5NG5 | pdb_00005ng5

multi-drug efflux; membrane transport; RND superfamily; Drug resistance

PDB DOI: https://doi.org/10.2210/pdb5NG5/pdb
EM Map EMD-3636: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2017-03-16 Released: 2017-04-19
Deposition Author(s): Wang, Z., Fan, G., Hryc, C.F., Blaza, J.N., Serysheva, I.I., Schmid, M.F., Chiu, W., Luisi, B.F., Du, D.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

An allosteric transport mechanism for the AcrAB-TolC Multidrug Efflux Pump.

Wang, Z., Fan, G., Hryc, C.F., Blaza, J.N., Serysheva, I.I., Schmid, M.F., Chiu, W., Luisi, B.F., Du, D.

(2017) Elife 6

PubMed: 28355133 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.24905
Primary Citation Related Structures:
5NC5, 5NG5, 5O66, 5V5S

PubMed Abstract:
Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell envelope. Here, we report the near-atomic resolution cryoEM structures of the Escherichia coli AcrAB-TolC multidrug efflux pump in resting and drug transport states, revealing a quaternary structural switch that allosterically couples and synchronizes initial ligand binding with channel opening. Within the transport-activated state, the channel remains open even though the pump cycles through three distinct conformations. Collectively, our data provide a dynamic mechanism for the assembly and operation of the AcrAB-TolC pump.

Organizational Affiliation

National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, United States.

Macromolecule Content

Total Structure Weight: 760.72 kDa
Atom Count: 49,806
Modeled Residue Count: 6,569
Deposited Residue Count: 7,026
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump subunit AcrA	A [auth E] B [auth D] C [auth G] D [auth H] E [auth A] A [auth E], B [auth D], C [auth G], D [auth H], E [auth A], F [auth B]	373	Escherichia coli	Mutation(s): 0 Gene Names: acrA, lir, mtcA, b0463, JW0452 Membrane Entity: Yes
UniProt
Find proteins for P0AE06 (Escherichia coli (strain K12)) Explore P0AE06 Go to UniProtKB: P0AE06
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AE06
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein TolC	G [auth F], H [auth I], I [auth C]	493	Escherichia coli	Mutation(s): 0 Gene Names: tolC, colE1-i, mtcB, mukA, refI, toc, weeA, b3035, JW5503 Membrane Entity: Yes
UniProt
Find proteins for P02930 (Escherichia coli (strain K12)) Explore P02930 Go to UniProtKB: P02930
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02930
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump subunit AcrB	J [auth K], K [auth L], O [auth J]	1,049	Escherichia coli	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump accessory protein AcrZ	L [auth M], M [auth N], N [auth O]	54	Escherichia coli	Mutation(s): 0 Gene Names: acrZ, ybhT, b0762, JW5102 Membrane Entity: Yes
UniProt
Find proteins for P0AAW9 (Escherichia coli (strain K12)) Explore P0AAW9 Go to UniProtKB: P0AAW9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AAW9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5QF Query on 5QF Download:Ideal Coordinates CCD File SDF format, chain Q [auth L] SDF format, chain R [auth J] SDF format, chain P [auth K] MOL2 format, chain Q [auth L] MOL2 format, chain R [auth J] MOL2 format, chain P [auth K] mmCIF format, chain Q [auth L] mmCIF format, chain R [auth J] mmCIF format, chain P [auth K]	P [auth K], Q [auth L], R [auth J]	6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)piperazin-1-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile C₂₈ H₃₈ N₄ O₄ S PJMAUCHUUURBGI-UHFFFAOYSA-N		Interactions Focus chain P [auth K] Focus chain Q [auth L] Focus chain R [auth J] Interactions & Density Focus chain P [auth K] Focus chain Q [auth L] Focus chain R [auth J]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 6.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-04-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-04-19
Type: Initial release
Version 1.1: 2017-08-02
Changes: Data collection, Refinement description
Version 1.2: 2025-04-09
Changes: Data collection, Database references, Structure summary
Version 1.3: 2025-10-01
Changes: Advisory, Data collection, Derived calculations