9J83 | pdb_00009j83

Cryo-EM structure of Aquifex aeolicus RseP E18Q mutant in complex with Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of the bacterial intramembrane metalloprotease RseP in the substrate-bound state.

Asahi, K.Hirose, M.Aruga, R.Shimizu, Y.Tajiri, M.Tanaka, T.Adachi, Y.Tanaka, Y.Kaneko, M.K.Kato, Y.Akashi, S.Akiyama, Y.Hizukuri, Y.Kato, T.Nogi, T.

(2025) Sci Adv 11: eadu0925-eadu0925

  • DOI: https://doi.org/10.1126/sciadv.adu0925
  • Primary Citation of Related Structures:  
    8ZAY, 9J82, 9J83

  • PubMed Abstract: 

    Site-2 proteases (S2Ps), conserved intramembrane metalloproteases that maintain cellular homeostasis, are associated with chronic infection and persistence leading to multidrug resistance in bacterial pathogens. A structural model of how S2Ps discriminate and accommodate substrates could help us develop selective antimicrobial agents. We previously proposed that the Escherichia coli S2P RseP unwinds helical substrate segments before cleavage, but the mechanism for accommodating a full-length membrane-spanning substrate remained unclear. Our present cryo-EM analysis of Aquifex aeolicus RseP ( Aa RseP) revealed that a substrate-like membrane protein fragment from the expression host occupied the active site while spanning a transmembrane cavity that is inaccessible via lateral diffusion. Furthermore, in vivo photocrosslinking supported that this substrate accommodation mode is recapitulated on the cell membrane. Our results suggest that the substrate accommodation by threading through a conserved membrane-associated region stabilizes the substrate-complex and contributes to substrate discrimination on the membrane.


  • Organizational Affiliation
    • Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative zinc metalloprotease aq_1964441Aquifex aeolicus VF5Mutation(s): 1 
Gene Names: aq_1964
EC: 3.4.24
Membrane Entity: Yes 
UniProt
Find proteins for O67776 (Aquifex aeolicus (strain VF5))
Explore O67776 
Go to UniProtKB:  O67776
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67776
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VH-CH1 region of mouse monoclonal antibody IgG 4A9B [auth H]239Mus musculusMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
L chain of mouse monoclonal antibody IgG 4A9C [auth L]214Mus musculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
unknown peptideD [auth C]15Escherichia coliMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A
L-PEPTIDE LINKINGC6 H11 N O3 SMET
SNN
Query on SNN
A
L-PEPTIDE LINKINGC4 H6 N2 O2ASN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC4.4.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan23K23825
Japan Society for the Promotion of Science (JSPS)Japan22H02561
Japan Society for the Promotion of Science (JSPS)Japan19H03170
Japan Society for the Promotion of Science (JSPS)Japan26291016
Japan Society for the Promotion of Science (JSPS)Japan22370039

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-03-12
    Changes: Data collection, Database references
  • Version 1.2: 2025-03-19
    Changes: Data collection, Database references, Structure summary