[English] 日本語
Yorodumi
- PDB-9wme: Cryo-EM structure of Clostridium perfringens pili CppA in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9wme
TitleCryo-EM structure of Clostridium perfringens pili CppA in complex with CppB
Components
  • Probable surface protein
  • SpaA-like prealbumin fold domain-containing protein
KeywordsPROTEIN FIBRIL / Shaft pilin / Tip pilin / Clostridium perfringens / surface protein / collagen binding protein
Function / homology
Function and homology information


Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / : / Fimbrial isopeptide formation D2 domain / Fibrogen-binding domain 1 / Prealbumin-like fold domain / Prealbumin-like fold domain / Adhesion domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Probable surface protein / SpaA-like prealbumin fold domain-containing protein
Similarity search - Component
Biological speciesClostridium perfringens str. 13 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsNonaka, Y. / Tamai, E. / Kamitori, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K04944 Japan
CitationJournal: FEBS J / Year: 2026
Title: Dynamic motion of bacterial surface pili based on structural analyses of covalently linked complexes formed by tip and shaft pili proteins from Clostridium perfringens.
Authors: Yasuhiro Nonaka / Eiji Tamai / Hiroshi Sekiya / Shigehiro Kamitori /
Abstract: The pathogenesis and infectivity of Gram-positive bacteria are mediated by many surface proteins covalently attached to the bacterial cell wall. Pili are types of surface appendages that play ...The pathogenesis and infectivity of Gram-positive bacteria are mediated by many surface proteins covalently attached to the bacterial cell wall. Pili are types of surface appendages that play important roles in the initial adhesion of bacterial cells to host tissues and bacterial colonization. The Gram-positive bacterium Clostridium perfringens (C. perfringens), one of the pathogenic clostridial species causing gas gangrene and food poisoning, has sortase-mediated pili composed of shaft/major pilin A (CppA) and tip/minor pilin B (CppB). The pilus shaft is formed by covalent polymerization of CppA, and CppB is covalently attached to the tip of the shaft involved in adhesion to the host cell. The formation of covalent bonds between CppB and CppA, as well as between CppA and CppA, is catalyzed by class C sortase (CpSrtC), a member of the cysteine transpeptidase family. Since pili consistently have CppB at their tip, CpSrtC is the enzyme that preferentially catalyzes the attachment of CppB (tip) to CppA (shaft) rather than polymerization of CppAs by an unknown mechanism. We determined the structures of complexes formed by covalently linking CppB and CppA by X-ray crystallography and cryo-EM analysis. The complexes have an elongated structure in which β-sandwich folded domains are sequentially arranged, and an amide bond between Thr688 of CppB and Lys174 of CppA was clearly identified. The determined structures allowed us to construct a three-dimensional structure model with dynamic motion of C. perfringens pili, and proposed new insights into the mechanism by which CppB is preferentially attached to CppA.
History
DepositionSep 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable surface protein
B: SpaA-like prealbumin fold domain-containing protein


Theoretical massNumber of molelcules
Total (without water)124,4662
Polymers124,4662
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Probable surface protein / CppA


Mass: 49983.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens str. 13 (bacteria)
Gene: CPE0156 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XP10
#2: Protein SpaA-like prealbumin fold domain-containing protein / CppB


Mass: 74482.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens str. 13 (bacteria)
Gene: CPE0155 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XP11
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Covalent complex of Clostridium perfringens pili proteins CppB and CppA
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Clostridium perfringens str. 13 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 20 mM Tris-HCl, 100 mM NaCl
SpecimenConc.: 0.26 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 3.88 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 3806

-
Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2Topazparticle selection
3EPUimage acquisition
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC4.4.13D reconstruction
14PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103291 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 5XCC

5xcc


Pdb chain-ID: A / Accession code: 5XCC / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 55.28 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00133512
ELECTRON MICROSCOPYf_angle_d0.33484749
ELECTRON MICROSCOPYf_chiral_restr0.0406546
ELECTRON MICROSCOPYf_plane_restr0.0017609
ELECTRON MICROSCOPYf_dihedral_angle_d2.4058471

+
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