BMRB Entry 31058

Name: Alpha7 nicotinic acetylcholine receptor intracellular and transmembrane domains bound to ivermectin in a desensitized state
Published: 2023-02-14

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PDB ID: 8f4v
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31058
MolProbity Validation Chart

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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: Alpha7 nicotinic acetylcholine receptor intracellular and transmembrane domains bound to ivermectin in a desensitized state PubMed: 36821490

Deposition date: 2022-11-11 Original release date: 2023-02-14

Authors: Bondarenko, V.; Chen, Q.; Tang, P.

Citation: Bondarenko, Vasyl; Chen, Qiang; Singewald, Kevin; Haloi, Nandan; Tillman, Tommy; Howard, Rebecca; Lindahl, Erik; Xu, Yan; Tang, Pei. "Structural Elucidation of Ivermectin Binding to Alpha7nAChR and the Induced Channel Desensitization" ACS Chem. Neurosci. 14, 1156-1165 (2023).

Assembly members:
entity_1, polymer, 272 residues, 29831.779 Da.
entity_IVM, non-polymer, 875.093 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pTBSG1-TMD+ICD

Entity Sequences (FASTA):
entity_1: SNAEEELYYGLNLLIPCVLI SALALLVFLLPADSGEKISL GITVLLSLTVFMLLVAEIMP STSDSSPSIAQYFASTMIIV GLSVVVTVIVLQYHHHDPDG GKMPKWTRVILLNWCAWFLR MKRPGEDKVRPACQHKQRRC SLASVEMSAVAPPPASNGNL LYIGFRGLDGVHCVPTPDSG VVCGRMACSPTHDEHLLHGG QPPEGDPDLAKILEEVRYIA NRFRCQDESEAVCSEWKFAA CVVDRLCLMAFSVFTIICTI GILMSAPNFVEE

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	764
15N chemical shifts	239
1H chemical shifts	1104

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1
3	unit_3	1
4	unit_4	1
5	unit_5	1
6	unit_6	2
7	unit_7	2
8	unit_8	2
9	unit_9	2
10	unit_10	2

Entities:

Entity 1, unit_1 272 residues - 29831.779 Da.

1

SER

ASN

ALA

GLU

LEU

TYR

GLY

2

LEU

ASN

LEU

ILE

PRO

CYS

VAL

LEU

ILE

3

SER

ALA

LEU

ALA

LEU

VAL

PHE

LEU

4

PRO

ALA

ASP

SER

GLY

GLU

LYS

ILE

SER

LEU

5

GLY

ILE

THR

VAL

LEU

SER

LEU

THR

VAL

6

PHE

MET

LEU

VAL

ALA

GLU

ILE

MET

PRO

7

SER

THR

SER

ASP

SER

PRO

SER

ILE

ALA

8

GLN

TYR

PHE

ALA

SER

THR

MET

ILE

VAL

9

GLY

LEU

SER

VAL

THR

VAL

ILE

VAL

10

LEU

GLN

TYR

HIS

ASP

PRO

ASP

GLY

11

GLY

LYS

MET

PRO

LYS

TRP

THR

ARG

VAL

ILE

12

LEU

ASN

TRP

CYS

ALA

TRP

PHE

LEU

ARG

13

MET

LYS

ARG

PRO

GLY

GLU

ASP

LYS

VAL

ARG

14

PRO

ALA

CYS

GLN

HIS

LYS

GLN

ARG

CYS

15

SER

LEU

ALA

SER

VAL

GLU

MET

SER

ALA

VAL

16

ALA

PRO

ALA

SER

ASN

GLY

ASN

LEU

17

LEU

TYR

ILE

GLY

PHE

ARG

GLY

LEU

ASP

GLY

18

VAL

HIS

CYS

VAL

PRO

THR

PRO

ASP

SER

GLY

19

VAL

CYS

GLY

ARG

MET

ALA

CYS

SER

PRO

20

THR

HIS

ASP

GLU

HIS

LEU

HIS

GLY

21

GLN

PRO

GLU

GLY

ASP

PRO

ASP

LEU

ALA

22

LYS

ILE

LEU

GLU

VAL

ARG

TYR

ILE

ALA

23

ASN

ARG

PHE

ARG

CYS

GLN

ASP

GLU

SER

GLU

24

ALA

VAL

CYS

SER

GLU

TRP

LYS

PHE

ALA

25

CYS

VAL

ASP

ARG

LEU

CYS

LEU

MET

ALA

26

PHE

SER

VAL

PHE

THR

ILE

CYS

THR

ILE

27

GLY

ILE

LEU

MET

SER

ALA

PRO

ASN

PHE

VAL

28

GLU

Entity 2, unit_6 - C48 H74 O14 - 875.093 Da.

1

IVM

Samples:

sample_1: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM

sample_2: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 30 uM; DMSO 0.1%

sample_3: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 100 uM; DMSO 0.3%

sample_4: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 250 uM; DMSO 0.55%

sample_5: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 500 uM; DMSO 0.95%

sample_6: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 500 uM; DMSO 0.8%

sample_7: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 500 uM; DMSO 0.8%

sample_8: alpha7nAChR C317 TMD+ICD, [U-15N], 0.25 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 500 uM; DMSO 0.8%

sample_9: alpha7nAChR C317 TMD+ICD, [U-15N], 0.20 ± 0.01 mM; sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 500 uM; DMSO 0.8%

sample_10: sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 220 uM; DMSO 0.4%; V311C-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.22 ± 0.01 mM

sample_11: sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; V311C-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.22 ± 0.01 mM

sample_12: sodium acetate 5 mM; LDAO 26 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 220 uM; DMSO 0.4%; C335-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.22 ± 0.01 mM

sample_13: sodium acetate 5 mM; LDAO 26 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; C335-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.22 ± 0.01 mM

sample_14: sodium acetate 5 mM; LDAO 26 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 200 uM; DMSO 0.4%; C342-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 mM

sample_15: sodium acetate 5 mM; LDAO 26 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; C342-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 %

sample_16: sodium acetate 5 mM; LDAO 44 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 200 uM; DMSO 0.4%; S350C-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 mM

sample_17: sodium acetate 5 mM; LDAO 44 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; S350C-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 mM

sample_18: sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 200 uM; DMSO 0.4%; C375-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 mM

sample_19: sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; C375-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 mM

sample_20: sodium acetate 5 mM; LDAO 44 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 250 uM; DMSO 0.4%; C390-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.25 ± 0.01 mM

sample_21: sodium acetate 5 mM; LDAO 44 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; C390-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.25 ± 0.01 mM

sample_22: sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 240 uM; DMSO 0.4%; L415C-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.24 ± 0.01 mM

sample_23: sodium acetate 5 mM; LDAO 35 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; L415C-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.24 ± 0.01 mM

sample_24: sodium acetate 5 mM; LDAO 22 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 200 uM; DMSO 0.4%; C435-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 mM

sample_25: sodium acetate 5 mM; LDAO 22 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; C435-MTSL alpha7nAChR TMD+ICD, [U-15N], 0.2 ± 0.01 mM

sample_26: alpha7nAChR C317 TMD+ICD, [U-13C; U-15N], 0.22 ± 0.01 mM; sodium acetate 5 mM; LDAO 44 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM; ivermectin 30 uM; DMSO 0.2%; PNU 30 uM

sample_27: alpha7nAChR C317 TMD+ICD, [U-13C; U-15N], 0.22 ± 0.01 mM; sodium acetate 5 mM; LDAO 44 mM; sodium chloride 25 mM; D2O 5%; DSS 20 uM

sample_conditions_1: ionic strength: 25 mM; pH: 4.7; pressure: 1 atm; temperature: 318 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY-HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-15N STD TROSY-HSQC	sample_6	isotropic	sample_conditions_1
2D 1H-15N STD TROSY-HSQC	sample_7	isotropic	sample_conditions_1
2D 1H-15N STD TROSY-HSQC	sample_8	isotropic	sample_conditions_1
2D NOESY	sample_9	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_10	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_11	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_12	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_13	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_14	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_15	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_16	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_17	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_18	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_19	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_20	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_21	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_22	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_23	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_24	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_25	isotropic	sample_conditions_1
3D TROSY-HNCO	sample_26	isotropic	sample_conditions_1
3D TROSY-HNCO	sample_27	isotropic	sample_conditions_1

Software:

TopSpin v3.2, Bruker Biospin - collection

NMRPipe v10.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

Sparky v3.190, Goddard - data analysis

NMRFAM-SPARKY v1.470, Lee, Tonelli and Markley - data analysis

CS-ROSETTA v3.17, Shen, Vernon, Baker and Bax - structure calculation

Rosetta v3.7, Rosetta - refinement, structure calculation

MolProbity, Richardson - refinement

NMR spectrometers:

Bruker AVANCE II 800 MHz

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