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- EMDB-66088: Cryo-EM structure of Clostridium perfringens pili CppA in complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-66088
TitleCryo-EM structure of Clostridium perfringens pili CppA in complex with CppB
Map data
Sample
  • Organelle or cellular component: Covalent complex of Clostridium perfringens pili proteins CppB and CppA
    • Protein or peptide: Probable surface protein
    • Protein or peptide: SpaA-like prealbumin fold domain-containing protein
KeywordsShaft pilin / Tip pilin / Clostridium perfringens / surface protein / collagen binding protein / PROTEIN FIBRIL
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsNonaka Y / Tamai E / Kamitori S
Funding support Japan, 1 items
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, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66088.png

Downloads & links

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Map

FileDownload / File: emd_66088.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 180 pix.
= 198. Å		1.1 Å/pix.
x 180 pix.
= 198. Å		1.1 Å/pix.
x 180 pix.
= 198. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-1.6056725 - 1.8036065
Average (Standard dev.)0.001057919 (±0.041772865)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 198.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66088_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66088_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Covalent complex of Clostridium perfringens pili proteins CppB an...

EntireName: Covalent complex of Clostridium perfringens pili proteins CppB and CppA
Components
  • Organelle or cellular component: Covalent complex of Clostridium perfringens pili proteins CppB and CppA
    • Protein or peptide: Probable surface protein
    • Protein or peptide: SpaA-like prealbumin fold domain-containing protein

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Supramolecule #1: Covalent complex of Clostridium perfringens pili proteins CppB an...

SupramoleculeName: Covalent complex of Clostridium perfringens pili proteins CppB and CppA
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium perfringens str. 13 (bacteria)

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Macromolecule #1: Probable surface protein

MacromoleculeName: Probable surface protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium perfringens str. 13 (bacteria)
Molecular weightTheoretical: 49.98332 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTPSISKDAP IKGSITISKK GATFTAYKLL DAIKSGDAYE YSVNSDLKDF FNNSNYGSYS QESIQKLNGE QVKEFAINLH KYILENKKS GQELKDGQKN TVDLGYYLVT ETSSDSEGAA VASTPIIVSV PQVSGDSWNY DVTINPKDNT PILEKNIVKE N QRVKTSSE ...String:
MTPSISKDAP IKGSITISKK GATFTAYKLL DAIKSGDAYE YSVNSDLKDF FNNSNYGSYS QESIQKLNGE QVKEFAINLH KYILENKKS GQELKDGQKN TVDLGYYLVT ETSSDSEGAA VASTPIIVSV PQVSGDSWNY DVTINPKDNT PILEKNIVKE N QRVKTSSE NIGDVVKYEV KASIPVYQKN AQNIMYKFTD TMSKGLTYDE KTGFKVTSGD KVFAKDTDYT VDVKKQEDGS TV ITINFVY ENIKAYAETG ITLNYQATLN KDAVISNKEN LGNTNNIQLD YTNNPHVKDS YKKLTDKVTT YTFGFGITKV DSE LNSKLL QGAEFSVKDA GGKIVAKYTY DEKGQVVYLS GNGVTNSKGI TTFLGLKEGK YFITEEVAPS GYSLLKNPVE VTIT ANKDE SGNYTGAATI EISNGNKAGQ IINDISEKDG NILFNVQIEN HAHHHHHH

UniProtKB: Probable surface protein

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Macromolecule #2: SpaA-like prealbumin fold domain-containing protein

MacromoleculeName: SpaA-like prealbumin fold domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium perfringens str. 13 (bacteria)
Molecular weightTheoretical: 74.482711 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEETKSVQND GAVEITSTTF ESNTVAKGIS NNLRIDYKIL NKDKLKDGDK IVISLPDIFK DIEPKCHDQH FKDFDVKDGV VTLTFNENV EKAVTGYMII RFVGNSNIRK GVSYPVSIDL NGKPSTVYIT GEEYSNSSSG AQYPLMYKTA DLPTAATDKE Q GREYYGEI ...String:
MEETKSVQND GAVEITSTTF ESNTVAKGIS NNLRIDYKIL NKDKLKDGDK IVISLPDIFK DIEPKCHDQH FKDFDVKDGV VTLTFNENV EKAVTGYMII RFVGNSNIRK GVSYPVSIDL NGKPSTVYIT GEEYSNSSSG AQYPLMYKTA DLPTAATDKE Q GREYYGEI VDRNKPIKYF VEINLGDGVN PNTRSYLSNA DFFDNIPKGM ALDVNSICIK RMGYYDERSS DVTKDFWESN RI KADTKHL EINFGDIRYE RYTVIYETRI TSTESGYLND AKLYYDDKEL PSKHYSKLSK DAGALNVYKY VDKTKVKNNL NDQ KIKYDI KFDSYGYFFK DTLNIIDKLD PRLSDIKITA TDQFITDFDE NTKELVIKNS NGDIDAKKPA YITIEASMKN VGPG EVVKN IAYVNGNPTN EVSTRKNPIV EIIKVSKDDV ESNLLEGAIF KLTTKDGKTV KDVYNKGVKT FTTSSEGSIR FELPN GDYK LEEIKAPNGY KLDQTPIEFT VNDESKIVKV VAKDDPLPTT CNLVINKINE KEIPILGAKF KLFEESNPKK VLKFSS QKN NYELNQNGVG KLTPSGKNAS FKINNLHYGN YILKEVQAPK GYKLSDDIYI TLGFEESFYR VGKQGEKIIL NKNTETN TY NISVENVPRI ILPET

UniProtKB: SpaA-like prealbumin fold domain-containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.26 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris-HCl, 100 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 3806 / Average exposure time: 3.88 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 103291
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5xcc


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9wme:
Cryo-EM structure of Clostridium perfringens pili CppA in complex with CppB

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