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Basic information

Entry
Database: EMDB / ID: EMD-58529
TitleCryoEM structure of a catalytically inactive CXC Chemokine-degrading protease SpyCEP from Streptococcus pyogenes complexed with an anti-N-terminal monoclonal antibody
Map data
Sample
  • Complex: SpyCEP complexed with 10B6C10
    • Protein or peptide: Streptococcus pyogenes cell envelope protease (SpyCEP) N-terminal D151A
    • Protein or peptide: Streptococcus pyogenes cell envelope protease (SpyCEP) C-terminal S617A
    • Protein or peptide: Anti-N-terminal monoclonal antibody (10B6C10) Light chain variable region
    • Protein or peptide: Anti-N-terminal monoclonal antibody (10B6C10) Heavy chain variable region
KeywordsBacterial / protease / complex / antibody / immune evasion / chemokine / PROTEIN BINDING
Biological speciesMus musculus (house mouse) / Streptococcus pyogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsLau RJ / Wu GHY / Barritt JD / Huemer CB / Matthews S
Funding support United Kingdom, 1 items
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 RJ / Giblin SP / Sugar A / Di Maio A / Tassini G / Huse K / Chorev D / Chen Y / Wu GHY / Huemer CB / Kim SY / Matthews J / Muloud B / Chen L / McKenna S / Xu Y / Massai L / Muzzi C / ...Authors: Lau RJ / Giblin SP / Sugar A / Di Maio A / Tassini G / Huse K / Chorev D / Chen Y / Wu GHY / Huemer CB / Kim SY / Matthews J / Muloud B / Chen L / McKenna S / Xu Y / Massai L / Muzzi C / Ferhati X / Necchi F / Moriel DG / Feizi T / Liu Y / Pease JE / Sriskandan S / Matthews S
History
DepositionJun 12, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58529.png

Downloads & links

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Map

FileReleased
Voxel sizeX=Y=Z: 1.16 Å
Density
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.25459588 - 0.9041056
Average (Standard dev.)0.00009264415 (±0.020034187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions344344344
Spacing344344344
CellA=B=C: 399.03998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : SpyCEP complexed with 10B6C10

EntireName: SpyCEP complexed with 10B6C10
Components
  • Complex: SpyCEP complexed with 10B6C10
    • Protein or peptide: Streptococcus pyogenes cell envelope protease (SpyCEP) N-terminal D151A
    • Protein or peptide: Streptococcus pyogenes cell envelope protease (SpyCEP) C-terminal S617A
    • Protein or peptide: Anti-N-terminal monoclonal antibody (10B6C10) Light chain variable region
    • Protein or peptide: Anti-N-terminal monoclonal antibody (10B6C10) Heavy chain variable region

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Supramolecule #1: SpyCEP complexed with 10B6C10

SupramoleculeName: SpyCEP complexed with 10B6C10 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: C1 symmetry
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 325 KDa

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Macromolecule #1: Streptococcus pyogenes cell envelope protease (SpyCEP) N-terminal...

MacromoleculeName: Streptococcus pyogenes cell envelope protease (SpyCEP) N-terminal D151A
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH ADELSTMSEP TITNHAQQQA QHLTNTELSS AESKSQDTSQ ITLKTNREKE QSQDLVSEPT TTELADTDAA SMANTGSDAT QKSASLPPVN TDVHDWVKTK GAWDKGYKGQ GKVVAVIATG IDPAHQSMRI SDVSTAKVKS KEDMLARQKA AGINYGSWIN ...String:
MGSSHHHHHH ADELSTMSEP TITNHAQQQA QHLTNTELSS AESKSQDTSQ ITLKTNREKE QSQDLVSEPT TTELADTDAA SMANTGSDAT QKSASLPPVN TDVHDWVKTK GAWDKGYKGQ GKVVAVIATG IDPAHQSMRI SDVSTAKVKS KEDMLARQKA AGINYGSWIN DKVVFAHNYV ENSDNIKENQ FEDFDEDWEN FEFDAEAEPK AIKKHKIYRP Q

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Macromolecule #2: Streptococcus pyogenes cell envelope protease (SpyCEP) C-terminal...

MacromoleculeName: Streptococcus pyogenes cell envelope protease (SpyCEP) C-terminal S617A
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSSTQAPK ETVIKTEETD GSHDIDWTQT DDDTKYESHG MHVTGIVAGN SKEAAATGER FLGIAPEAQV MFMRVFANDI MGSAESLFIK AIEDAVALGA DVINLSLGTA NGAQLSGSKP LMEAIEKAKK AGVSVVVAAG NERVYGSDHD DPLATNPDYG LVGSPSTGRT ...String:
MGSSSTQAPK ETVIKTEETD GSHDIDWTQT DDDTKYESHG MHVTGIVAGN SKEAAATGER FLGIAPEAQV MFMRVFANDI MGSAESLFIK AIEDAVALGA DVINLSLGTA NGAQLSGSKP LMEAIEKAKK AGVSVVVAAG NERVYGSDHD DPLATNPDYG LVGSPSTGRT PTSVAAINSK WVIQRLMTVK ELENRADLNH GKAIYSESVD FKDIKDSLGY DKSHQFAYVK ESTDAGYNAQ DVKGKIALIE RDPNKTYDEM IALAKKHGAL GVLIFNNKPG QSNRSMRLTA NGMGIPSAFI SHEFGKAMSQ LNGNGTGSLE FDSVVSKAPS QKGNEMNHFS NWGLTSDGYL KPDITAPGGD IYSTYNDNHY GSQTGTSMAS PQIAGASLLV KQYLEKTQPN LPKEKIADIV KNLLMSNAQI HVNPETKTTT SPRQQGAGLL NIDGAVTSGL YVTGKDNYGS ISLGNITDTM TFDVTVHNLS NKDKTLRYDT ELLTDHVDPQ KGRFTLTSHS LKTYQGGEVT VPANGKVTVR VTMDVSQFTK ELTKQMPNGY YLEGFVRFRD SQDDQLNRVN IPFVGFKGQF ENLAVAEESI YRLKSQGKTG FYFDESGPKD DIYVGKHFTG LVTLGSETNV STKTISDNGL HTLGTFKNAD GKFILEKNAQ GNPVLAISPN GDNNQNFAAF KGVFLRKYQG LKASVYHASD KEHKNPLWVS PESFKGDKNF NSDIRFAKST TLLGTAFSGK SLTGAELPDG HYHYVVSYYP DVVGAKRQEM TFDMILDRQK PVLSQATFDP ETNRFKPEPL KDRGLAGVRK DSAFYLERKD NKPYTVTIND SYKYVSVEDN KTFVERQADG SFILPLDKAK LGDFYYMVED FAGNVAIAKL GDHLPQTLGK TPIKLKLTDG NYQTKETLKD NLEMTQSDTG LVTNQAQLAV VHRNQPQSQL TKMNQDFFIS PNEDGNKDFV AFKGLKNNVY NDLTVNVYAK DDHQKQTPIW SSQAGASVSA IESTAWYGIT ARGSKVMPGD YQYVVTYRDE HGKEHQKQYT ISVNDKKPMI TQGRFDTING VDHFTPDKTK ALGSSGIVRE EVFYLAKKNG RKFDVTEGKD GITVSDNKVY IPKNPDGSYT ISKRDGVTLS DYYYLVEDRA GNVSFATLRD LKAVGKDKAV VNFGLDLPVP EDKQIVNFTY LVRDADGKPI ENLEYYNNSG NSLILPYGKY TVELLTYDTN AAKLESDKIV SFTLSADNNF QQVTFKITML ATSQITAHFD HLLPEGSRVS LKTAQDQLIP LEQSLYVPKA YGKTVQEGTY EVVVSLPKGY RIEGNTKVNT LPNEVHELSL RLVKVGDASD STGDHKVMSK NNSQALTASA TPTKSTTSAT AKAALEHHHH HH

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Macromolecule #3: Anti-N-terminal monoclonal antibody (10B6C10) Light chain variabl...

MacromoleculeName: Anti-N-terminal monoclonal antibody (10B6C10) Light chain variable region
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
SequenceString:
DAVMTQTPLS LPVSLGDQAS ISCRSSQSLE NSNGNTYLNW YLQKPGQSPQ LLIYRVSNRF SGVLDRFSGS GSGTDFTLKI SRVEAEDLGV YFCLQVTHVP LTFGAGTKLE LK

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Macromolecule #4: Anti-N-terminal monoclonal antibody (10B6C10) Heavy chain variabl...

MacromoleculeName: Anti-N-terminal monoclonal antibody (10B6C10) Heavy chain variable region
type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
SequenceString:
EVKLVESGGG LVQPGGSLRL SCATSGFTFT DYYMSWVRQP PGKALEWLGF IRNKANGYTI EYSASVKGRF TISRDNSQSI LYLQMNTLRV EDSATYYCAR ALDYWGLGTT LTVSS

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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

Concentration1.625 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
20.0 mMTris-HCLtris hydrochloride
0.03 %DDMn dodecyl beta D maltoside

Details: 20 mM Tris pH 7.0, 200 mM NaCl, 0.003% DDM
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1182 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 100000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 223716
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 44200
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementOverall B value: 102.9

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