[English] 日本語
Yorodumi
- PDB-2pzd: Crystal Structure of the HtrA2/Omi PDZ Domain Bound to a Phage-De... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pzd
TitleCrystal Structure of the HtrA2/Omi PDZ Domain Bound to a Phage-Derived Ligand (WTMFWV)
ComponentsSerine protease HTRA2
KeywordsHYDROLASE / PDZ domain / serine protease / apoptosis / mitochondria / peptide-binding module
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 / Roll / Peptidase S1, PA clan / Mainly Beta
Similarity search - Domain/homology
Serine protease HTRA2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsAppleton, B.A. / Wiesmann, C.
CitationJournal: Protein Sci. / Year: 2007
Title: Structural and functional analysis of the ligand specificity of the HtrA2/Omi PDZ domain.
Authors: Zhang, Y. / Appleton, B.A. / Wu, P. / Wiesmann, C. / Sidhu, S.S.
History
DepositionMay 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999SEQUENCE The peptide ligand was fused to the C-terminus of the linker

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine protease HTRA2
B: Serine protease HTRA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3114
Polymers25,1872
Non-polymers1242
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-25 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.105, 90.105, 83.516
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGTHRTHRAA359 - 3685 - 14
21ARGARGTHRTHRBB359 - 3685 - 14
32GLYGLYTHRTHRAA390 - 45736 - 103
42GLYGLYTHRTHRBB390 - 45736 - 103
53GLYGLYVALVALAA461 - 467107 - 113
63GLYGLYVALVALBB461 - 467107 - 113

-
Components

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


Mass: 12593.536 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA2 / Production host: Escherichia coli (E. coli) / References: UniProt: O43464, HtrA2 peptidase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.36 Å3/Da / Density % sol: 63.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 5.6
Details: 0.1 M sodium citrate, 1.0 M monoammonium dihydrogen phosphate, pH 5.6, VAPOR DIFFUSION, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.975 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 9406 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rsym value: 0.071 / Χ2: 1.077 / Net I/σ(I): 11.2
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 901 / Rsym value: 0.594 / Χ2: 1.036 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCY

1lcy


Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / SU B: 11.77 / SU ML: 0.228 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.521 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 453 4.8 %RANDOM
Rwork0.208 ---
obs0.21 8898 99.98 %-
all-8900 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.281 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 8 9 1695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211716
X-RAY DIFFRACTIONr_bond_other_d0.0020.021642
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.962326
X-RAY DIFFRACTIONr_angle_other_deg0.76833782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3865208
X-RAY DIFFRACTIONr_chiral_restr0.0670.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021862
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02344
X-RAY DIFFRACTIONr_nbd_refined0.1850.2279
X-RAY DIFFRACTIONr_nbd_other0.2210.21800
X-RAY DIFFRACTIONr_nbtor_other0.0840.21134
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0870.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1720.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0120.22
X-RAY DIFFRACTIONr_mcbond_it2.2792.51054
X-RAY DIFFRACTIONr_mcangle_it3.78851712
X-RAY DIFFRACTIONr_scbond_it2.5182.5662
X-RAY DIFFRACTIONr_scangle_it3.9775614
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
497TIGHT POSITIONAL0.030.05
838LOOSE POSITIONAL0.935
497TIGHT THERMAL0.080.5
838LOOSE THERMAL2.0610
LS refinement shellResolution: 2.75→2.807 Å / Total num. of bins used: 25
RfactorNum. reflection
Rfree0.378 26
Rwork0.327 501
obs-527
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)
17.47813.64420.7185.00860.22753.5831-0.57090.7822-0.0728-0.86770.62410.00580.28240.3537-0.05320.27680.0069-0.0770.0863-0.05190.051526.356256.13123.8997
23.6278-0.14370.12842.85181.91353.31330.228-0.3396-0.16170.5045-0.21420.21880.4806-0.2391-0.01380.1525-0.0069-0.03280.04830.02120.108816.27348.660728.0365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA359 - 4575 - 103
2X-RAY DIFFRACTION1BB461 - 467107 - 113
3X-RAY DIFFRACTION2AA461 - 467107 - 113
4X-RAY DIFFRACTION2BB359 - 4575 - 103

+
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://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