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- PDB-5v1d: Complex structure of the bovine PERK luminal domain and its subst... -

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Basic information

Entry
Database: PDB / ID: 5v1d
TitleComplex structure of the bovine PERK luminal domain and its substrate peptide
Components
  • 12-mer peptide
  • eIF2AK3 protein
KeywordsTRANSFERASE/SUBSTRATE / PERK / luminal domain / substrate peptide / complex structure / TRANSFERASE-SUBSTRATE complex
Function / homology
Function and homology information


PERK regulates gene expression / regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / eukaryotic translation initiation factor 2alpha kinase activity / endocrine pancreas development / cellular response to cold / positive regulation of transcription by RNA polymerase I / ER overload response / positive regulation of vascular endothelial growth factor production / cellular response to glucose starvation / endoplasmic reticulum unfolded protein response ...PERK regulates gene expression / regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / eukaryotic translation initiation factor 2alpha kinase activity / endocrine pancreas development / cellular response to cold / positive regulation of transcription by RNA polymerase I / ER overload response / positive regulation of vascular endothelial growth factor production / cellular response to glucose starvation / endoplasmic reticulum unfolded protein response / cellular response to amino acid starvation / ossification / angiogenesis / protein phosphatase binding / protein autophosphorylation / endoplasmic reticulum membrane / 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
PRKR-like endoplasmic reticulum kinase
Similarity search - Component
Biological speciesBos taurus (cattle)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.799 Å
AuthorsWang, P. / Li, J. / Sha, B.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The luminal domain of the ER stress sensor protein PERK binds misfolded proteins and thereby triggers PERK oligomerization
Authors: Wang, P. / Li, J. / Tao, J. / Sha, B.
History
DepositionMar 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: eIF2AK3 protein
E: 12-mer peptide
B: eIF2AK3 protein
C: eIF2AK3 protein
F: 12-mer peptide
D: eIF2AK3 protein
G: 12-mer peptide


Theoretical massNumber of molelcules
Total (without water)150,0087
Polymers150,0087
Non-polymers00
Water3,117173
1
A: eIF2AK3 protein
E: 12-mer peptide
D: eIF2AK3 protein
G: 12-mer peptide


Theoretical massNumber of molelcules
Total (without water)75,7574
Polymers75,7574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-38 kcal/mol
Surface area22610 Å2
MethodPISA
2
B: eIF2AK3 protein
C: eIF2AK3 protein
F: 12-mer peptide


Theoretical massNumber of molelcules
Total (without water)74,2513
Polymers74,2513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-26 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.750, 161.547, 104.780
Angle α, β, γ (deg.)90.00, 106.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
eIF2AK3 protein


Mass: 36372.723 Da / Num. of mol.: 4 / Fragment: PERK luminal domain, UNP residues 96-421 / Mutation: C337S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: EIF2AK3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: A5D791
#2: Protein/peptide 12-mer peptide


Mass: 1505.677 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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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: 3.28 Å3/Da / Density % sol: 62.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES, 1% PEG4000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.799→47.89 Å / Num. obs: 47641 / % possible obs: 91.43 % / Redundancy: 1.6 % / Net I/σ(I): 10.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.799→47.89 Å / Cross valid method: THROUGHOUT / σ(F): 65.59 / Phase error: 31.09 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2909 2119 4.87 %
Rwork0.24 --
obs0.2447 43538 91.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.799→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7097 0 0 173 7270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057233
X-RAY DIFFRACTIONf_angle_d0.719757
X-RAY DIFFRACTIONf_dihedral_angle_d16.5634276
X-RAY DIFFRACTIONf_chiral_restr0.0481096
X-RAY DIFFRACTIONf_plane_restr0.0051205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8003-2.87030.31291560.32493090X-RAY DIFFRACTION91
2.8703-2.94790.38661460.31263089X-RAY DIFFRACTION92
2.9479-3.03460.37041530.313151X-RAY DIFFRACTION92
3.0346-3.13250.34031540.27913051X-RAY DIFFRACTION91
3.1325-3.24440.3481510.27173146X-RAY DIFFRACTION92
3.2444-3.37430.32411420.26493103X-RAY DIFFRACTION91
3.3743-3.52780.31791520.25493049X-RAY DIFFRACTION91
3.5278-3.71370.327940.27951854X-RAY DIFFRACTION55
3.7137-3.94620.25111380.2382861X-RAY DIFFRACTION84
3.9462-4.25070.32431450.22643071X-RAY DIFFRACTION90
4.2507-4.6780.24231500.18483046X-RAY DIFFRACTION89
4.678-5.35380.25061420.19812962X-RAY DIFFRACTION88
5.3538-6.74120.28171520.24273022X-RAY DIFFRACTION88
6.7412-43.31570.25661490.24492983X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: -44.3275 Å / Origin y: -24.2662 Å / Origin z: 45.1435 Å
111213212223313233
T0.4629 Å2-0.0116 Å20.0225 Å2-0.487 Å20.0442 Å2--0.353 Å2
L0.0541 °20.0146 °2-0.0346 °2--0.116 °20.1152 °2--1.4293 °2
S0.0106 Å °-0.0171 Å °-0.009 Å °0.0091 Å °0.0067 Å °-0.0014 Å °-0.035 Å °0.0925 Å °-0.0037 Å °
Refinement TLS groupSelection details: all

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