6XJB | pdb_00006xjb

IgA1 Protease


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6XJB

This is version 1.2 of the entry. See complete history

Literature

Mechanism and inhibition of Streptococcus pneumoniae IgA1 protease.

Wang, Z.Rahkola, J.Redzic, J.S.Chi, Y.C.Tran, N.Holyoak, T.Zheng, H.Janoff, E.Eisenmesser, E.

(2020) Nat Commun 11: 6063-6063

  • DOI: https://doi.org/10.1038/s41467-020-19887-3
  • Primary Citation Related Structures: 
    6XJA, 6XJB, 7JGJ

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO, 80045, USA.

Macromolecule Content 

  • Total Structure Weight: 144.43 kDa 
  • Atom Count: 10,070 
  • Modeled Residue Count: 1,277 
  • Deposited Residue Count: 1,285 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunoglobulin A1 protease1,285Streptococcus pneumoniae R6Mutation(s): 0 
Gene Names: igaspr1042
EC: 3.4.24.13
UniProt
Find proteins for Q59947 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q59947 
Go to UniProtKB:  Q59947
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59947
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI146295

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-21
    Changes: Data collection, Structure summary