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- EMDB-22205: IgA1 Protease -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-22205
TitleIgA1 Protease
Map datafree IgA1 Protease
Sample
  • Complex: IgA1 Protease
    • Protein or peptide: Immunoglobulin A1 protease
Keywordsmetalloprotease / IgA1 / IMMUNE SYSTEM
Function / homology
Function and homology information


IgA-specific metalloendopeptidase / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / TFIIIC-class transcription factor complex binding / metalloendopeptidase activity / proteolysis / zinc ion binding / extracellular region / membrane
Similarity search - Function
Peptidase M26, N-terminal domain / GLUG / Peptidase M26, C-terminal domain / M26 IgA1-specific Metallo-endopeptidase N-terminal region / M26 IgA1-specific Metallo-endopeptidase C-terminal region / The GLUG motif / G5 domain / G5 domain / G5 domain profile. / G5 ...Peptidase M26, N-terminal domain / GLUG / Peptidase M26, C-terminal domain / M26 IgA1-specific Metallo-endopeptidase N-terminal region / M26 IgA1-specific Metallo-endopeptidase C-terminal region / The GLUG motif / G5 domain / G5 domain / G5 domain profile. / G5 / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Immunoglobulin A1 protease
Similarity search - Component
Biological speciesStreptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsEisenmesser EZ / Zheng H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI146295 United States
CitationJournal: Nat Commun / Year: 2020
Title: Mechanism and inhibition of Streptococcus pneumoniae IgA1 protease.
Authors: Zhiming Wang / Jeremy Rahkola / Jasmina S Redzic / Ying-Chih Chi / Norman Tran / Todd Holyoak / Hongjin Zheng / Edward Janoff / Elan Eisenmesser /
Abstract: Opportunistic pathogens such as Streptococcus pneumoniae secrete a giant metalloprotease virulence factor responsible for cleaving host IgA1, yet the molecular mechanism has remained unknown since ...Opportunistic pathogens such as Streptococcus pneumoniae secrete a giant metalloprotease virulence factor responsible for cleaving host IgA1, yet the molecular mechanism has remained unknown since their discovery nearly 30 years ago despite the potential for developing vaccines that target these enzymes to block infection. Here we show through a series of cryo-electron microscopy single particle reconstructions how the Streptococcus pneumoniae IgA1 protease facilitates IgA1 substrate recognition and how this can be inhibited. Specifically, the Streptococcus pneumoniae IgA1 protease subscribes to an active-site-gated mechanism where a domain undergoes a 10.0 Å movement to facilitate cleavage. Monoclonal antibody binding inhibits this conformational change, providing a direct means to block infection at the host interface. These structural studies explain decades of biological and biochemical studies and provides a general strategy to block Streptococcus pneumoniae IgA1 protease activity to potentially prevent infection.
History
DepositionJun 23, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0128
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0128
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xjb
  • Surface level: 0.0128
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22205.png

Downloads & links

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Map

FileDownload / File: emd_22205.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfree IgA1 Protease
Voxel sizeX=Y=Z: 0.864 Å
Density
Contour LevelBy AUTHOR: 0.0128 / Movie #1: 0.0128
Minimum - Maximum-0.025127375 - 0.05874301
Average (Standard dev.)0.00009318504 (±0.0012928853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 290.30402 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8640.8640.864
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z290.304290.304290.304
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS336336336
D min/max/mean-0.0250.0590.000

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Supplemental data

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Sample components

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Entire : IgA1 Protease

EntireName: IgA1 Protease
Components
  • Complex: IgA1 Protease
    • Protein or peptide: Immunoglobulin A1 protease

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Supramolecule #1: IgA1 Protease

SupramoleculeName: IgA1 Protease / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)

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Macromolecule #1: Immunoglobulin A1 protease

MacromoleculeName: Immunoglobulin A1 protease / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: IgA-specific metalloendopeptidase
Source (natural)Organism: Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6
Molecular weightTheoretical: 144.431078 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TEPEKKLELR NVSDIELYSQ TNGTYRQHVS LDGIPENTDT YFVKVKSSAF KDVYIPVASI TEEKRNGQSV YKITAKAEKL QQELENKYV DNFTFYLDKK AKEENTNFTS FSNLVKAINQ NPSGTYHLAA SLNANEVELG PDERSYIKDT FTGRLIGEKD G KNYAIYNL ...String:
TEPEKKLELR NVSDIELYSQ TNGTYRQHVS LDGIPENTDT YFVKVKSSAF KDVYIPVASI TEEKRNGQSV YKITAKAEKL QQELENKYV DNFTFYLDKK AKEENTNFTS FSNLVKAINQ NPSGTYHLAA SLNANEVELG PDERSYIKDT FTGRLIGEKD G KNYAIYNL KKPLFENLSG ATVEKLSLKN VAISGKNDIG SLANEATNGT KIKQVHVDGV LAGERGVGGL LAKADQSSIA ES SFKGRIV NTYETTDAYN IGGLVGHLTG KNASIAKSKA TVTISSNTNR SDQTVGGLAG LVDQDAHIQN SYAEGDINNV KHF GKVAGV AGYLWDRTSG EEKHAGELTN VLSDVNVTNG NAITGYHYTG MKVANTFSSK ANRVFNVTLE KDEVVSKESF EERG TMLDA SQIVSKKAEI NPLTLPTVEP LSTSGKKDSD FSKIAHYQAN RALVYKNIEK LLPFYNKSTI VKYGNLVKEN SLLYQ KELL SAVMMKDDQV ITDIVSNKQT ANKLLLHYND HSSEKFDLKY QTDFANLAEY NLGNTGLLYT PNQFLYDRDS IVKEVL PEL QKLDYQSDAI RKTLGISPEV KLTELYLEDQ FSKTKQNLGD SLKKLLSADA GLAADNSVTR GYLVDKIKNN KEALLLG LT YLERWYNFNY GQVNVKDLVM YHPDFFGKGN TSPLDTLIEL GKSGFNNLLA KNNVDTYGIS LASQHGATDL FSTLEHYR K VFLPNTSNND WFKSETKAYI VEEKSTIEEV KTKQGLAGTK YSIGVYDRIT SATWKYRNMV LPLLTLPERS VFVISTMSS LGFGAYDRYR SSDHKAGKAL NDFVEENARE TAKRQRDHYD YWYRILDEQS REKLYRTILL YDAYKFGDDT TSGKATAEAK FDSSNPAMK NFFGPVGNKV VHNQHGAYAT GDGVYYMSYR MLDKDGAITY THEMTHDSDQ DIYLGGYGRR NGLGPEFFAK G LLQAPDQP SDATITINSI LKHSKSDSTE GSRLQVLDPT ERFQNAADLQ NYVHNMFDLI YMMEYLEGQS IVNKLSVYQK MA ALRKIEN KYVKDPADGN EVYATNVVKE LTEAEARNLN SFESLIDHNI LSAREYQSGD YERNGYYTIK LFAPIYSALS SEK GTPGDL MGRRIAYELL AAKGFKDGMV PYISNQYEED AKQQGQTINL YGKERGLVTD ELVLKKVFDG KYKTWAEFKT AMYQ ERVDQ FGNLKQVTFK DPTKPWPSYG TKTINNVDEL QALMDQAVLK DAEGPRWSNY DPEIDSAVHK LKRAIFKAYL DQTND FRSS I

UniProtKB: Immunoglobulin A1 protease

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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

BufferpH: 7 / Details: 20 mM Hepes, pH 7 50 mM NaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Number images used: 200000
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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