-1.31321.02253.3563-0.04770.70910.13980.284-0.0001-0.3251-0.0561-0.62640.30910.857-0.23420.64710.28840.02471.1935-0.08560.927968.255236.701148.5448
54.86380.2510.38670.8146-0.27967.6362-0.2671-1.24120.4308-0.1894-0.6095-0.5426-1.12950.98750.36810.7227-0.09990.0310.7034-0.35171.182340.337465.115165.761
67.2586-1.21980.55532.7667-4.20258.8312-0.69420.4801-0.2734-0.09310.1845-1.2685-0.1786-0.78521.13850.7679-0.22890.01560.82920.06330.681936.59861.704241.6613
78.8109-2.54822.07252.9264-2.53648.3781-0.2006-0.72580.25630.08320.1929-0.59620.26131.1741-0.17150.4773-0.1259-0.11280.6812-0.19960.830249.884155.45758.9233
87.04551.3646-0.52953.4708-1.0299.1715-0.30290.47050.0403-0.7471-0.3187-0.05160.048-0.11160.1860.62580.12920.04760.7747-0.07450.769649.552558.160554.3407
96.0749-3.3591-0.70218.15361.36514.2167-0.8517-0.8116-1.18420.3334-0.19871.7607-0.5386-1.18931.08180.42120.08330.12211.3197-0.15460.969527.521359.793171.0968
106.1499-4.4625-4.62463.84341.91567.25360.038-1.16650.07670.0990.12790.148-0.35090.4662-0.30180.4716-0.09930.04910.7974-0.02880.991828.764763.253470.5829
111.70130.7454-1.27511.7086-3.03635.4471-0.6384-0.397-2.65090.1240.15160.1119-1.68890.08420.14160.55760.16640.05460.5669-0.09041.062818.639256.839158.3154
123.99625.31970.83828.5621-1.13213.62880.4086-0.46570.4586-0.1754-0.34790.2982-0.65050.11190.08030.79950.18130.14060.6687-0.16441.199928.488261.752351.0155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 104 through 160 )
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 204 )
3X-RAY DIFFRACTION3chain 'A' and (resid 205 through 244 )
4X-RAY DIFFRACTION4chain 'A' and (resid 245 through 400 )
5X-RAY DIFFRACTION5chain 'B' and (resid 104 through 155 )
6X-RAY DIFFRACTION6chain 'B' and (resid 156 through 169 )
7X-RAY DIFFRACTION7chain 'B' and (resid 170 through 235 )
8X-RAY DIFFRACTION8chain 'B' and (resid 236 through 268 )
9X-RAY DIFFRACTION9chain 'B' and (resid 269 through 316 )
10X-RAY DIFFRACTION10chain 'B' and (resid 317 through 352 )
11X-RAY DIFFRACTION11chain 'B' and (resid 353 through 373 )
12X-RAY DIFFRACTION12chain 'B' and (resid 374 through 400 )

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