6ur8

CryoEM structure of human alpha4beta2 nicotinic acetylcholine receptor in complex with varenicline

Method: ELECTRON MICROSCOPY Dmax: 138.9 Å Quality: REASONABLE

1. Protein Identity and Related Structures Protein Identity & Related Structures

Chimera of soluble cytochrome b562 (BRIL) and neuronal acetylcholine receptor subunit alpha-4

Homo sapiens

UniProt P0ABE7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 23–123 Chain D; UniProt 23–123 Not recorded Neuronal acetylcholine receptor subunit beta-2 × 3 (P17787) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 QMR VARENICLINE × 2 BMA beta-D-mannopyranose × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.71 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

714 other PDB entries and 822 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 343–443; UniProt 23–123 Author chain D; PDBConstruct 343–443; UniProt 23–123

Chimera of soluble cytochrome b562 (BRIL) and neuronal acetylcholine receptor subunit alpha-4

Homo sapiens

UniProt P43681

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 27–364 Chain A; UniProt 589–627 Chain D; UniProt 27–364 Chain D; UniProt 589–627 Not recorded Neuronal acetylcholine receptor subunit beta-2 × 3 (P17787) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 QMR VARENICLINE × 2 BMA beta-D-mannopyranose × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.71 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACHA4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–338; UniProt 27–364 Author chain A; PDBConstruct 449–487; UniProt 589–627 Author chain D; PDBConstruct 1–338; UniProt 27–364 Author chain D; PDBConstruct 449–487; UniProt 589–627

Neuronal acetylcholine receptor subunit beta-2

Homo sapiens

UniProt P17787

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 26–351 Chain B; UniProt 442–502 Chain C; UniProt 26–351 Chain C; UniProt 442–502 Chain E; UniProt 26–351 Chain E; UniProt 442–502 Not recorded Chimera of soluble cytochrome b562 (BRIL) and neuronal acetylcholine receptor subunit alpha-4 × 2 (P43681,P0ABE7) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 QMR VARENICLINE × 2 BMA beta-D-mannopyranose × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.71 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACHB2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–326; UniProt 26–351 Author chain B; PDBConstruct 327–387; UniProt 442–502 Author chain C; PDBConstruct 1–326; UniProt 26–351 Author chain C; PDBConstruct 327–387; UniProt 442–502 Author chain E; PDBConstruct 1–326; UniProt 26–351 Author chain E; PDBConstruct 327–387; UniProt 442–502

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6ur8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6ur8
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id6ur8
Deposition date deposition_date2019-10-22
Structure title titleCryoEM structure of human alpha4beta2 nicotinic acetylcholine receptor in complex with varenicline
Keywords keywordsacetylcholine receptor, nicotine, varenicline, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier42.44
Radius of gyration Rg (electron density) rg_electron41.82
Forward intensity I(0) i0565568000.00
Molecular weight molecular_weight211020.0 kDa
Excluded volume excluded_volume270390 ų
Envelope volume envelope_volume370590 ų
Hydration-shell volume shell_volume73716 ų
Envelope diameter envelope_diameter135.8
Shell Rg shell_rg47.58
Envelope Rg envelope_rg41.18
Shape Rg shape_rg41.84
Total Rg total_rg42.05
Total atoms total_atoms14880
Residues n_residues1798
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax138.9
Rg (real space) rg_real42.45
Rg uncertainty (real space) rg_real_error0.93
I(0) (real space) i0_real5.6560e+08
I(0) uncertainty (real space) i0_real_error9.1230e+06
Rg (reciprocal space) rg_reciprocal42.44
I(0) (reciprocal space) i0_reciprocal565600000.0000
Solution quality estimate total_estimate0.6519
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.8
Skewness Skewness skewness0.393
Kurtosis Kurtosis kurtosis-0.331
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha77400000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 0.083; Positv: 1.000; Valcen: 0.998; Smooth: 0.748

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id6ur8A01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id6ur8B01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id6ur8C01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id6ur8D01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id6ur8E01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain

8. Citations (1)

9. Files and Curves (10)