[English] 日本語
Yorodumi
- PDB-1lcy: Crystal Structure of the Mitochondrial Serine Protease HtrA2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lcy
TitleCrystal Structure of the Mitochondrial Serine Protease HtrA2
ComponentsHtrA2 serine protease
KeywordsHYDROLASE / apoptosis / serine protease / PDZ domain / caspase activation / IAP-binding
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 / 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 / MAD / Resolution: 2 Å
AuthorsLi, W. / Srinivasula, S.M. / Chai, J. / Li, P. / Wu, J.W. / Zhang, Z. / Alnemri, E.S. / Shi, Y.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structural insights into the pro-apoptotic function of mitochondrial serine protease HtrA2/Omi.
Authors: Li, W. / Srinivasula, S.M. / Chai, J. / Li, P. / Wu, J.W. / Zhang, Z. / Alnemri, E.S. / Shi, Y.
History
DepositionApr 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HtrA2 serine protease


Theoretical massNumber of molelcules
Total (without water)35,0021
Polymers35,0021
Non-polymers00
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HtrA2 serine protease

A: HtrA2 serine protease

A: HtrA2 serine protease


Theoretical massNumber of molelcules
Total (without water)105,0053
Polymers105,0053
Non-polymers00
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 area5940 Å2
ΔGint-19 kcal/mol
Surface area39080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.42, 85.42, 127.16
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein HtrA2 serine protease


Mass: 35001.820 Da / Num. of mol.: 1 / Mutation: S173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21b / Production host: Escherichia coli (E. coli)
References: UniProt: O43464, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: lithium sulfate, sodium chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMcitrate1reservoirpH5.8
21.0 Mlithium sulfate1reservoir
31.0 M1reservoirNaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1, 0.9788, 0.9791, 0.9638
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jul 1, 2001
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97881
30.97911
40.96381
ReflectionResolution: 2→99 Å / Num. all: 23376 / Num. obs: 23282 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / % possible all: 99.5
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 99 Å / % possible obs: 99.4 % / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.1

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MADSYSphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2→2.03 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.274 49 RANDOM
Rwork0.235 --
all0.247 23282 -
obs0.237 23282 -
Refinement stepCycle: LAST / Resolution: 2→2.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 0 302 2561
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 2→2.03 Å
RfactorNum. reflection
Rfree0.274 48
Rwork0.235 -
obs-1052
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.215 / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor obs: 0.235

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more