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- PDB-5tny: HTRA2 G399S mutant -

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Basic information

Entry
Database: PDB / ID: 5tny
TitleHTRA2 G399S mutant
ComponentsSerine protease HTRA2, mitochondrial
KeywordsHYDROLASE / Serine Protease / Parkinson Disease / Mitochondria / PDZ Dynamics
Function / homology
Function and homology information


HtrA2 peptidase / pentacyclic triterpenoid metabolic process / negative regulation of mitophagy in response to mitochondrial depolarization / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / regulation of autophagy of mitochondrion / ceramide metabolic process / CD40 receptor complex / : / programmed cell death / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand ...HtrA2 peptidase / pentacyclic triterpenoid metabolic process / negative regulation of mitophagy in response to mitochondrial depolarization / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / regulation of autophagy of mitochondrion / ceramide metabolic process / CD40 receptor complex / : / programmed cell death / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / serine-type endopeptidase complex / adult walking behavior / response to herbicide / positive regulation of protein targeting to mitochondrion / execution phase of apoptosis / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein autoprocessing / regulation of multicellular organism growth / negative regulation of cell cycle / neuron development / cellular response to interferon-beta / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / forebrain development / cellular response to retinoic acid / 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 / cellular response to oxidative stress / cellular response to heat / peptidase activity / neuron apoptotic process / negative regulation of neuron apoptotic process / cytoskeleton / positive regulation of apoptotic process / serine-type endopeptidase activity / chromatin / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / proteolysis / membrane / identical protein binding / 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: 1.7 Å
AuthorsMerski, M. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF)PortoNeuroDRIve@i3S Portugal
CitationJournal: Cell Death Dis / Year: 2017
Title: Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2.
Authors: Merski, M. / Moreira, C. / Abreu, R.M. / Ramos, M.J. / Fernandes, P.A. / Martins, L.M. / Pereira, P.J.B. / Macedo-Ribeiro, S.
History
DepositionOct 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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)36,2032
Polymers36,0081
Non-polymers1951
Water2,072115
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)108,6096
Polymers108,0243
Non-polymers5863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area6250 Å2
ΔGint-18 kcal/mol
Surface area35790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.424, 84.424, 127.294
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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: 36007.914 Da / Num. of mol.: 1 / Mutation: G399S
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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


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


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES pH 6.0, 1 M LiCl, and 15-20% (w/v) PEG-6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→63.4 Å / Num. obs: 37190 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 5 / Num. unique all: 5454 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCY

1lcy


Resolution: 1.7→31.7 Å / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 28.34 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1871 1882 5.06 %
Rwork0.1613 --
obs0.1644 37189 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 12 115 2220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112172
X-RAY DIFFRACTIONf_angle_d1.052975
X-RAY DIFFRACTIONf_dihedral_angle_d13.9781318
X-RAY DIFFRACTIONf_chiral_restr0.061368
X-RAY DIFFRACTIONf_plane_restr0.006385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7004-1.74630.28371310.2582741X-RAY DIFFRACTION95
1.7463-1.79770.2591550.24122695X-RAY DIFFRACTION95
1.7977-1.85570.2181200.23352704X-RAY DIFFRACTION96
1.8557-1.9220.23251330.222740X-RAY DIFFRACTION95
1.922-1.99890.21481690.19992694X-RAY DIFFRACTION94
1.9989-2.08980.21011440.19332738X-RAY DIFFRACTION95
2.0898-2.19980.21051440.19352687X-RAY DIFFRACTION95
2.1998-2.33750.20441580.19872699X-RAY DIFFRACTION94
2.3375-2.51770.22481530.18362718X-RAY DIFFRACTION95
2.5177-2.77060.17211480.19112699X-RAY DIFFRACTION95
2.7706-3.17030.1961480.1642727X-RAY DIFFRACTION95
3.1703-3.98990.16911420.13062725X-RAY DIFFRACTION95
3.9899-21.1350.15611370.10632706X-RAY DIFFRACTION95
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)
10.7850.0942-0.20381.0370.24691.3586-0.09020.10490.05480.02820.0693-0.1371-0.04130.1738-0.02940.09260.03050.00240.08920.01560.111316.9442-44.2617-14.6069
22.06290.85741.90770.33440.77951.72620.2684-0.2339-0.12230.0015-0.03920.00520.4262-0.209-0.24710.1728-0.0018-0.02880.2338-0.00830.21827.5184-36.89091.3165
32.15320.49061.31351.54370.3183.1113-0.1047-0.03490.32690.0751-0.0404-0.2806-0.16760.37140.13680.1575-0.0498-0.05450.20960.02280.241223.3577-30.246-9.6649
43.26180.63580.09081.29430.61042.550.002-0.22450.10760.1488-0.0303-0.02920.00510.00890.02640.122-0.0051-0.0220.0919-0.0060.10046.5447-37.1625-10.7354
50.92420.27421.35070.76590.95252.9609-0.1085-0.1210.4334-0.0979-0.15520.0609-0.24890.10650.23370.20040.0038-0.09180.1862-0.04780.325210.1731-24.796-4.7024
65.32380.83930.940.17460.47422.5656-0.2048-0.66920.43010.1701-0.48030.5659-0.2016-0.52810.48620.2907-0.0067-0.17530.4308-0.1820.6954-1.6079-32.26875.076
74.7978-0.77320.63392.11511.11731.57050.2724-0.2627-0.4285-0.4519-0.21150.8887-0.1555-0.2-0.05880.31810.0011-0.13890.3106-0.07880.43339.105-22.3629.9489
82.14170.1304-0.67223.6992-0.85745.34860.00530.1614-0.5240.2853-0.07720.3407-0.1106-0.32570.09720.2418-0.0343-0.07620.3479-0.19120.448111.2099-19.679214.8932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 142 through 170 )
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 188 )
3X-RAY DIFFRACTION3chain 'A' and (resid 189 through 247 )
4X-RAY DIFFRACTION4chain 'A' and (resid 248 through 329 )
5X-RAY DIFFRACTION5chain 'A' and (resid 330 through 370 )
6X-RAY DIFFRACTION6chain 'A' and (resid 371 through 396 )
7X-RAY DIFFRACTION7chain 'A' and (resid 397 through 433 )
8X-RAY DIFFRACTION8chain 'A' and (resid 434 through 457 )

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