[English] 日本語
Yorodumi
- PDB-7wh5: Crystal structure of human ClpP in complex with ZG180 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wh5
TitleCrystal structure of human ClpP in complex with ZG180
ComponentsATP-dependent Clp protease proteolytic subunit, mitochondrial
KeywordsHYDROLASE / protease
Function / homology
Function and homology information


membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding ...membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix / serine-type endopeptidase activity / mitochondrion / proteolysis / identical protein binding
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
Chem-9DF / ATP-dependent Clp protease proteolytic subunit, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsWei, B.Y. / Gan, J.H. / Yang, C.-G.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22037007 China
National Natural Science Foundation of China (NSFC)21725801 China
National Natural Science Foundation of China (NSFC)22107109 China
CitationJournal: Nat Commun / Year: 2022
Title: Anti-infective therapy using species-specific activators of Staphylococcus aureus ClpP.
Authors: Wei, B. / Zhang, T. / Wang, P. / Pan, Y. / Li, J. / Chen, W. / Zhang, M. / Ji, Q. / Wu, W. / Lan, L. / Gan, J. / Yang, C.G.
History
DepositionDec 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit, mitochondrial
B: ATP-dependent Clp protease proteolytic subunit, mitochondrial
C: ATP-dependent Clp protease proteolytic subunit, mitochondrial
D: ATP-dependent Clp protease proteolytic subunit, mitochondrial
E: ATP-dependent Clp protease proteolytic subunit, mitochondrial
F: ATP-dependent Clp protease proteolytic subunit, mitochondrial
G: ATP-dependent Clp protease proteolytic subunit, mitochondrial
H: ATP-dependent Clp protease proteolytic subunit, mitochondrial
I: ATP-dependent Clp protease proteolytic subunit, mitochondrial
J: ATP-dependent Clp protease proteolytic subunit, mitochondrial
K: ATP-dependent Clp protease proteolytic subunit, mitochondrial
L: ATP-dependent Clp protease proteolytic subunit, mitochondrial
M: ATP-dependent Clp protease proteolytic subunit, mitochondrial
N: ATP-dependent Clp protease proteolytic subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,94329
Polymers338,65914
Non-polymers7,28415
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Analytical gel filtration indicatges ClpP as a tetradecamer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50600 Å2
ΔGint-254 kcal/mol
Surface area81270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.890, 97.025, 131.420
Angle α, β, γ (deg.)90.000, 93.700, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit, mitochondrial / Endopeptidase Clp


Mass: 24189.912 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLPP / Production host: Escherichia coli (E. coli) / References: UniProt: Q16740, endopeptidase Clp
#2: Chemical
ChemComp-9DF / (6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide


Mass: 518.571 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C27H33F3N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3350
PH range: 7.0-8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.13→54.38 Å / Num. obs: 156976 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
2.13-2.196.51.2311569761100
9.53-54.386.90.042156976199.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TG6

1tg6


Resolution: 2.13→54.33 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.868 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 7770 5 %RANDOM
Rwork0.23 ---
obs0.2318 148823 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 158.65 Å2 / Biso mean: 51.405 Å2 / Biso min: 23.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-1.06 Å2
2---2.52 Å20 Å2
3---3.83 Å2
Refinement stepCycle: final / Resolution: 2.13→54.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18299 0 519 254 19072
Biso mean--75.33 44.66 -
Num. residues----2399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01919208
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218092
X-RAY DIFFRACTIONr_angle_refined_deg1.6442.01226112
X-RAY DIFFRACTIONr_angle_other_deg1.008341960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80352357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.10224.417686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.307153220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6921580
X-RAY DIFFRACTIONr_chiral_restr0.0920.23026
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02120773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023471
LS refinement shellResolution: 2.13→2.182 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.401 508 -
Rwork0.381 10627 -
obs--96.12 %

+
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