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- PDB-6xjb: IgA1 Protease -

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Basic information

Entry
Database: PDB / ID: 6xjb
TitleIgA1 Protease
ComponentsImmunoglobulin A1 protease
KeywordsIMMUNE SYSTEM / metalloprotease / IgA1
Function / homology
Function and homology information


IgA-specific metalloendopeptidase / metalloendopeptidase activity / proteolysis / extracellular region / zinc ion binding / 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 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsEisenmesser, E.Z. / Zheng, H.
Funding support United States, 1items
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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.0Dec 9, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 9, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 9, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 9, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 9, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 21, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: Immunoglobulin A1 protease


Theoretical massNumber of molelcules
Total (without water)144,4311
Polymers144,4311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area49850 Å2

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Components

#1: Protein Immunoglobulin A1 protease / IgA1 protease / IgA-specific zinc metalloproteinase


Mass: 144431.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6 / Gene: iga, spr1042 / Production host: Escherichia coli (E. coli)
References: UniProt: Q59947, IgA-specific metalloendopeptidase
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: IgA1 Protease / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7 / Details: 20 mM Hepes, pH 7 50 mM NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: OTHER / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18rc5_3822: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Num. of particles: 200000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210259
ELECTRON MICROSCOPYf_angle_d0.41313865
ELECTRON MICROSCOPYf_dihedral_angle_d17.8251394
ELECTRON MICROSCOPYf_chiral_restr0.0391523
ELECTRON MICROSCOPYf_plane_restr0.0031803

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