[English] 日本語
Yorodumi
- EMDB-58555: Unknown entry -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-58555
TitleCryoEM structure of a catalytically inactive CXC Chemokine-degrading protease SpyCEP from Streptococcus pyogenes complexed with an anti-PA-domain monoclonal antibody
Map data
Sample
  • Complex: SpyCEP complexed with 3F2G10
    • Protein or peptide: Cell envelope proteinase A
    • Protein or peptide: Cell envelope proteinase A
    • Protein or peptide: Anti-PA-domain monoclonal antibody (3F2G10) Heavy chain variable region
    • Protein or peptide: Anti-PA-domain monoclonal antibody (3F2G10) Light chain variable region
KeywordsBacterial / protease / complex / antibody / immune evasion / chemokine / PROTEIN BINDING
Biological speciesStreptococcus pyogenes (bacteria) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsLau RJ / Barritt JD / Wu GHY / 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

-
Structure visualization

Supplemental images

emd_58555.png

Downloads & links

-
Map

FileReleased
Voxel sizeX=Y=Z: 0.75 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.12438007 - 0.28537354
Average (Standard dev.)-0.0002792762 (±0.004808477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 375.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : SpyCEP complexed with 3F2G10

EntireName: SpyCEP complexed with 3F2G10
Components
  • Complex: SpyCEP complexed with 3F2G10
    • Protein or peptide: Cell envelope proteinase A
    • Protein or peptide: Cell envelope proteinase A
    • Protein or peptide: Anti-PA-domain monoclonal antibody (3F2G10) Heavy chain variable region
    • Protein or peptide: Anti-PA-domain monoclonal antibody (3F2G10) Light chain variable region

-
Supramolecule #1: SpyCEP complexed with 3F2G10

SupramoleculeName: SpyCEP complexed with 3F2G10 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 325 KDa

-
Macromolecule #1: Cell envelope proteinase A

MacromoleculeName: Cell envelope proteinase A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 24.609822 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH ADELSTMSEP TITNHAQQQA QHLTNTELSS AESKSQDTSQ ITLKTNREKE QSQDLVSEPT TTELADTDAA SMANTGSDA TQKSASLPPV NTDVHDWVKT KGAWDKGYKG QGKVVAVIAT GIDPAHQSMR ISDVSTAKVK SKEDMLARQK A AGINYGSW ...String:
MGSSHHHHHH ADELSTMSEP TITNHAQQQA QHLTNTELSS AESKSQDTSQ ITLKTNREKE QSQDLVSEPT TTELADTDAA SMANTGSDA TQKSASLPPV NTDVHDWVKT KGAWDKGYKG QGKVVAVIAT GIDPAHQSMR ISDVSTAKVK SKEDMLARQK A AGINYGSW INDKVVFAHN YVENSDNIKE NQFEDFDEDW ENFEFDAEAE PKAIKKHKIY RPQ

UniProtKB: Cell envelope proteinase A

-
Macromolecule #2: Cell envelope proteinase A

MacromoleculeName: Cell envelope proteinase A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 148.494438 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSSTQAPK ETVIKTEETD GSHDIDWTQT DDDTKYESHG MHVTGIVAGN SKEAAATGER FLGIAPEAQV MFMRVFANDI MGSAESLFI KAIEDAVALG ADVINLSLGT ANGAQLSGSK PLMEAIEKAK KAGVSVVVAA GNERVYGSDH DDPLATNPDY G LVGSPSTG ...String:
MGSSSTQAPK ETVIKTEETD GSHDIDWTQT DDDTKYESHG MHVTGIVAGN SKEAAATGER FLGIAPEAQV MFMRVFANDI MGSAESLFI KAIEDAVALG ADVINLSLGT ANGAQLSGSK PLMEAIEKAK KAGVSVVVAA GNERVYGSDH DDPLATNPDY G LVGSPSTG RTPTSVAAIN SKWVIQRLMT VKELENRADL NHGKAIYSES VDFKDIKDSL GYDKSHQFAY VKESTDAGYN AQ DVKGKIA LIERDPNKTY DEMIALAKKH GALGVLIFNN KPGQSNRSMR LTANGMGIPS AFISHEFGKA MSQLNGNGTG SLE FDSVVS KAPSQKGNEM NHFSNWGLTS DGYLKPDITA PGGDIYSTYN DNHYGSQTGT AMASPQIAGA SLLVKQYLEK TQPN LPKEK IADIVKNLLM SNAQIHVNPE TKTTTSPRQQ GAGLLNIDGA VTSGLYVTGK DNYGSISLGN ITDTMTFDVT VHNLS NKDK TLRYDTELLT DHVDPQKGRF TLTSHSLKTY QGGEVTVPAN GKVTVRVTMD VSQFTKELTK QMPNGYYLEG FVRFRD SQD DQLNRVNIPF VGFKGQFENL AVAEESIYRL KSQGKTGFYF DESGPKDDIY VGKHFTGLVT LGSETNVSTK TISDNGL HT LGTFKNADGK FILEKNAQGN PVLAISPNGD NNQNFAAFKG VFLRKYQGLK ASVYHASDKE HKNPLWVSPE SFKGDKNF N SDIRFAKSTT LLGTAFSGKS LTGAELPDGH YHYVVSYYPD VVGAKRQEMT FDMILDRQKP VLSQATFDPE TNRFKPEPL KDRGLAGVRK DSAFYLERKD NKPYTVTIND SYKYVSVEDN KTFVERQADG SFILPLDKAK LGDFYYMVED FAGNVAIAKL GDHLPQTLG KTPIKLKLTD GNYQTKETLK DNLEMTQSDT GLVTNQAQLA VVHRNQPQSQ LTKMNQDFFI SPNEDGNKDF V AFKGLKNN VYNDLTVNVY AKDDHQKQTP IWSSQAGASV SAIESTAWYG ITARGSKVMP GDYQYVVTYR DEHGKEHQKQ YT ISVNDKK PMITQGRFDT INGVDHFTPD KTKALGSSGI VREEVFYLAK KNGRKFDVTE GKDGITVSDN KVYIPKNPDG SYT ISKRDG VTLSDYYYLV EDRAGNVSFA TLRDLKAVGK DKAVVNFGLD LPVPEDKQIV NFTYLVRDAD GKPIENLEYY NNSG NSLIL PYGKYTVELL TYDTNAAKLE SDKIVSFTLS ADNNFQQVTF KITMLATSQI TAHFDHLLPE GSRVSLKTAQ DQLIP LEQS LYVPKAYGKT VQEGTYEVVV SLPKGYRIEG NTKVNTLPNE VHELSLRLVK VGDALEHHHH HH

UniProtKB: Cell envelope proteinase A

-
Macromolecule #3: Anti-PA-domain monoclonal antibody (3F2G10) Heavy chain variable ...

MacromoleculeName: Anti-PA-domain monoclonal antibody (3F2G10) Heavy chain variable region
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.333943 KDa
SequenceString:
EVRLVESGGG LVKPGGSLKL SCAASGFTLN SYAMSWVRQT PEKRLEWVAS ISRGGSTFYP DDVRGRFTFS RDNARNILYL QMSSLRSED TAMYYCARGI LGNYGIFGAI DNWGQGTSVT VSS

-
Macromolecule #4: Anti-PA-domain monoclonal antibody (3F2G10) Light chain variable ...

MacromoleculeName: Anti-PA-domain monoclonal antibody (3F2G10) Light chain variable region
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.324799 KDa
SequenceString:
DIVMTQSPSS LAMSVGQKVT MSCKSSQNLL NSSNQKNYLA WYQQKPGQSP KLLVFFASSR ESGVPDRFIG SGSGTDFTLT ISSVQAEDL ADYFCQQHSS IPFTFGSGTK LEMK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.625 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
20.0 mMTris-HCLtris hydrochloride

Details: 20 mM Tris pH 8.0, 200 mM NaCl
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

-
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: 1959 / Average electron dose: 40.0 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: 79000
Sample stageCooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 1351301
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold 3 prediction of SpyCEP + 3F2G10
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 660420
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsFlexible fitting all performed in ISOLDE
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 129.9
Output model

PDB-31mr:
CryoEM structure of a catalytically inactive CXC Chemokine-degrading protease SpyCEP from Streptococcus pyogenes complexed with an anti-PA-domain monoclonal antibody

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more