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- PDB-9vo5: X-ray structure of Clostridium perfringens pili CppB-D3D4D5-CppA ... -

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Basic information

Entry
Database: PDB / ID: 9vo5
TitleX-ray structure of Clostridium perfringens pili CppB-D3D4D5-CppA covalent complex
Components
  • Probable surface protein
  • SpaA-like prealbumin fold domain-containing protein
KeywordsSTRUCTURAL PROTEIN / pili / tip pilin / major pilin
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKamitori, S. / Nonaka, Y. / Tamai, E.
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
DepositionJul 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2026Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)181,8534
Polymers181,8534
Non-polymers00
Water28,1931565
1
A: Probable surface protein
B: SpaA-like prealbumin fold domain-containing protein


Theoretical massNumber of molelcules
Total (without water)90,9272
Polymers90,9272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Probable surface protein
D: SpaA-like prealbumin fold domain-containing protein


Theoretical massNumber of molelcules
Total (without water)90,9272
Polymers90,9272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.360, 70.710, 110.590
Angle α, β, γ (deg.)93.63, 107.20, 89.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Probable surface protein / CppA


Mass: 49983.320 Da / Num. of mol.: 2
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: 40943.406 Da / Num. of mol.: 2
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1565 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Magnesium formate dihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→48.36 Å / Num. obs: 156433 / % possible obs: 95.6 % / Redundancy: 1.8 % / CC1/2: 0.996 / Net I/σ(I): 8.98
Reflection shellResolution: 1.85→1.9 Å / Num. unique obs: 20342 / CC1/2: 0.854

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.85→48.36 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.252 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21619 7902 5.1 %RANDOM
Rwork0.18923 ---
obs0.19058 148531 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.952 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.15 Å2-0.14 Å2
2---0.24 Å2-0.18 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.85→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12506 0 0 1565 14071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.01212722
X-RAY DIFFRACTIONr_bond_other_d00.01612151
X-RAY DIFFRACTIONr_angle_refined_deg0.51.82417209
X-RAY DIFFRACTIONr_angle_other_deg0.2151.77828190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.651590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.239512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.402102353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0270.21963
X-RAY DIFFRACTIONr_gen_planes_refined00.0214581
X-RAY DIFFRACTIONr_gen_planes_other00.022641
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8832.1336372
X-RAY DIFFRACTIONr_mcbond_other2.8832.1336372
X-RAY DIFFRACTIONr_mcangle_it3.8233.8257958
X-RAY DIFFRACTIONr_mcangle_other3.8233.8257959
X-RAY DIFFRACTIONr_scbond_it4.3862.6326350
X-RAY DIFFRACTIONr_scbond_other4.3862.6326351
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4834.5839252
X-RAY DIFFRACTIONr_long_range_B_refined8.42129.3514225
X-RAY DIFFRACTIONr_long_range_B_other8.34724.7913720
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 592 -
Rwork0.283 10825 -
obs--94.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1688-0.0306-0.41450.31780.10611.1840.0712-0.00630.0446-0.02440.03410.0027-0.09750.0055-0.10520.08880.02810.05180.11010.03050.0661-4.60744.062911.8001
20.22010.1474-0.33470.4279-0.57450.89310.0574-0.0015-0.01450.0508-0.06110.008-0.08210.09070.00370.0948-0.00860.00680.10890.00620.0523-7.8497-15.867845.6495
30.21290.3646-0.07970.7694-0.32660.4077-0.00660.0321-0.01460.0450.03670.01090.0001-0.0265-0.03010.08410.01220.01150.09040.00370.0826-26.0524-40.00567.4053
40.2791-0.09380.23460.7058-0.71331.91160.08990.03110.0978-0.0167-0.02270.0221-0.03060.0474-0.06720.10280.03020.02330.07780.02580.05948.605336.4893-99.7124
50.49820.21990.18431.2281-1.18821.72810.0414-0.0648-0.02250.0224-0.1421-0.0461-0.08970.08320.10070.1265-0.02430.01560.0849-0.01880.047318.211224.9234-63.1216
60.2142-0.0092-0.06450.0791-0.00920.3564-0.04230.01390.00510.02710.04150.04790.01070.07610.00080.07690.02370.00920.09010.01310.09547.01794.2425-24.3491
70.26480.1049-0.36640.2075-0.49041.3688-0.0860.0065-0.00670.07040.0811-0.0152-0.0551-0.11870.00490.1540.0425-0.0040.1344-0.00130.0166-50.1655-24.910820.4135
80.29250.091-0.30430.1758-0.17140.5185-0.0185-0.00220.03070.00410.0177-0.0160.0646-0.0270.00080.08590.00410.00190.09670.01370.0743-38.4507-19.6396-16.4365
90.82770.2598-0.51540.218-0.19790.6713-0.0330.05270.0215-0.01420.0129-0.02410.01390.00260.02010.05590.01020.00480.09180.01960.0898-13.8722-7.3269-41.4174
100.13660.0858-0.47810.4385-0.29522.20640.01070.0504-0.0470.0966-0.03760.0017-0.0618-0.03960.02690.0727-0.01820.02620.1363-0.04160.0638-71.7948-72.704128.5386
110.58330.15250.14710.21590.30261.6149-0.0667-0.03560.0636-0.05530.011-0.0165-0.10030.03570.05570.0692-0.01830.01870.0834-0.00620.0823-64.8297-69.263989.5622
120.0444-0.04020.05160.12170.08353.06440.06810.00420.0376-0.03560.0321-0.05930.3626-0.3599-0.10020.1483-0.05120.02480.12440.03260.0548-49.4682-47.606351.2511
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 174
2X-RAY DIFFRACTION2A175 - 337
3X-RAY DIFFRACTION3A338 - 476
4X-RAY DIFFRACTION4B331 - 452
5X-RAY DIFFRACTION5B453 - 551
6X-RAY DIFFRACTION6B552 - 688
7X-RAY DIFFRACTION7C38 - 174
8X-RAY DIFFRACTION8C175 - 337
9X-RAY DIFFRACTION9C338 - 476
10X-RAY DIFFRACTION10D333 - 452
11X-RAY DIFFRACTION11D453 - 551
12X-RAY DIFFRACTION12D552 - 688

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