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- PDB-7vge: Structure of the PDZ deleted variant of HtrA2 protease (S306A) -

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Basic information

Entry
Database: PDB / ID: 7vge
TitleStructure of the PDZ deleted variant of HtrA2 protease (S306A)
Components(Serine protease HTRA2, mitochondrial) x 3
KeywordsHYDROLASE / Serine protease / HtrA / PDZ / oligomer
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 / ceramide metabolic process / regulation of autophagy of mitochondrion / mitochondrial protein catabolic process / CD40 receptor complex / : / programmed cell death ...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 / 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 / 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 / protein autoprocessing / negative regulation of cell cycle / regulation of multicellular organism growth / neuron development / cellular response to interferon-beta / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / cellular response to retinoic acid / forebrain development / Mitochondrial protein degradation / serine-type peptidase activity / 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 heat / cellular response to oxidative stress / 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 / identical protein binding / membrane / nucleus / cytosol
Similarity search - Function
PDZ domain 6 / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Serine protease HTRA2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsParui, A.L. / Mishra, V. / Bhaumik, P. / Bose, K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/HRD/NWBA/37/01/2015 India
CitationJournal: Structure / Year: 2022
Title: Inter-subunit crosstalk via PDZ synergistically governs allosteric activation of proapoptotic HtrA2.
Authors: Parui, A.L. / Mishra, V. / Dutta, S. / Bhaumik, P. / Bose, K.
History
DepositionSep 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 14, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease HTRA2, mitochondrial
B: Serine protease HTRA2, mitochondrial
C: Serine protease HTRA2, mitochondrial
D: Serine protease HTRA2, mitochondrial
E: Serine protease HTRA2, mitochondrial
F: Serine protease HTRA2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)129,5256
Polymers129,5256
Non-polymers00
Water00
1
A: Serine protease HTRA2, mitochondrial
B: Serine protease HTRA2, mitochondrial
C: Serine protease HTRA2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)65,0063
Polymers65,0063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-14 kcal/mol
Surface area23860 Å2
MethodPISA
2
D: Serine protease HTRA2, mitochondrial
E: Serine protease HTRA2, mitochondrial
F: Serine protease HTRA2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)64,5193
Polymers64,5193
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-12 kcal/mol
Surface area24530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.880, 82.880, 395.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 21668.580 Da / Num. of mol.: 3 / Mutation: S306A
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: 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: 21555.422 Da / Num. of mol.: 2 / Mutation: S306A
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
#3: 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: 21408.248 Da / Num. of mol.: 1 / Mutation: S306A
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

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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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.5 M Sodium acetate trihydrate pH 6.0, 2.0 M Sodium formate, 3% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 4→40 Å / Num. obs: 11300 / % possible obs: 90.7 % / Redundancy: 4.24 % / Biso Wilson estimate: 76.05 Å2 / CC1/2: 0.967 / Net I/σ(I): 4.36
Reflection shellResolution: 4→4.1 Å / Redundancy: 3.78 % / Mean I/σ(I) obs: 1.27 / Num. unique obs: 1441 / CC1/2: 0.251 / % possible all: 90.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCY

1lcy


Resolution: 4→39.53 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.754 / SU B: 189.057 / SU ML: 1.065 / Cross valid method: THROUGHOUT / ESU R Free: 1.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33642 595 5 %RANDOM
Rwork0.26511 ---
obs0.26859 11300 94.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 108.477 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2---1.03 Å2-0 Å2
3---2.06 Å2
Refinement stepCycle: 1 / Resolution: 4→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8149 0 0 0 8149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138271
X-RAY DIFFRACTIONr_bond_other_d0.0040.0158089
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.64211271
X-RAY DIFFRACTIONr_angle_other_deg1.1861.57218505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25251070
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.14421.316418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.941151262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9321572
X-RAY DIFFRACTIONr_chiral_restr0.0560.21159
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021853
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6876.8864346
X-RAY DIFFRACTIONr_mcbond_other1.6866.8854345
X-RAY DIFFRACTIONr_mcangle_it2.86310.3255394
X-RAY DIFFRACTIONr_mcangle_other2.86310.3265395
X-RAY DIFFRACTIONr_scbond_it1.2227.0173925
X-RAY DIFFRACTIONr_scbond_other1.2227.0173926
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.26210.4855878
X-RAY DIFFRACTIONr_long_range_B_refined5.61431038
X-RAY DIFFRACTIONr_long_range_B_other5.61431039
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4→4.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 43 -
Rwork0.385 820 -
obs--97.51 %
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)
15.3434-0.41613.46383.2465-0.63615.15420.17630.4393-0.1323-0.1835-0.01080.20280.0022-0.0147-0.16550.401-0.0806-0.05730.37340.08580.0426-26.8139-29.238517.6688
22.6451.1918-2.81116.9367-3.39986.4913-0.1467-0.4146-0.5360.20410.11110.45840.2890.09910.03560.25410.0303-0.00290.62850.11940.2248-24.1486-43.353650.0794
37.5022-1.7589-2.7712.95162.05973.5832-0.17830.0933-0.65410.11210.0112-0.21240.34650.20870.16710.385-0.0459-0.110.60610.14860.19423.5242-43.706427.847
45.05610.553-1.71654.2314-1.31053.11590.17720.23510.2773-0.2346-0.1775-0.35890.1870.34060.00030.43010.1812-0.07940.6972-0.00770.0833-12.7192-60.18793.3678
53.33560.18711.90713.18710.64256.95740.079-0.5173-0.07230.20850.0637-0.0647-0.03130.3912-0.14270.43250.1895-0.03470.50120.21650.3314-16.2036-74.695135.6947
66.5233-3.0950.40676.2863-1.58853.5316-0.1192-0.48180.15610.58210.45180.2941-0.2988-0.3337-0.33260.289-0.0969-0.09070.46270.17720.15-44.0319-57.798721.6345
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A140 - 342
2X-RAY DIFFRACTION2B140 - 342
3X-RAY DIFFRACTION3C140 - 342
4X-RAY DIFFRACTION4D140 - 341
5X-RAY DIFFRACTION5E140 - 340
6X-RAY DIFFRACTION6F140 - 341

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