5NC5

Crystal structure of AcrBZ in complex with antibiotic puromycin

PDB DOI: https://doi.org/10.2210/pdb5NC5/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12, Escherichia coli, Escherichia coli O157:H7
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2017-03-03 Released: 2017-04-12
Deposition Author(s): Du, D., Luisi, B.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.245
R-Value Work: 0.183
R-Value Observed: 0.186

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

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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.7554/eLife.24905
Primary Citation of 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: 402.49 kDa
Atom Count: 27,397
Modelled Residue Count: 3,528
Deposited Residue Count: 3,632
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump subunit AcrB	A, B, C	1,049	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31224
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPin	D, E	169	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump accessory protein AcrZ	F, G, H	49	Escherichia coli O157:H7	Mutation(s): 0 Gene Names: acrZ, Z0932, ECs0790 Membrane Entity: Yes
UniProt
Find proteins for P0AAX1 (Escherichia coli O157:H7) Explore P0AAX1 Go to UniProtKB: P0AAX1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AAX1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain S [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain S [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain S [auth A]	I [auth A], J [auth A], S [auth A]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth A]
PUY Query on PUY Download Ideal Coordinates CCD File SDF format, chain PA [auth B] MOL2 format, chain PA [auth B] mmCIF format, chain PA [auth B]	PA [auth B]	PUROMYCIN C₂₂ H₂₉ N₇ O₅ RXWNCPJZOCPEPQ-NVWDDTSBSA-N		Interactions Focus chain PA [auth B] Interactions & Density Focus chain PA [auth B]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain QA [auth B] SDF format, chain T [auth A] SDF format, chain UA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain Z [auth B] SDF format, chain ZA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth C]	K [auth A] QA [auth B] T [auth A] UA [auth C] XA [auth C] K [auth A], QA [auth B], T [auth A], UA [auth C], XA [auth C], YA [auth C], Z [auth B], ZA [auth C]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain QA [auth B] Focus chain T [auth A] Focus chain UA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain K [auth A] Focus chain QA [auth B] Focus chain T [auth A] Focus chain UA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CB [auth C] SDF format, chain DA [auth B] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FA [auth B] SDF format, chain FB [auth C] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain HB [auth C] SDF format, chain IA [auth B] SDF format, chain IB [auth C] SDF format, chain JA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain RA [auth B] SDF format, chain TA [auth C] SDF format, chain VA [auth C] SDF format, chain W [auth B] SDF format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B]	AA [auth B] CB [auth C] DA [auth B] DB [auth C] EB [auth C] AA [auth B], CB [auth C], DA [auth B], DB [auth C], EB [auth C], FA [auth B], FB [auth C], GA [auth B], GB [auth C], HB [auth C], IA [auth B], IB [auth C], JA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], P [auth A], Q [auth A], RA [auth B], TA [auth C], VA [auth C], W [auth B], Y [auth B]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RA [auth B] Focus chain TA [auth C] Focus chain VA [auth C] Focus chain W [auth B] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RA [auth B] Focus chain TA [auth C] Focus chain VA [auth C] Focus chain W [auth B] Focus chain Y [auth B]
DD9 Query on DD9 Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain CA [auth B] SDF format, chain EA [auth B] SDF format, chain HA [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain R [auth A] SDF format, chain SA [auth C] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain X [auth B] SDF format, chain KA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain X [auth B] MOL2 format, chain KA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain X [auth B] mmCIF format, chain KA [auth B]	AB [auth C] BA [auth B] BB [auth C] CA [auth B] EA [auth B] AB [auth C], BA [auth B], BB [auth C], CA [auth B], EA [auth B], HA [auth B], KA [auth B], O [auth A], OA [auth B], R [auth A], SA [auth C], U [auth A], V [auth A], X [auth B]	nonane C₉ H₂₀ BKIMMITUMNQMOS-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain EA [auth B] Focus chain HA [auth B] Focus chain KA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain R [auth A] Focus chain SA [auth C] Focus chain U [auth A] Focus chain V [auth A] Focus chain X [auth B] Interactions & Density Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain EA [auth B] Focus chain HA [auth B] Focus chain KA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain R [auth A] Focus chain SA [auth C] Focus chain U [auth A] Focus chain V [auth A] Focus chain X [auth B]
HEX Query on HEX Download Ideal Coordinates CCD File SDF format, chain WA [auth C] MOL2 format, chain WA [auth C] mmCIF format, chain WA [auth C]	WA [auth C]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain WA [auth C] Interactions & Density Focus chain WA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.245
R-Value Work: 0.183
R-Value Observed: 0.186
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.245	α = 90
b = 167.646	β = 90
c = 249.98	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-04-12

Deposition Author(s):

Du, D.

Luisi, B.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	RG61065

Revision History (Full details and data files)

Version 1.0: 2017-04-12
Type: Initial release
Version 1.1: 2017-04-19
Changes: Atomic model
Version 1.2: 2019-10-16
Changes: Data collection
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Refinement description