BMRB Entry 31121

Name: EmrE structure in the TPP-bound state (WT/E14Q heterodimer)
Published: 2024-05-23

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PDB ID: 8uoz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31121
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

EmrE structure in the TPP-bound state (WT/E14Q heterodimer)

Deposition date:

2023-10-20

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, 11962.293 Da.
entity_P4P, non-polymer, 339.389 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 CASFWLLAQTLAYIPTGIAY AIWSGVGIVLISLLSWGFFG QRLDLPAIIGMMLICAGVLI INLLSRSTPH
entity_2: MNPYIYLGGAILAQVIGTTL MKFSEGFTRLWPSVGTIICY CASFWLLAQTLAYIPTGIAY AIWSGVGIVLISLLSWGFFG QRLDLPAIIGMMLICAGVLI INLLSRSTPH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
13C chemical shifts	900
15N chemical shifts	363
1H chemical shifts	191

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
3	unit_3	3

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	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

Entity 2, unit_2 110 residues - 11962.293 Da.

1	MET	ASN	PRO	TYR	ILE	TYR	LEU	GLY	GLY	ALA
2	ILE	LEU	ALA	GLN	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

Entity 3, unit_3 - C24 H20 P - 339.389 Da.

1

P4P

Samples:

sample_1: EmrE, [U-15N; U-2H; 13CH3-ILV], 0.5 mM; EmrE(E14Q), [U-2H], 0.8 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 37.2 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 112.7 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 10.4 mM

sample_2: EmrE, [U-15N; U-2H; 13CH3-ILV], 0.4 mM; EmrE(E14Q), [U-2H], 0.7 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 30.8 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 93.2 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 8.8 mM

sample_3: EmrE, [U-15N; U-2H; 13CH3-ILV], 0.76 mM; EmrE(E14Q), [U-2H], 1.24 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 63.7 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 198.5 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 16 mM

sample_4: EmrE, [U-15N; U-2H; 13CH3-ILV], 0.6 mM; EmrE(E14Q), [U-2H], 0.4 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 25.7 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 78.0 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 8.0 mM

sample_5: EmrE, [U-2H], 0.5 mM; EmrE(E14Q), [U-15N; U-2H; 13CH3-ILV], 0.3 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 20 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 60.7 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 6.4 mM

sample_6: EmrE, [U-2H], 0.5 mM; EmrE(E14Q), [U-15N; U-2H; 13CH3-ILV], 0.3 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 28.8 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 90.2 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 6.4 mM

sample_7: EmrE, [U-2H], 0.7 mM; EmrE(E14Q), [U-15N; U-2H; 13CH3-ILV], 0.45 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 34.9 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 108.2 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 9.2 mM

sample_8: EmrE, [U-2H], 0.5 mM; EmrE(E14Q), [U-15N; U-2H; 13CH3-ILV], 0.3 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 22.2 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 67.2 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 6.4 mM

sample_9: EmrE, [U-2H], 0.83 mM; EmrE(E14Q), [U-15N; U-2H; 13CH3-ILV], 0.51 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 55.0 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 171.1 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 10.72 mM

sample_10: EmrE, [U-2H], 0.72 mM; EmrE(E14Q), [U-15N; U-2H; 13CH3-ILV], 0.43 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 34.9 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 108.2 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 9.2 mM

sample_11: EmrE, [U-15N; U-2H; 13CH3-ILV], 0.4 mM; EmrE(E14Q), [U-2H], 0.7 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 30.8 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 93.2 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 8.8 mM

sample_12: EmrE, [U-15N; U-2H; 13CH3-ILV], 0.3 mM; EmrE(E14Q), [U-2H], 0.5 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 22.2 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 67.2 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 6.4 mM

sample_13: EmrE, [U-15N; U-2H; 13CH3-ILV], 0.67 mM; EmrE(E14Q), [U-2H], 1.2 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 55.0 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 194.0 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 14.96 mM

sample_15: EmrE, [U-15N; U-2H; U-13C], 0.5 mM; EmrE(E14Q), [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; TPP 10.4 mM

sample_16: EmrE, [U-15N; U-2H; 13CH3-ILV], 0.87 mM; EmrE(E14Q), [U-2H], 1.57 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 72.4 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 225.5 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 19.5 mM

sample_17: EmrE, [U-2H], 0.8 mM; EmrE(E14Q), [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; TPP 10.4 mM

sample_18: EmrE, [U-15N; U-13C], 10.7 mM; EmrE(E14Q) 16 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 213.6 mM; 1;2-dimyristoyl-sn-glycero-3-phosphocholine, nature abundance, 491.7 mM

sample_19: EmrE 16 mM; EmrE(E14Q), [U-15N; U-13C], 10.7 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 213.6 mM; 1,2-dimyristoyl-sn-glycero-3-phosphocholine, nature abundance, 491.7 mM

sample_20: EmrE, [U-15N; 1,3-13C glycerol], 10.7 mM; EmrE(E14Q), nature abundance, 16 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 213.6 mM; 1,2-dimyristoyl-sn-glycero-3-phosphocholine, nature abundance, 491.7 mM

sample_21: EmrE, nature abundance, 16 mM; EmrE(E14Q), [U-15N; 1,3-13C glycerol], 10.7 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 213.6 mM; 1,2-dimyristoyl-sn-glycero-3-phosphocholine, nature abundance, 491.7 mM

sample_22: EmrE, [U-15N; 2-13C glycerol], 10.7 mM; EmrE(E14Q), nature abundance, 16 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 213.6 mM; 1,2-dimyristoyl-sn-glycero-3-phosphocholine, nature abundance, 491.7 mM

sample_23: EmrE, nature abundance, 16 mM; EmrE(E14Q), [U-15N; 2-13C glycerol], 10.7 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 213.6 mM; 1,2-dimyristoyl-sn-glycero-3-phosphocholine, nature abundance, 491.7 mM

sample_24: EmrE, [U-2H], 1.47 mM; EmrE(E14Q), [U-15N; U-2H; 13CH3-ILV], 0.89 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 63.4 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 197.4 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 18.9 mM

sample_25: EmrE, [U-15N; U-2H; 13CH3-ILV], 0.74 mM; EmrE(E14Q), [U-2H], 1.45 mM; 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine, 2H-54, 57.5 mM; 1,2-dihexanoyl-d22-sn-glycero-3-phosphocholine, 2H-22, 178.6 mM; sodium chloride 20 mM; Na2HPO4 150 mM; TPP 18.9 mM

sample_26: EmrE, [U-15N]-amino acid, 2 mM; sodium chloride 20 mM; TPP 16 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: 5.6; 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
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	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-13C HSQC	sample_7	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_7	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_8	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_8	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_9	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_9	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_10	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_10	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_11	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_11	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_12	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_12	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_13	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_13	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_16	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_16	isotropic	sample_conditions_1
3D HNCA	sample_15	isotropic	sample_conditions_1
3D HNCA	sample_17	isotropic	sample_conditions_1
3D HNCO	sample_15	isotropic	sample_conditions_1
3D HNCO	sample_17	isotropic	sample_conditions_1
3D HN(CO)CA	sample_15	isotropic	sample_conditions_1
3D HN(CO)CA	sample_17	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_25	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_24	isotropic	sample_conditions_1
3D NCACX	sample_18	isotropic	sample_conditions_2
3D NCACX	sample_19	isotropic	sample_conditions_2
3D NCOCX	sample_18	isotropic	sample_conditions_2
3D NCOCX	sample_19	isotropic	sample_conditions_2
3D CANCOCX	sample_18	isotropic	sample_conditions_2
3D CANCOCX	sample_19	isotropic	sample_conditions_2
3D CANCO	sample_18	isotropic	sample_conditions_2
3D CANCO	sample_19	isotropic	sample_conditions_2
2D 13C/13C DARR	sample_18	isotropic	sample_conditions_2
2D 13C/13C DARR	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 13C/13C PDSD	sample_22	isotropic	sample_conditions_2
2D 13C/13C PDSD	sample_23	isotropic	sample_conditions_2
2D 1H/15N PISEMA	sample_26	anisotropic	sample_conditions_3

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