[English] 日本語
Yorodumi
- PDB-9mk5: Crystal structure of Neisseria meningitidis ClpP protease complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mk5
TitleCrystal structure of Neisseria meningitidis ClpP protease complex with small molecule activator, Dioctatin
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / small molecule / inhibitor / activator / metabolite
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm
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
: / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMabanglo, M.F. / Houry, W.A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-148564 Canada
CitationJournal: Structure / Year: 2025
Title: Small molecule dysregulation of ClpP activity via bidirectional allosteric pathways.
Authors: Barghash, M.M. / Mabanglo, M.F. / Hoff, S.E. / Brozdnychenko, D. / Wong, K.S. / Binepal, G. / Ip, P. / Shen, J. / Furukawa, T. / Katayama, H. / Trudel, V. / Tan, J. / Yudin, A.K. / Gray- ...Authors: Barghash, M.M. / Mabanglo, M.F. / Hoff, S.E. / Brozdnychenko, D. / Wong, K.S. / Binepal, G. / Ip, P. / Shen, J. / Furukawa, T. / Katayama, H. / Trudel, V. / Tan, J. / Yudin, A.K. / Gray-Owen, S.D. / Sakuda, S. / Batey, R.A. / Vahidi, S. / Bonomi, M. / Houry, W.A.
History
DepositionDec 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)345,55619
Polymers343,76814
Non-polymers1,7875
Water14,862825
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.435, 127.304, 119.091
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

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


Mass: 24554.881 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: clpP, NMB1312 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JZ38, endopeptidase Clp
#2: Chemical
ChemComp-A1BMH / N-{(3S)-3-[(3S)-3-aminooctanamido]octanoyl}glycine / Dioctatin


Mass: 357.488 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H35N3O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 825 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium thiocyanate or potassium acetate, pH 7.5, 40% (+/-)-2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1.5212 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5212 Å / Relative weight: 1
ReflectionResolution: 1.9→119.09 Å / Num. obs: 225163 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.85 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.127 / Net I/σ(I): 9.8
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 1.8 / Num. unique obs: 224880 / CC1/2: 0.353

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→97.43 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 11332 5.04 %Random selection
Rwork0.2022 ---
obs0.2034 224879 98.99 %-
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→97.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19921 0 125 825 20871
LS refinement shellResolution: 1.9→1.94 Å
RfactorNum. reflection
Rfree0.4052 -
Rwork0.3594 -
obs-10725

+
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