BMRB Entry 31125

Name: EmrE structure in the proton-bound state (WT/L51I heterodimer)
Published: 2024-05-23

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PDB ID: 8uwu
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31125
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

EmrE structure in the proton-bound state (WT/L51I heterodimer)

Deposition date:

2023-11-08

Original release date:

2024-05-23

Authors:

Li, J.; Sae Her, A.; Besch, A.; Ramirez, B.; Crames, M.; Banigan, J.; Mueller, C.; Marsiglia, W.; Zhang, Y.; Traaseth, N.

Citation:

Citation: Li, J.; Sae Her, A.; Besch, A.; Ramirez, B.; Crames, M.; Banigan, J.; Mueller, C.; Marsiglia, W.; Zhang, Y.; Traaseth, N.. "Dynamics underlie the drug recognition mechanism by the efflux transporter EmrE" Nat. Commun. 15, 4537-4537 (2024).
PubMed: 38806470

Assembly members:

Assembly members:
entity_1, polymer, 110 residues, 11963.278 Da.
entity_2, polymer, 110 residues, 11963.278 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MNPYIYLGGAILAEVIGTTL MKFSEGFTRLWPSVGTIICY CASFWLLAQTIAYIPTGIAY AIWSGVGIVLISLLSWGFFG QRLDLPAIIGMMLICAGVLI INLLSRSTPH
entity_2: MNPYIYLGGAILAEVIGTTL MKFSEGFTRLWPSVGTIICY CASFWLLAQTLAYIPTGIAY AIWSGVGIVLISLLSWGFFG QRLDLPAIIGMMLICAGVLI INLLSRSTPH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	534
15N chemical shifts	204
1H chemical shifts	169

Additional metadata:

Assembly
Samples and Experiments
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 110 residues - 11963.278 Da.

1	MET	ASN	PRO	TYR	ILE	TYR	LEU	GLY	GLY	ALA
2	ILE	LEU	ALA	GLU	VAL	ILE	GLY	THR	THR	LEU
3	MET	LYS	PHE	SER	GLU	GLY	PHE	THR	ARG	LEU
4	TRP	PRO	SER	VAL	GLY	THR	ILE	ILE	CYS	TYR
5	CYS	ALA	SER	PHE	TRP	LEU	LEU	ALA	GLN	THR
6	ILE	ALA	TYR	ILE	PRO	THR	GLY	ILE	ALA	TYR
7	ALA	ILE	TRP	SER	GLY	VAL	GLY	ILE	VAL	LEU
8	ILE	SER	LEU	LEU	SER	TRP	GLY	PHE	PHE	GLY
9	GLN	ARG	LEU	ASP	LEU	PRO	ALA	ILE	ILE	GLY
10	MET	MET	LEU	ILE	CYS	ALA	GLY	VAL	LEU	ILE
11	ILE	ASN	LEU	LEU	SER	ARG	SER	THR	PRO	HIS

Entity 2, unit_2 110 residues - 11963.278 Da.

1	MET	ASN	PRO	TYR	ILE	TYR	LEU	GLY	GLY	ALA
2	ILE	LEU	ALA	GLU	VAL	ILE	GLY	THR	THR	LEU
3	MET	LYS	PHE	SER	GLU	GLY	PHE	THR	ARG	LEU
4	TRP	PRO	SER	VAL	GLY	THR	ILE	ILE	CYS	TYR
5	CYS	ALA	SER	PHE	TRP	LEU	LEU	ALA	GLN	THR
6	LEU	ALA	TYR	ILE	PRO	THR	GLY	ILE	ALA	TYR
7	ALA	ILE	TRP	SER	GLY	VAL	GLY	ILE	VAL	LEU
8	ILE	SER	LEU	LEU	SER	TRP	GLY	PHE	PHE	GLY
9	GLN	ARG	LEU	ASP	LEU	PRO	ALA	ILE	ILE	GLY
10	MET	MET	LEU	ILE	CYS	ALA	GLY	VAL	LEU	ILE
11	ILE	ASN	LEU	LEU	SER	ARG	SER	THR	PRO	HIS

Samples:

sample_1: EmrE, [U-15N; U-2H; U-13C], 0.5 mM; EmrE (L51I), [U-2H], 0.8 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 35.8 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 108.3 mM; sodium chloride 20 mM; Na2HPO4 150 mM

sample_2: EmrE, [U-2H], 0.8 mM; EmrE (L51I), [U-15N; U-2H; U-13C], 0.5 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 35.8 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 108.3 mM; sodium chloride 20 mM; Na2HPO4 150 mM

sample_3: EmrE, [U-15N; U-2H; 13CH3-ILV], 0.5 mM; EmrE (L51I), [U-2H], 0.8 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 35.8 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 108.3 mM; sodium chloride 20 mM; Na2HPO4 150 mM

sample_4: EmrE, [U-15N; U-2H; 13CH3-ILV], 0.5 mM; EmrE (L51I), [U-2H], 0.8 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 35.8 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 108.3 mM; sodium chloride 20 mM; Na2HPO4 150 mM

sample_5: EmrE, [U-15N; U-2H; 13CH3-ILV], 0.5 mM; EmrE (L51I), [U-2H], 0.8 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 35.8 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 108.3 mM; sodium chloride 20 mM; Na2HPO4 150 mM

sample_6: EmrE, [U-2H], 0.5 mM; EmrE (L51I), [U-15N; U-2H; 13CH3-ILV], 0.3 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 21.5 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 65.1 mM; sodium chloride 20 mM; Na2HPO4 150 mM

sample_8: EmrE, [U-2H], 0.8 mM; EmrE (L51I), [U-15N; U-2H; 13CH3-ILV], 0.5 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 35.8 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 108.3 mM; sodium chloride 20 mM; Na2HPO4 150 mM

sample_9: EmrE, [U-2H], 0.6 mM; EmrE (L51I), [U-15N; U-2H; 13CH3-ILV], 0.4 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 28.6 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 86.8 mM; sodium chloride 20 mM; Na2HPO4 150 mM

sample_10: EmrE, [U-15N; U-2H; 13CH3-ILV], 0.5 mM; EmrE (L51I), [U-2H], 0.8 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 35.8 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 108.3 mM; sodium chloride 20 mM; Na2HPO4 150 mM

sample_11: EmrE, [U-2H], 0.6 mM; EmrE (L51I), [U-15N; U-2H; 13CH3-ILV], 0.4 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 28.6 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 86.8 mM; sodium chloride 20 mM; Na2HPO4 150 mM

sample_12: EmrE, [U-2H], 0.6 mM; EmrE (L51I), [U-15N; U-2H; 13CH3-ILV], 0.4 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 28.6 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 86.8 mM; sodium chloride 20 mM; Na2HPO4 150 mM

sample_13: EmrE, [U-2H], 0.6 mM; EmrE (L51I), [U-15N; U-2H; 13CH3-ILV], 0.4 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 28.6 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 86.8 mM; sodium chloride 20 mM; Na2HPO4 150 mM

sample_14: EmrE, [U-2H], 0.6 mM; EmrE (L51I), [U-15N; U-2H; 13CH3-ILV], 0.4 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 28.6 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 86.8 mM; sodium chloride 20 mM; Na2HPO4 150 mM

sample_15: EmrE, [U-15N; U-2H; 13CH3-ILV], 0.4 mM; EmrE (L51I), [U-2H], 0.6 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 28.6 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 86.8 mM; sodium chloride 20 mM; Na2HPO4 150 mM

sample_16: EmrE, [U-15N; U-13C], 6.7 mM; EmrE (L51I) 10.7 mM; sodium chloride 20 mM; Na2HPO4 150 mM; 1,2-dimyristoyl-sn-glycero-3-phosphocholine 513.3 mM

sample_17: EmrE 14.2 mM; EmrE (L51I), [U-15N; U-13C], 8.9 mM; sodium chloride 20 mM; Na2HPO4 150 mM; 1,2-dimyristoyl-sn-glycero-3-phosphocholine 511.1 mM

sample_18: EmrE, [U-15N; 1,3-13C glycerol], 6.7 mM; EmrE (L51I) 10.7 mM; sodium chloride 20 mM; Na2HPO4 150 mM; 1,2-dimyristoyl-sn-glycero-3-phosphocholine 513.3 mM

sample_19: EmrE 12.5 mM; EmrE (L51I), [U-15N; 1,3-13C glycerol], 7.8 mM; sodium chloride 20 mM; Na2HPO4 150 mM; 1,2-dimyristoyl-sn-glycero-3-phosphocholine 512.2 mM

sample_20: EmrE, [U-15N; 2-13C glycerol], 6.7 mM; EmrE (L51I) 10.7 mM; sodium chloride 20 mM; Na2HPO4 150 mM; 1,2-dimyristoyl-sn-glycero-3-phosphocholine 513.3 mM

sample_21: EmrE 12.5 mM; EmrE (L51I), [U-15N; 2-13C glycerol], 7.8 mM; sodium chloride 20 mM; Na2HPO4 150 mM; 1,2-dimyristoyl-sn-glycero-3-phosphocholine 512.2 mM

sample_22: EmrE, [U-15N]-amino acid, 2 mM; sodium chloride 20 mM; 1,2-di-O-tetradecyl-sn-glycero-3-phosphocholine 321 mM; 1,2-dihexanoyl-sn-glycero-3-phosphocholine 91.6 mM; YbCl3 8 mM; HEPES 80 mM

sample_conditions_1: ionic strength: 20 mM; pH: 5.6; pressure: 1 atm; temperature: 310 K

sample_conditions_2: ionic strength: 20 mM; pH: 5; pressure: 1 atm; temperature: 273 K

sample_conditions_3: ionic strength: 20 mM; pH: 6; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCA	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
2D 1H/15N PISEMA	sample_22	anisotropic	sample_conditions_3
2D 15N/13C NCA	sample_16	isotropic	sample_conditions_2
3D HNCO	sample_1	isotropic	sample_conditions_1
3D NCACX	sample_16	isotropic	sample_conditions_2
3D NCOCX	sample_16	isotropic	sample_conditions_2
3D CANCOCX	sample_16	isotropic	sample_conditions_2
3D CANCO	sample_16	isotropic	sample_conditions_2
2D 15N/13C NCO	sample_16	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_3	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_2	isotropic	sample_conditions_1
2D 13C/13C PDSD	sample_18	isotropic	sample_conditions_2
2D 13C/13C PDSD	sample_19	isotropic	sample_conditions_2
2D 13C/13C PDSD	sample_20	isotropic	sample_conditions_2
2D 13C/13C PDSD	sample_21	isotropic	sample_conditions_2
2D 15N/13C NCA	sample_17	isotropic	sample_conditions_2
2D 15N/13C NCO	sample_17	isotropic	sample_conditions_2
3D NCACX	sample_17	isotropic	sample_conditions_2
3D NCOCX	sample_17	isotropic	sample_conditions_2
3D CANCOCX	sample_17	isotropic	sample_conditions_2
3D CANCO	sample_17	isotropic	sample_conditions_2
2D 13C/13C DARR	sample_16	isotropic	sample_conditions_2
3D CANCO	sample_17	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_10	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_10	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_6	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_6	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_9	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_9	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_8	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_11	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_14	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_13	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_13	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_12	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_12	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_11	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_15	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_14	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_15	isotropic	sample_conditions_1

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks