6WK9 | pdb_00006wk9

Crystal structure of Gdx-Clo from Small Multidrug Resistance family of transporters in complex with octylguanidinium

PDB DOI: https://doi.org/10.2210/pdb6WK9/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Clostridiales bacterium oral taxon 876 str. F0540, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-04-15 Released: 2020-10-28
Deposition Author(s): Kermani, A.A., Stockbridge, R.B.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.286 (Depositor), 0.286 (DCC)
R-Value Work:
0.246 (Depositor), 0.246 (DCC)
R-Value Observed:
0.248 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The structural basis of promiscuity in small multidrug resistance transporters.

Kermani, A.A., Macdonald, C.B., Burata, O.E., Ben Koff, B., Koide, A., Denbaum, E., Koide, S., Stockbridge, R.B.

(2020) Nat Commun 11: 6064-6064

PubMed: 33247110 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-020-19820-8
Primary Citation Related Structures:
6WK5, 6WK8, 6WK9

PubMed Abstract:
By providing broad resistance to environmental biocides, transporters from the small multidrug resistance (SMR) family drive the spread of multidrug resistance cassettes among bacterial populations. A fundamental understanding of substrate selectivity by SMR transporters is needed to identify the types of selective pressures that contribute to this process. Using solid-supported membrane electrophysiology, we find that promiscuous transport of hydrophobic substituted cations is a general feature of SMR transporters. To understand the molecular basis for promiscuity, we solved X-ray crystal structures of a SMR transporter Gdx-Clo in complex with substrates to a maximum resolution of 2.3 Å. These structures confirm the family's extremely rare dual topology architecture and reveal a cleft between two helices that provides accommodation in the membrane for the hydrophobic substituents of transported drug-like cations.

Organizational Affiliation

Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.

Macromolecule Content

Total Structure Weight: 88.91 kDa
Atom Count: 6,262
Modeled Residue Count: 774
Deposited Residue Count: 784
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug resistance protein, SMR family	A [auth B], B [auth A], E [auth F], F [auth E]	105	Clostridiales bacterium oral taxon 876 str. F0540	Mutation(s): 0 Gene Names: HMPREF1982_00479
UniProt
Find proteins for A0ACD6B9S6 (Clostridiales bacterium oral taxon 876 str. F0540) Explore A0ACD6B9S6 Go to UniProtKB: A0ACD6B9S6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9S6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L10 monobody	C, D, G, H	91	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMU Query on DMU Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain O [auth C] SDF format, chain U [auth G] SDF format, chain Q [auth F] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] MOL2 format, chain U [auth G] MOL2 format, chain Q [auth F] mmCIF format, chain I [auth B] mmCIF format, chain O [auth C] mmCIF format, chain U [auth G] mmCIF format, chain Q [auth F]	I [auth B], O [auth C], Q [auth F], U [auth G]	DECYL-BETA-D-MALTOPYRANOSIDE C₂₂ H₄₂ O₁₁ WOQQAWHSKSSAGF-WXFJLFHKSA-N		Interactions Focus chain I [auth B] Focus chain O [auth C] Focus chain Q [auth F] Focus chain U [auth G] Interactions & Density Focus chain I [auth B] Focus chain O [auth C] Focus chain Q [auth F] Focus chain U [auth G]
U4G (Subject of Investigation/LOI) Query on U4G Download:Ideal Coordinates CCD File SDF format, chain T [auth E] SDF format, chain W [auth G] SDF format, chain V [auth G] SDF format, chain S [auth F] SDF format, chain R [auth F] SDF format, chain P [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth A] SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain T [auth E] MOL2 format, chain W [auth G] MOL2 format, chain V [auth G] MOL2 format, chain S [auth F] MOL2 format, chain R [auth F] MOL2 format, chain P [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain T [auth E] mmCIF format, chain W [auth G] mmCIF format, chain V [auth G] mmCIF format, chain S [auth F] mmCIF format, chain R [auth F] mmCIF format, chain P [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	J [auth B] K [auth B] L [auth A] M [auth C] N [auth C] J [auth B], K [auth B], L [auth A], M [auth C], N [auth C], P [auth C], R [auth F], S [auth F], T [auth E], V [auth G], W [auth G]	N-octylguanidine C₉ H₂₁ N₃ XPYXSZDENRDLKD-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth C] Focus chain R [auth F] Focus chain S [auth F] Focus chain T [auth E] Focus chain V [auth G] Focus chain W [auth G] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth C] Focus chain R [auth F] Focus chain S [auth F] Focus chain T [auth E] Focus chain V [auth G] Focus chain W [auth G]