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- PDB-9pr9: Crystal structure of the Clostridiodes difficile CspA homodimer -

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Basic information

Entry
Database: PDB / ID: 9pr9
TitleCrystal structure of the Clostridiodes difficile CspA homodimer
ComponentsGermination-specific protease
KeywordsSIGNALING PROTEIN / Pseudoproteases / homodimer / signaling proteins
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
Csp protease B, prodomain / Csp protease B prodomain / CspA-like domain / : / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
Germination-specific protease
Similarity search - Component
Biological speciesClostridia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.26 Å
AuthorsHeldwein, E.E. / Gonzalez-Del Pino, G.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM108684-08 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K12GM133314 United States
CitationJournal: To Be Published
Title: The CspC:CspA heterodimer transduces germinant and co-germinant signals during C. difficile spore germination.
Authors: McNellis, M.E. / Gonzalez-Del Pino, G.L. / Serrano-Jimenez, J.A. / Forster, E.R. / Stoica, A.I. / Heldwein, E.E. / Shen, A.
History
DepositionJul 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Germination-specific protease
B: Germination-specific protease
C: Germination-specific protease
D: Germination-specific protease


Theoretical massNumber of molelcules
Total (without water)245,3184
Polymers245,3184
Non-polymers00
Water00
1
A: Germination-specific protease
B: Germination-specific protease


Theoretical massNumber of molelcules
Total (without water)122,6592
Polymers122,6592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-13 kcal/mol
Surface area39350 Å2
MethodPISA
2
C: Germination-specific protease
D: Germination-specific protease


Theoretical massNumber of molelcules
Total (without water)122,6592
Polymers122,6592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-11 kcal/mol
Surface area38930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.980, 131.930, 155.327
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein
Germination-specific protease


Mass: 61329.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridia (bacteria) / Gene: cspBA, CDR20291_2147 / Production host: Escherichia (bacteria) / References: UniProt: A0A9R0BLF4
Has protein modificationN

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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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.2 M lithium sulfate, 0.1 M morpholinoethane sulfonic acid (MES) pH 6.0, and 20% w/v polyethylene glycol (PEG) 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.22→100.6 Å / Num. obs: 42547 / % possible obs: 99.8 % / Redundancy: 7.9 % / CC1/2: 0.967 / Net I/σ(I): 3.09
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
3.22-3.330950.3271
3.3-3.3930220.3921
3.39-3.4929260.4941
3.49-3.628840.5711
3.6-3.7227640.681
3.72-3.8526900.761
3.85-3.9926160.8751
3.99-4.1624860.9021
4.16-4.3424270.9541
4.34-4.5522900.9611
4.55-4.821920.9761
4.8-5.0920860.9621
5.09-5.4419480.9511
5.44-5.8818380.9621
5.88-6.4416960.9571
6.44-7.215530.9791
7.2-8.3113820.9871

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.26→100.55 Å / SU ML: 0.5399 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.0581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3215 1934 4.76 %
Rwork0.2789 38655 -
obs0.281 40589 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.36 Å2
Refinement stepCycle: LAST / Resolution: 3.26→100.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15720 0 0 0 15720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005316033
X-RAY DIFFRACTIONf_angle_d1.018121815
X-RAY DIFFRACTIONf_chiral_restr0.05912509
X-RAY DIFFRACTIONf_plane_restr0.00862819
X-RAY DIFFRACTIONf_dihedral_angle_d10.4915673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.26-3.340.44551300.38142515X-RAY DIFFRACTION91.49
3.34-3.430.40751340.37042666X-RAY DIFFRACTION96.59
3.43-3.530.42681370.34662711X-RAY DIFFRACTION98.82
3.53-3.650.40221460.32352753X-RAY DIFFRACTION99.15
3.65-3.780.3531260.31882752X-RAY DIFFRACTION99.69
3.78-3.930.35961420.29242762X-RAY DIFFRACTION99.69
3.93-4.110.29021280.27862753X-RAY DIFFRACTION99.72
4.11-4.320.29921440.25052761X-RAY DIFFRACTION99.62
4.32-4.590.2631350.23322773X-RAY DIFFRACTION99.59
4.59-4.950.2761380.23572791X-RAY DIFFRACTION99.59
4.95-5.450.27881390.25512787X-RAY DIFFRACTION99.59
5.45-6.240.311450.27142819X-RAY DIFFRACTION99.8
6.24-7.850.30311420.27382850X-RAY DIFFRACTION99.93
7.86-100.550.311480.26142962X-RAY DIFFRACTION99.27

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