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- PDB-31mr: CryoEM structure of a catalytically inactive CXC Chemokine-degrad... -

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Basic information

Entry
Database: PDB / ID: 31mr
TitleCryoEM structure of a catalytically inactive CXC Chemokine-degrading protease SpyCEP from Streptococcus pyogenes complexed with an anti-PA-domain monoclonal antibody
Components
  • (Cell envelope proteinase A) x 2
  • Anti-PA-domain monoclonal antibody (3F2G10) Heavy chain variable region
  • Anti-PA-domain monoclonal antibody (3F2G10) Light chain variable region
KeywordsPROTEIN BINDING / Bacterial / protease / complex / antibody / immune evasion / chemokine
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Fn3-like domain / C5a peptidase-like domain / Fn3-like domain / : / PA domain / PA domain superfamily / PA domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Peptidase S8, subtilisin, His-active site ...Fn3-like domain / C5a peptidase-like domain / Fn3-like domain / : / PA domain / PA domain superfamily / PA domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Gram-positive cocci surface proteins LPxTG motif profile. / Peptidase S8, subtilisin-related / LPXTG cell wall anchor domain / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Immunoglobulin-like fold
Similarity search - Domain/homology
Cell envelope proteinase A
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsLau, R.J. / Barritt, J.D. / Wu, G.H.Y. / Huemer, C.B. / Matthews, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)UKRI682 United Kingdom
CitationJournal: PNAS / Year: 2026
Title: SpyCEP dismantles neutrophil immunity via disorder-driven chemokine remodeling and GAG targeting
Authors: Lau, R.J. / Giblin, S.P. / Sugar, A. / Di Maio, A. / Tassini, G. / Huse, K. / Chorev, D. / Chen, Y. / Wu, G.H.Y. / Huemer, C.B. / Kim, S.Y. / Matthews, J. / Muloud, B. / Chen, L. / McKenna, ...Authors: Lau, R.J. / Giblin, S.P. / Sugar, A. / Di Maio, A. / Tassini, G. / Huse, K. / Chorev, D. / Chen, Y. / Wu, G.H.Y. / Huemer, C.B. / Kim, S.Y. / Matthews, J. / Muloud, B. / Chen, L. / McKenna, S. / Xu, Y. / Massai, L. / Muzzi, C. / Ferhati, X. / Necchi, F. / Moriel, D.G. / Feizi, T. / Liu, Y. / Pease, J.E. / Sriskandan, S. / Matthews, S.
History
DepositionJun 12, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell envelope proteinase A
B: Cell envelope proteinase A
H: Anti-PA-domain monoclonal antibody (3F2G10) Heavy chain variable region
L: Anti-PA-domain monoclonal antibody (3F2G10) Light chain variable region


Theoretical massNumber of molelcules
Total (without water)198,7634
Polymers198,7634
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Cell envelope proteinase A / Peptidase S8 PrtS/CepA protein


Mass: 24609.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: cepA, SP119_0326 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q201Z7
#2: Protein Cell envelope proteinase A / Peptidase S8 PrtS/CepA protein


Mass: 148494.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: cepA, SP119_0326 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q201Z7
#3: Antibody Anti-PA-domain monoclonal antibody (3F2G10) Heavy chain variable region


Mass: 13333.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Antibody Anti-PA-domain monoclonal antibody (3F2G10) Light chain variable region


Mass: 12324.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: SpyCEP complexed with 3F2G10 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.325 MDa / Experimental value: YES
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8 / Details: 20 mM Tris pH 8.0, 200 mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMsodium chlorideNaCl1
220 mMtris hydrochlorideTris-HCL1
SpecimenConc.: 1.625 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 294.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 79000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1959
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7ISOLDEmodel fitting
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1351301
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 660420 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 129.9 / Protocol: FLEXIBLE FIT / Space: REAL / Details: Flexible fitting all performed in ISOLDE
Atomic model buildingSource name: AlphaFold / Type: in silico model

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