6ZOB | pdb_00006zob

3-Formylrifamycin SV binding to the access pocket of AcrB L protomer

PDB DOI: https://doi.org/10.2210/pdb6ZOB/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12, synthetic construct
Expression System: Escherichia coli BL21(DE3), Escherichia coli K-12
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2020-07-07 Released: 2021-05-19
Deposition Author(s): Tam, H.K., Foong, W.E., Pos, K.M.
Funding Organization(s): German Research Foundation (DFG), German-Israeli Foundation for Research and Development, European Communitys Seventh Framework Programme

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.262 (Depositor), 0.263 (DCC)
R-Value Work:
0.238 (Depositor), 0.240 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Allosteric drug transport mechanism of multidrug transporter AcrB.

Tam, H.K., Foong, W.E., Oswald, C., Herrmann, A., Zeng, H., Pos, K.M.

(2021) Nat Commun 12: 3889-3889

PubMed: 34188038 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-24151-3
Primary Citation Related Structures:
6ZO5, 6ZO6, 6ZO7, 6ZO8, 6ZO9, 6ZOA, 6ZOB, 6ZOC, 6ZOD, 6ZOE, 6ZOF, 6ZOG, 6ZOH

PubMed Abstract:
Gram-negative bacteria maintain an intrinsic resistance mechanism against entry of noxious compounds by utilizing highly efficient efflux pumps. The E. coli AcrAB-TolC drug efflux pump contains the inner membrane H ⁺/drug antiporter AcrB comprising three functionally interdependent protomers, cycling consecutively through the loose (L), tight (T) and open (O) state during cooperative catalysis. Here, we present 13 X-ray structures of AcrB in intermediate states of the transport cycle. Structure-based mutational analysis combined with drug susceptibility assays indicate that drugs are guided through dedicated transport channels toward the drug binding pockets. A co-structure obtained in the combined presence of erythromycin, linezolid, oxacillin and fusidic acid shows binding of fusidic acid deeply inside the T protomer transmembrane domain. Thiol cross-link substrate protection assays indicate that this transmembrane domain-binding site can also accommodate oxacillin or novobiocin but not erythromycin or linezolid. AcrB-mediated drug transport is suggested to be allosterically modulated in presence of multiple drugs.

Organizational Affiliation

Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany. tamhk60@hotmail.com.

Macromolecule Content

Total Structure Weight: 386.25 kDa
Atom Count: 26,439
Modeled Residue Count: 3,410
Deposited Residue Count: 3,509
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump subunit AcrB	A, B, C	1,057	Escherichia coli K-12	Mutation(s): 0 Gene Names: acrB, acrE, b0462, JW0451 Membrane Entity: Yes
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224 Go to UniProtKB: P31224
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31224
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPIN	D, E	169	synthetic construct	Mutation(s): 0 Gene Names: ARTIFICIAL GENE

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3YI (Subject of Investigation/LOI) Query on 3YI Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	(2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-heptam ethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl acetate C₃₈ H₄₇ N O₁₃ BBNQHOMJRFAQBN-UPZFVJMDSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C]	F [auth A] G [auth A] H [auth A] K [auth A] O [auth B] F [auth A], G [auth A], H [auth A], K [auth A], O [auth B], T [auth C]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain T [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain T [auth C]
DDR Query on DDR Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	(2S)-3-hydroxypropane-1,2-diyl didecanoate C₂₃ H₄₄ O₅ GNSDEDOVXZDMKM-NRFANRHFSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
ETE Query on ETE Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₉ H₂₀ O₅ ZNYRFEPBTVGZDN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
DDQ Query on DDQ Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	DECYLAMINE-N,N-DIMETHYL-N-OXIDE C₁₂ H₂₇ N O ZRKZFNZPJKEWPC-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain U [auth C] MOL2 format, chain U [auth C] mmCIF format, chain U [auth C]	U [auth C]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain U [auth C] Interactions & Density Focus chain U [auth C]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain S [auth B] SDF format, chain V [auth C] SDF format, chain X [auth D] MOL2 format, chain J [auth A] MOL2 format, chain S [auth B] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] mmCIF format, chain J [auth A] mmCIF format, chain S [auth B] mmCIF format, chain V [auth C] mmCIF format, chain X [auth D]	J [auth A], S [auth B], V [auth C], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain S [auth B] Focus chain V [auth C] Focus chain X [auth D] Interactions & Density Focus chain J [auth A] Focus chain S [auth B] Focus chain V [auth C] Focus chain X [auth D]
HEX Query on HEX Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth C] MOL2 format, chain W [auth C] mmCIF format, chain W [auth C]	W [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain W [auth C] Interactions & Density Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.262 (Depositor), 0.263 (DCC)
R-Value Work: 0.238 (Depositor), 0.240 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.361	α = 90
b = 160.195	β = 90
c = 244.341	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-19

Deposition Author(s):

Tam, H.K.

Foong, W.E.

Pos, K.M.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	DFG-EXC115
German-Israeli Foundation for Research and Development	Germany	I-1202-248.9/2012
European Communitys Seventh Framework Programme	European Union	FP7/2007-2013

Revision History (Full details and data files)

Version 1.0: 2021-05-19
Type: Initial release
Version 1.1: 2021-07-07
Changes: Database references
Version 1.2: 2021-07-14
Changes: Database references
Version 1.3: 2024-01-31
Changes: Data collection, Database references, Refinement description