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- PDB-5wyn: HtrA2 Pathogenic Mutant -

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Basic information

Entry
Database: PDB / ID: 5wyn
TitleHtrA2 Pathogenic Mutant
ComponentsSerine protease HTRA2, mitochondrial
KeywordsHYDROLASE / Neurodegeneration / Pathogenic Mutant
Function / homology
Function and homology information


HtrA2 peptidase / pentacyclic triterpenoid metabolic process / negative regulation of mitophagy in response to mitochondrial depolarization / ceramide metabolic process / regulation of autophagy of mitochondrion / mitochondrial protein catabolic process / CD40 receptor complex / programmed cell death / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein serine/threonine kinase inhibitor activity ...HtrA2 peptidase / pentacyclic triterpenoid metabolic process / negative regulation of mitophagy in response to mitochondrial depolarization / ceramide metabolic process / regulation of autophagy of mitochondrion / mitochondrial protein catabolic process / CD40 receptor complex / programmed cell death / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein serine/threonine kinase inhibitor activity / serine-type endopeptidase complex / adult walking behavior / response to herbicide / positive regulation of protein targeting to mitochondrion / execution phase of apoptosis / positive regulation of execution phase of apoptosis / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / ubiquitin ligase inhibitor activity / protein autoprocessing / negative regulation of cell cycle / regulation of multicellular organism growth / cellular response to interferon-beta / neuron development / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / cellular response to retinoic acid / forebrain development / Mitochondrial protein degradation / serine-type peptidase activity / mitochondrion organization / mitochondrial membrane / protein catabolic process / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / cellular response to growth factor stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / unfolded protein binding / peptidase activity / cellular response to oxidative stress / cellular response to heat / neuron apoptotic process / negative regulation of neuron apoptotic process / cytoskeleton / intracellular signal transduction / positive regulation of apoptotic process / serine-type endopeptidase activity / endoplasmic reticulum membrane / chromatin / endoplasmic reticulum / mitochondrion / proteolysis / identical protein binding / membrane / nucleus / cytosol
Similarity search - Function
PDZ domain 6 / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...PDZ domain 6 / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine protease HTRA2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWagh, A.R. / Bose, K.
CitationJournal: Biosci. Rep. / Year: 2018
Title: Structural basis of inactivation of human counterpart of mouse motor neuron degeneration 2 mutant in serine protease HtrA2
Authors: Wagh, A.R. / Bose, K.
History
DepositionJan 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 22, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease HTRA2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4258
Polymers36,0171
Non-polymers4087
Water3,387188
1
A: Serine protease HTRA2, mitochondrial
hetero molecules

A: Serine protease HTRA2, mitochondrial
hetero molecules

A: Serine protease HTRA2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,27524
Polymers108,0513
Non-polymers1,22421
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6790 Å2
ΔGint-73 kcal/mol
Surface area36880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.646, 85.646, 126.306
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-678-

HOH

21A-683-

HOH

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Components

#1: Protein Serine protease HTRA2, mitochondrial / High temperature requirement protein A2 / HtrA2 / Omi stress-regulated endoprotease / Serine ...High temperature requirement protein A2 / HtrA2 / Omi stress-regulated endoprotease / Serine protease 25 / Serine proteinase OMI


Mass: 36016.988 Da / Num. of mol.: 1 / Mutation: S143C,Y295W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA2, OMI, PRSS25 / Production host: Escherichia coli (E. coli) / References: UniProt: O43464, HtrA2 peptidase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Sodium phosphate monobasic monohydrate Potassium phosphate monobasic Sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.22
ReflectionResolution: 2.05→48.08 Å / Num. obs: 21668 / % possible obs: 99.8 % / Redundancy: 4.2 % / Net I/σ(I): 16.4
Reflection shell% possible obs: 94.1 % / Mean I/σ(I) obs: 1.23 / CC1/2: 0.391

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCY

1lcy


Resolution: 2.05→42.823 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.57
RfactorNum. reflection% reflection
Rfree0.1854 1111 5.13 %
Rwork0.1526 --
obs0.1568 21663 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→42.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 18 188 2421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082264
X-RAY DIFFRACTIONf_angle_d1.1253084
X-RAY DIFFRACTIONf_dihedral_angle_d13.73828
X-RAY DIFFRACTIONf_chiral_restr0.041371
X-RAY DIFFRACTIONf_plane_restr0.005400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0501-2.14320.26151300.23842576X-RAY DIFFRACTION95
2.1432-2.25580.23221350.20792558X-RAY DIFFRACTION95
2.2558-2.39660.20941300.19552575X-RAY DIFFRACTION95
2.3966-2.58080.24421580.18832554X-RAY DIFFRACTION94
2.5808-2.8390.21511480.17022541X-RAY DIFFRACTION94
2.839-3.24630.19231260.15112591X-RAY DIFFRACTION95
3.2463-4.07660.16121550.12832536X-RAY DIFFRACTION94
4.0766-15.1080.151270.12382574X-RAY DIFFRACTION95

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