BMRB Entry 31121

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31121
MolProbity Validation Chart

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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:
Data typeCount
13C chemical shifts900
15N chemical shifts363
1H chemical shifts191

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_33

Entities:

Entity 1, unit_1 110 residues - 11963.278 Da.

1   METASNPROTYRILETYRLEUGLYGLYALA
2   ILELEUALAGLUVALILEGLYTHRTHRLEU
3   METLYSPHESERGLUGLYPHETHRARGLEU
4   TRPPROSERVALGLYTHRILEILECYSTYR
5   CYSALASERPHETRPLEULEUALAGLNTHR
6   LEUALATYRILEPROTHRGLYILEALATYR
7   ALAILETRPSERGLYVALGLYILEVALLEU
8   ILESERLEULEUSERTRPGLYPHEPHEGLY
9   GLNARGLEUASPLEUPROALAILEILEGLY
10   METMETLEUILECYSALAGLYVALLEUILE
11   ILEASNLEULEUSERARGSERTHRPROHIS

Entity 2, unit_2 110 residues - 11962.293 Da.

1   METASNPROTYRILETYRLEUGLYGLYALA
2   ILELEUALAGLNVALILEGLYTHRTHRLEU
3   METLYSPHESERGLUGLYPHETHRARGLEU
4   TRPPROSERVALGLYTHRILEILECYSTYR
5   CYSALASERPHETRPLEULEUALAGLNTHR
6   LEUALATYRILEPROTHRGLYILEALATYR
7   ALAILETRPSERGLYVALGLYILEVALLEU
8   ILESERLEULEUSERTRPGLYPHEPHEGLY
9   GLNARGLEUASPLEUPROALAILEILEGLY
10   METMETLEUILECYSALAGLYVALLEUILE
11   ILEASNLEULEUSERARGSERTHRPROHIS

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:

NameSampleSample stateSample conditions
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-15N TROSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-15N TROSYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 1H-15N TROSYsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
2D 1H-15N TROSYsample_4isotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
2D 1H-15N TROSYsample_5isotropicsample_conditions_1
2D 1H-13C HSQCsample_6isotropicsample_conditions_1
2D 1H-15N TROSYsample_6isotropicsample_conditions_1
2D 1H-13C HSQCsample_7isotropicsample_conditions_1
2D 1H-15N TROSYsample_7isotropicsample_conditions_1
2D 1H-13C HSQCsample_8isotropicsample_conditions_1
2D 1H-15N TROSYsample_8isotropicsample_conditions_1
2D 1H-13C HSQCsample_9isotropicsample_conditions_1
2D 1H-15N TROSYsample_9isotropicsample_conditions_1
2D 1H-13C HSQCsample_10isotropicsample_conditions_1
2D 1H-15N TROSYsample_10isotropicsample_conditions_1
2D 1H-13C HSQCsample_11isotropicsample_conditions_1
2D 1H-15N TROSYsample_11isotropicsample_conditions_1
2D 1H-13C HSQCsample_12isotropicsample_conditions_1
2D 1H-15N TROSYsample_12isotropicsample_conditions_1
2D 1H-13C HSQCsample_13isotropicsample_conditions_1
2D 1H-15N TROSYsample_13isotropicsample_conditions_1
2D 1H-13C HSQCsample_16isotropicsample_conditions_1
2D 1H-15N TROSYsample_16isotropicsample_conditions_1
3D HNCAsample_15isotropicsample_conditions_1
3D HNCAsample_17isotropicsample_conditions_1
3D HNCOsample_15isotropicsample_conditions_1
3D HNCOsample_17isotropicsample_conditions_1
3D HN(CO)CAsample_15isotropicsample_conditions_1
3D HN(CO)CAsample_17isotropicsample_conditions_1
3D 1H-13C NOESYsample_25isotropicsample_conditions_1
3D 1H-13C NOESYsample_24isotropicsample_conditions_1
3D NCACXsample_18isotropicsample_conditions_2
3D NCACXsample_19isotropicsample_conditions_2
3D NCOCXsample_18isotropicsample_conditions_2
3D NCOCXsample_19isotropicsample_conditions_2
3D CANCOCXsample_18isotropicsample_conditions_2
3D CANCOCXsample_19isotropicsample_conditions_2
3D CANCOsample_18isotropicsample_conditions_2
3D CANCOsample_19isotropicsample_conditions_2
2D 13C/13C DARRsample_18isotropicsample_conditions_2
2D 13C/13C DARRsample_19isotropicsample_conditions_2
2D 13C/13C PDSDsample_20isotropicsample_conditions_2
2D 13C/13C PDSDsample_21isotropicsample_conditions_2
2D 13C/13C PDSDsample_22isotropicsample_conditions_2
2D 13C/13C PDSDsample_23isotropicsample_conditions_2
2D 1H/15N PISEMAsample_26anisotropicsample_conditions_3

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift assignment

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

GROMACS, Lindahl, Abraham, Hess, van der Spoel - refinement

Sparky, Goddard - peak picking

NMR spectrometers:

  • Bruker AVANCE III 600 MHz
  • Bruker AVANCE III 700 MHz
  • Agilent Direct Drive 600 MHz

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