[English] 日本語
Yorodumi
- EMDB-49273: Cryo-EM structure of ClpX from Pseudomonas aeruginosa -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49273
TitleCryo-EM structure of ClpX from Pseudomonas aeruginosa
Map data
Sample
  • Complex: ClpX
KeywordsClpXP / full-engaged state / AAA protease / CHAPERONE
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsGhanbarpour A / Sauer RT / Davis JH
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01-GM144542 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM141517 United States
National Science Foundation (NSF, United States)2046778 United States
CitationJournal: Protein Sci / Year: 2025
Title: Structural insights into the Pseudomonas aeruginosa ClpP1•ClpP2 heterocomplex and its interactions with the AAA+ ClpX unfoldase.
Authors: Alireza Ghanbarpour / Jia Jia Zhang / Joseph H Davis / Tania A Baker / Robert T Sauer /
Abstract: ClpXP and other AAA+ proteases play central roles in bacterial proteostasis by degrading misfolded and regulatory proteins. In Pseudomonas aeruginosa, ClpXP consists of the ClpX unfoldase and ClpP ...ClpXP and other AAA+ proteases play central roles in bacterial proteostasis by degrading misfolded and regulatory proteins. In Pseudomonas aeruginosa, ClpXP consists of the ClpX unfoldase and ClpP peptidase, which influence critical adaptive processes contributing to stress resistance. P. aeruginosa ClpP1 and ClpP2 paralogs assemble into homomeric (ClpP1•ClpP1) and heteromeric (ClpP1•ClpP2) complexes. ClpP2 is only active in the ClpP1•ClpP2 heterocomplex. Here, we present a cryo-EM structure of ClpX•ClpP1•ClpP2, revealing how ClpX binds ClpP1, which in turn interacts with ClpP2. Comparison of the active heterocomplex with an inactive ClpP2 crystal structure shows that ClpP1 binding induces conformational changes in ClpP2, stabilizing an active catalytic triad. Differences in ClpP1 and ClpP2 substrate-binding residues and an unstructured ClpP2 N-terminal segment that protrudes into the peptidase chamber likely contribute to distinct peptide-cleavage specificities of ClpX•ClpP1•ClpP2 and ClpX•ClpP1•ClpP1. Given the role of ClpP1•ClpP2 in biofilm formation and virulence, these structural insights may provide a foundation for developing selective inhibitors to combat P. aeruginosa infections.
History
DepositionFeb 18, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49273.png

Downloads & links

-
Map

FileDownload / File: emd_49273.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 256 pix.
= 287.77 Å		1.12 Å/pix.
x 256 pix.
= 287.77 Å		1.12 Å/pix.
x 256 pix.
= 287.77 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1241 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0797
Minimum - Maximum-0.2086447 - 0.5479093
Average (Standard dev.)0.00080272893 (±0.0151440175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 287.7696 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_49273_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_49273_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_49273_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ClpX

EntireName: ClpX
Components
  • Complex: ClpX

-
Supramolecule #1: ClpX

SupramoleculeName: ClpX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.67 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionDetails: Patch CTF estimation, cryoSPARC / Type: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135056
Initial angle assignmentType: PROJECTION MATCHING / Details: Ab-initio reconstruction, cryoSPARC
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

-
Atomic model buiding 1

SoftwareName: cryoSPARC (ver. 4.4.1)

+
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