6PV8

Human alpha3beta4 nicotinic acetylcholine receptor in complex with AT-1001


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Agonist Selectivity and Ion Permeation in the alpha 3 beta 4 Ganglionic Nicotinic Receptor.

Gharpure, A.Teng, J.Zhuang, Y.Noviello, C.M.Walsh Jr., R.M.Cabuco, R.Howard, R.J.Zaveri, N.T.Lindahl, E.Hibbs, R.E.

(2019) Neuron 104: 501

  • DOI: https://doi.org/10.1016/j.neuron.2019.07.030
  • Primary Citation of Related Structures:  
    6PV7, 6PV8

  • PubMed Abstract: 

    Nicotinic acetylcholine receptors are pentameric ion channels that mediate fast chemical neurotransmission. The α3β4 nicotinic receptor subtype forms the principal relay between the central and peripheral nervous systems in the autonomic ganglia. This receptor is also expressed focally in brain areas that affect reward circuits and addiction. Here, we present structures of the α3β4 nicotinic receptor in lipidic and detergent environments, using functional reconstitution to define lipids appropriate for structural analysis. The structures of the receptor in complex with nicotine, as well as the α3β4-selective ligand AT-1001, complemented by molecular dynamics, suggest principles of agonist selectivity. The structures further reveal much of the architecture of the intracellular domain, where mutagenesis experiments and simulations define residues governing ion conductance.


  • Organizational Affiliation

    Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion protein of Neuronal acetylcholine receptor subunit alpha-3 and Soluble cytochrome b562
A, D
525Homo sapiensEscherichia coli O11Mutation(s): 0 
Gene Names: CHRNA3NACHRA3CWJ32_12820
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P32297 (Homo sapiens)
Explore P32297 
Go to UniProtKB:  P32297
PHAROS:  P32297
GTEx:  ENSG00000080644 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32297
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P32297-2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion protein of Neuronal acetylcholine receptor subunit beta-4 and Soluble cytochrome b562
B, C, E
538Homo sapiensEscherichia coli O11Mutation(s): 0 
Gene Names: CHRNB4CWJ32_12820
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P30926 (Homo sapiens)
Explore P30926 
Go to UniProtKB:  P30926
PHAROS:  P30926
GTEx:  ENSG00000117971 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30926
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P30926-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
IgG2b Fab heavy chain
F, H
219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Kappa Fab light chain
G, I
213Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, P
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K, M, O, Q, S
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
L, N, R
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01
Query on Y01

Download Ideal Coordinates CCD File 
DA [auth C]
EA [auth C]
GA [auth D]
HA [auth D]
KA [auth E]
DA [auth C],
EA [auth C],
GA [auth D],
HA [auth D],
KA [auth E],
LA [auth E],
U [auth A],
V [auth A],
Y [auth B],
Z [auth B]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
P1M (Subject of Investigation/LOI)
Query on P1M

Download Ideal Coordinates CCD File 
FA [auth D],
T [auth A]
(3-endo)-N-(2-bromophenyl)-9-methyl-9-azabicyclo[3.3.1]nonan-3-amine
C15 H21 Br N2
UZJWAFOJOSGEKL-CLLJXQQHSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
IA [auth E]
JA [auth E]
W [auth B]
BA [auth C],
CA [auth C],
IA [auth E],
JA [auth E],
W [auth B],
X [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Welch FoundationUnited StatesI-1812
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesT32DA07290
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM008203
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesDA037492
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesDA042072
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS095899

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Database references
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary