+Open data
-Basic information
Entry | Database: PDB / ID: 7uvk | ||||||
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Title | G. haemolysans IgA1 protease | ||||||
Components | IgA1 Protease | ||||||
Keywords | IMMUNE SYSTEM / protease | ||||||
Function / homology | Function and homology information serine-type peptidase activity / metalloendopeptidase activity / proteolysis / zinc ion binding / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Gemella haemolysans (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å | ||||||
Authors | Eisenmesser, E.Z. / Zheng, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Commun Biol / Year: 2022 Title: A substrate-induced gating mechanism is conserved among Gram-positive IgA1 metalloproteases. Authors: Jasmina S Redzic / Jeremy Rahkola / Norman Tran / Todd Holyoak / Eunjeong Lee / Antonio Javier Martín-Galiano / Nancy Meyer / Hongjin Zheng / Elan Eisenmesser / Abstract: The mucosal adaptive immune response is dependent on the production of IgA antibodies and particularly IgA1, yet opportunistic bacteria have evolved mechanisms to specifically block this response by ...The mucosal adaptive immune response is dependent on the production of IgA antibodies and particularly IgA1, yet opportunistic bacteria have evolved mechanisms to specifically block this response by producing IgA1 proteases (IgA1Ps). Our lab was the first to describe the structures of a metal-dependent IgA1P (metallo-IgA1P) produced from Gram-positive Streptococcus pneumoniae both in the absence and presence of its IgA1 substrate through cryo-EM single particle reconstructions. This prior study revealed an active-site gating mechanism reliant on substrate-induced conformational changes to the enzyme that begged the question of whether such a mechanism is conserved among the wider Gram-positive metallo-IgA1P subfamily of virulence factors. Here, we used cryo-EM to characterize the metallo-IgA1P of a more distantly related family member from Gemella haemolysans, an emerging opportunistic pathogen implicated in meningitis, endocarditis, and more recently bacteremia in the elderly. While the substrate-free structures of these two metallo-IgA1Ps exhibit differences in the relative starting positions of the domain responsible for gating substrate, the enzymes have similar domain orientations when bound to IgA1. Together with biochemical studies that indicate these metallo-IgA1Ps have similar binding affinities and activities, these data indicate that metallo-IgA1P binding requires the specific IgA1 substrate to open the enzymes for access to their active site and thus, largely conform to an "induced fit" model. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uvk.cif.gz | 255.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uvk.ent.gz | 192.4 KB | Display | PDB format |
PDBx/mmJSON format | 7uvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uvk_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7uvk_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7uvk_validation.xml.gz | 48.8 KB | Display | |
Data in CIF | 7uvk_validation.cif.gz | 70.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/7uvk ftp://data.pdbj.org/pub/pdb/validation_reports/uv/7uvk | HTTPS FTP |
-Related structure data
Related structure data | 26812MC 7uvlC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 246235.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gemella haemolysans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: C5NYF3 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Gemella haemolysans IgA protease apo / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Source (natural) | Organism: Gemella haemolysans (bacteria) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: cryoSPARC / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 443908 / Symmetry type: POINT | ||||||||||||||||||||||||
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