6ZO5 | pdb_00006zo5

Fusidic acid binding to the TM1/TM2 groove of AcrB-G619P_G621P

PDB DOI: https://doi.org/10.2210/pdb6ZO5/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12, synthetic construct
Expression System: Escherichia coli BL21(DE3), Escherichia coli K-12
Mutation(s): Yes
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: 2.50 Å
R-Value Free:
0.252 (Depositor), 0.221 (DCC)
R-Value Work:
0.226 (Depositor)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
View more details

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: 392.65 kDa
Atom Count: 27,620
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): 2 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 15 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTY Query on PTY Download:Ideal Coordinates CCD File SDF format, chain QA [auth C] MOL2 format, chain QA [auth C] mmCIF format, chain QA [auth C]	QA [auth C]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain QA [auth C] Interactions & Density Focus chain QA [auth C]
FUA (Subject of Investigation/LOI) Query on FUA Download:Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	FUSIDIC ACID C₃₁ H₄₈ O₆ IECPWNUMDGFDKC-MZJAQBGESA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain RA [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain RA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] RA [auth C] G [auth A], H [auth A], I [auth A], J [auth A], RA [auth C], W [auth B], X [auth B], Y [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain RA [auth C] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain RA [auth C] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
XPE Query on XPE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL C₂₀ H₄₂ O₁₁ DTPCFIHYWYONMD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
LPX Query on LPX Download:Ideal Coordinates CCD File SDF format, chain OA [auth C] SDF format, chain MA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain MA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain MA [auth C]	MA [auth C], OA [auth C]	(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate C₂₁ H₄₄ N O₇ P YVYMBNSKXOXSKW-FQEVSTJZSA-N		Interactions Focus chain MA [auth C] Focus chain OA [auth C] Interactions & Density Focus chain MA [auth C] Focus chain OA [auth C]
DDR Query on DDR Download:Ideal Coordinates CCD File SDF format, chain U [auth B] MOL2 format, chain U [auth B] mmCIF format, chain U [auth B]	U [auth B]	(2S)-3-hydroxypropane-1,2-diyl didecanoate C₂₃ H₄₄ O₅ GNSDEDOVXZDMKM-NRFANRHFSA-N		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]
C14 Query on C14 Download:Ideal Coordinates CCD File SDF format, chain UA [auth C] SDF format, chain TA [auth C] SDF format, chain AA [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain AA [auth B]	AA [auth B], TA [auth C], UA [auth C]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain TA [auth C] Focus chain UA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain TA [auth C] Focus chain UA [auth C]
D12 Query on D12 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain SA [auth C] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], SA [auth C], Z [auth B]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain SA [auth C] Focus chain Z [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain SA [auth C] Focus chain Z [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain PA [auth C] SDF format, chain NA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain NA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain NA [auth C]	NA [auth C], PA [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain NA [auth C] Focus chain PA [auth C] Interactions & Density Focus chain NA [auth C] Focus chain PA [auth C]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain VA [auth C] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain CA [auth B] SDF format, chain BA [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain VA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B]	BA [auth B], CA [auth B], M [auth A], N [auth A], VA [auth C]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain VA [auth C] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain VA [auth C]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain DB [auth C] MOL2 format, chain DB [auth C] mmCIF format, chain DB [auth C]	DB [auth C]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain DB [auth C] Interactions & Density Focus chain DB [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain WA [auth C] SDF format, chain EA [auth B] SDF format, chain DA [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain WA [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B]	DA [auth B], EA [auth B], WA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Focus chain WA [auth C] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B] Focus chain WA [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain YA [auth C] SDF format, chain XA [auth C] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain FA [auth B] SDF format, chain AB [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain AB [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain AB [auth C]	AB [auth C] FA [auth B] O [auth A] P [auth A] Q [auth A] AB [auth C], FA [auth B], O [auth A], P [auth A], Q [auth A], XA [auth C], YA [auth C], ZA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain FA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain FA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]
HEX Query on HEX Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain IA [auth B] SDF format, chain HA [auth B] SDF format, chain GA [auth B] SDF format, chain CB [auth C] SDF format, chain BB [auth C] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain BB [auth C] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain BB [auth C]	BB [auth C] CB [auth C] GA [auth B] HA [auth B] IA [auth B] BB [auth C], CB [auth C], GA [auth B], HA [auth B], IA [auth B], R [auth A], S [auth A]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain BB [auth C] Focus chain CB [auth C] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain BB [auth C] Focus chain CB [auth C] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain R [auth A] Focus chain S [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain LA [auth B] SDF format, chain KA [auth B] SDF format, chain JA [auth B] SDF format, chain GB [auth D] SDF format, chain FB [auth C] SDF format, chain EB [auth C] MOL2 format, chain T [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain FB [auth C] MOL2 format, chain EB [auth C] mmCIF format, chain T [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain GB [auth D] mmCIF format, chain FB [auth C] mmCIF format, chain EB [auth C]	EB [auth C] FB [auth C] GB [auth D] JA [auth B] KA [auth B] EB [auth C], FB [auth C], GB [auth D], JA [auth B], KA [auth B], LA [auth B], T [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth D] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain T [auth A] Interactions & Density Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth D] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain T [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.252 (Depositor), 0.221 (DCC)
R-Value Work: 0.226 (Depositor)
R-Value Observed: 0.227 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.234	α = 90
b = 159.703	β = 90
c = 245.486	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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