PDB-8z1u: Crystal structure of aminoglycoside efflux transporter MexY from ...

ID or keywords:

Entry

Database: PDB / ID: 8z1u

Title

Crystal structure of aminoglycoside efflux transporter MexY from Pseudomonas aeruginosa

Components

Efflux pump membrane transporter

Keywords

MEMBRANE PROTEIN / multidrug efflux transporter membrane transport RND superfamily antimicrobial resistance aminoglycoside / TRANSPORT PROTEIN

Function / homology

Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / plasma membrane / Efflux pump membrane transporter

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.89 Å

Authors

Murakami, S. / Yamashita, E. / Okada, U. / Aoki, M.

Funding support

Japan, 3items

Organization	Grant number	Country
Japan Society for the Promotion of Science (JSPS)	JP21H02412	Japan
Japan Society for the Promotion of Science (JSPS)	JP21K19337	Japan
Japan Society for the Promotion of Science (JSPS)	JP18K06079	Japan

Citation

Journal: To Be Published
Title: Crystal structure of aminoglycoside efflux transporter MexY from Pseudomonas aeruginosa
Authors: Murakami, S. / Okada, U. / Yamashita, E.

History

Deposition	Apr 12, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 15, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8z1u.cif.gz	486.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8z1u.ent.gz	336 KB	Display	PDB format
PDBx/mmJSON format	8z1u.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8z1u_validation.pdf.gz	454.4 KB	Display	wwPDB validaton report
Full document	8z1u_full_validation.pdf.gz	486.6 KB	Display
Data in XML	8z1u_validation.xml.gz	43.1 KB	Display
Data in CIF	8z1u_validation.cif.gz	55.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z1/8z1u ftp://data.pdbj.org/pub/pdb/validation_reports/z1/8z1u	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#95 - Nov 2007 Multidrug Resistance Transporters similarity (4)

Deposited unit

A: Efflux pump membrane transporter

hetero molecules

115 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: assay for oligomerization

Unit cell

Length a, b, c (Å)	186.432, 186.432, 374.011
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22
Space group name Hall	P6₁2(x,y,z+5/12)
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/6 #3: y,-x+y,z+5/6 #4: -y,x-y,z+1/3 #5: -x+y,-x,z+2/3 #6: x-y,-y,-z #7: -x,-x+y,-z+2/3 #8: -x,-y,z+1/2 #9: y,x,-z+1/3 #10: -y,-x,-z+5/6 #11: -x+y,y,-z+1/2 #12: x,x-y,-z+1/6

#1: Protein	Efflux pump membrane transporter / MexY Mass: 114039.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: amrB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RG59
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 8.26 Å³/Da / Density % sol: 85.1 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium phosphate (pH 6.5), 2.0 - 2.3 M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 23, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.89→161.45 Å / Num. obs: 81724 / % possible obs: 95.9 % / Redundancy: 303 % / B_iso Wilson estimate: 87.28 Å² / CC_1/2: 0.99 / Net I/σ(I): 32.1
Reflection shell	Resolution: 2.89→2.99 Å / Num. unique obs: 4086 / CC_1/2: 0.618

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
PHENIX		phasing
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.89→161.45 Å / SU ML: 0.3694 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7455
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2699	4060	4.97 %
R_work	0.2531	77648	-
obs	0.2539	81708	94.21 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 93.58 Å²

Refinement step

Cycle: LAST / Resolution: 2.89→161.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7798	0	55	87	7940

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0037	7993
X-RAY DIFFRACTION	f_angle_d	0.6838	10873
X-RAY DIFFRACTION	f_chiral_restr	0.042	1270
X-RAY DIFFRACTION	f_plane_restr	0.0058	1392
X-RAY DIFFRACTION	f_dihedral_angle_d	4.9377	1118

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.89-2.92	0.5135	21	0.5045	422	X-RAY DIFFRACTION	15.01
2.92-2.95	0.4962	52	0.4593	1312	X-RAY DIFFRACTION	46.71
2.95-2.99	0.4626	113	0.4166	2149	X-RAY DIFFRACTION	77.1
2.99-3.03	0.4036	123	0.3578	2574	X-RAY DIFFRACTION	91.8
3.03-3.07	0.3652	145	0.3228	2780	X-RAY DIFFRACTION	99.19
3.07-3.12	0.3282	151	0.2925	2791	X-RAY DIFFRACTION	100
3.12-3.16	0.3168	145	0.289	2815	X-RAY DIFFRACTION	100
3.16-3.21	0.3171	147	0.2799	2793	X-RAY DIFFRACTION	100
3.21-3.27	0.3282	151	0.2868	2790	X-RAY DIFFRACTION	100
3.27-3.32	0.3203	142	0.283	2801	X-RAY DIFFRACTION	100
3.32-3.38	0.3178	152	0.2881	2810	X-RAY DIFFRACTION	100
3.38-3.45	0.3023	147	0.2952	2814	X-RAY DIFFRACTION	100
3.45-3.52	0.3173	149	0.3036	2827	X-RAY DIFFRACTION	100
3.52-3.59	0.3325	148	0.322	2798	X-RAY DIFFRACTION	100
3.59-3.68	0.3145	147	0.2758	2794	X-RAY DIFFRACTION	100
3.68-3.77	0.261	148	0.2575	2830	X-RAY DIFFRACTION	100
3.77-3.87	0.2425	148	0.2303	2815	X-RAY DIFFRACTION	100
3.87-3.99	0.2744	147	0.222	2835	X-RAY DIFFRACTION	100
3.99-4.11	0.2433	151	0.2156	2812	X-RAY DIFFRACTION	100
4.11-4.26	0.2612	152	0.2218	2857	X-RAY DIFFRACTION	99.97
4.26-4.43	0.2582	148	0.2322	2834	X-RAY DIFFRACTION	100
4.43-4.63	0.2271	152	0.2218	2850	X-RAY DIFFRACTION	100
4.63-4.88	0.2288	151	0.2002	2856	X-RAY DIFFRACTION	100
4.88-5.18	0.2164	149	0.1969	2876	X-RAY DIFFRACTION	100
5.18-5.58	0.2387	152	0.222	2869	X-RAY DIFFRACTION	100
5.58-6.15	0.2726	152	0.2507	2898	X-RAY DIFFRACTION	100
6.15-7.04	0.2776	153	0.2441	2925	X-RAY DIFFRACTION	99.97
7.04-8.86	0.2057	158	0.2221	2971	X-RAY DIFFRACTION	100
8.86-161.45	0.2898	166	0.2951	3150	X-RAY DIFFRACTION	99.43

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.435839323709	0.225346801036	0.156346561859	0.747282244615	0.197672426296	0.423013034185	0.153537872042	-0.0213429785361	0.0696007048392	0.0177306356877	0.0661691098861	-0.214002185598	-0.238103150396	0.356120035013	-0.0183211128974	0.840616008505	-0.248592838658	0.154336846796	0.246179366857	0.0674276401136	0.373465332133	21.4339748092	16.3459809729	-7.72680406702
2	1.20103942419	0.0318731496951	0.481385873951	0.92476510025	0.0789096454438	1.58353964777	0.0249096096833	-0.0493046450917	-0.142711891646	0.0564247802648	0.188491787021	-0.356836254558	0.0935195892727	0.227407194822	-0.065664980479	0.805672555578	0.0566118752092	-0.0725967724736	0.437203944629	-0.0817223063546	0.649225464163	19.7591340802	-19.3786651099	-11.6831479671
3	1.25493944924	-0.0458799415509	0.160363592839	1.39282527209	0.284858557942	1.45234627874	0.123917318399	-0.0463733512128	0.170653162166	0.108004647534	0.0269037486756	-0.271575056043	-0.158511406028	0.347835284894	-0.0636708469794	0.665203246347	-0.241312976717	-0.0267150489856	0.442318295982	0.108106135445	0.550204068122	36.5478431486	9.6538606334	-11.0926922748
4	0.20370348226	0.180788666185	-0.003118658364	0.38480149748	0.00613957636191	0.0316302696607	0.0306424938514	0.0507256429873	0.257207248266	0.0530927484768	-0.0734357878168	-0.254092310873	-0.238956011606	0.0614881834269	-0.13259981519	1.28696451062	-0.841386736881	0.106541029263	0.475268565765	0.0763670825756	0.781419833521	44.2903551543	53.3427082216	-17.3259477549
5	0.369862402393	0.0589883741946	-0.257243147834	0.523386897041	-0.208897846972	0.229146173977	0.0116593003801	0.18848222286	0.256111936638	-0.0752321435004	-0.048533012671	-0.321026799932	-0.314403272169	0.264522142299	-0.11515866156	1.10071305618	-0.455650725717	0.153268739329	0.676478181661	0.285797391392	1.16038804235	36.8426844264	42.8656681142	-34.8861283379
6	0.783238297748	-0.18235094399	-0.0285837219207	0.688742754544	-0.0872674800367	0.761367479382	0.0887827959169	0.190424757427	0.234009884964	-0.0841082550582	0.257592411766	-0.146374307813	-0.347583364885	0.0521511877456	-0.129306199669	0.819959651926	-0.271409744541	0.101219254468	0.477384055665	0.0941188675106	0.774946177255	22.2216164129	16.959812867	-30.1387836551
7	1.23285633073	1.00479213654	-1.06861347027	1.08960006135	-1.37636609814	2.05415950514	0.116175189237	-0.00631101036481	0.0245770191243	-0.00716507956355	0.0801243600809	0.298957639573	0.0535155299623	-0.324673235782	-0.169452181297	0.651677586224	-0.322028587084	-0.0359830559905	0.420346533428	0.151798358347	0.573831515684	-3.81359435311	-8.45233754277	-14.6002952113
8	-0.017155577908	0.0211105804384	-0.0114526910724	-0.000922010880022	-0.013759642861	0.0244776575338	0.234814652414	0.12160119069	0.194159648179	-0.0604658126051	0.0721153957963	-0.0586828649312	-0.17715918744	0.0976656765816	0.772303950219	1.07845718896	-0.636811259825	0.327279537896	0.396378620726	0.363243717892	1.22511130451	25.9704344203	49.1659291047	-29.3332734388

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Selection details	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 215 )	1 - 215	1 - 215
2	2	chain 'A' and (resid 216 through 271 )	216 - 271	216 - 271
3	3	chain 'A' and (resid 272 through 327 )	272 - 327	272 - 327
4	4	chain 'A' and (resid 328 through 495 )	328 - 495	328 - 495
5	5	chain 'A' and (resid 496 through 598 )	496 - 598	496 - 598
6	6	chain 'A' and (resid 599 through 716 )	599 - 716	599 - 716
7	7	chain 'A' and (resid 717 through 799 )	717 - 799	717 - 799
8	8	chain 'A' and (resid 800 through 1027 )	800 - 1027	800 - 1027

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