8ZAY | pdb_00008zay

Crystal structure of Fab from mouse monoclonal antibody 4A9 against Aquifex aeolicus RseP PDZ tandem

PDB DOI: https://doi.org/10.2210/pdb8ZAY/pdb

Classification: PROTEIN BINDING
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-04-25 Released: 2025-03-05
Deposition Author(s): Adachi, Y., Nogi, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.269 (Depositor), 0.269 (DCC)
R-Value Work:
0.218 (Depositor), 0.217 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 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

PubMed: 40009668 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adu0925
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 96.85 kDa
Atom Count: 6,893
Modeled Residue Count: 863
Deposited Residue Count: 880
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VH-CH1 region of antibody of anti-RseP orthologue from A aeolicus	A [auth H], B [auth I]	226	Mus musculus	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of antibody of anti-RseP orthologue from A aeolicus	C [auth L], D [auth M]	214	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain G [auth I] SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain M SDF format, chain N [auth M] SDF format, chain L [auth M] SDF format, chain H [auth I] SDF format, chain F [auth H] MOL2 format, chain E [auth H] MOL2 format, chain G [auth I] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain M MOL2 format, chain N [auth M] MOL2 format, chain L [auth M] MOL2 format, chain H [auth I] MOL2 format, chain F [auth H] mmCIF format, chain E [auth H] mmCIF format, chain G [auth I] mmCIF format, chain I [auth L] mmCIF format, chain J [auth L] mmCIF format, chain K [auth L] mmCIF format, chain M mmCIF format, chain N [auth M] mmCIF format, chain L [auth M] mmCIF format, chain H [auth I] mmCIF format, chain F [auth H]	E [auth H] F [auth H] G [auth I] H [auth I] I [auth L] E [auth H], F [auth H], G [auth I], H [auth I], I [auth L], J [auth L], K [auth L], L [auth M], M, N [auth M]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth I] Focus chain H [auth I] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L [auth M] Focus chain M Focus chain N [auth M] Interactions & Density Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth I] Focus chain H [auth I] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L [auth M] Focus chain M Focus chain N [auth M]