6PV8

Human alpha3beta4 nicotinic acetylcholine receptor in complex with AT-1001

PDB DOI: https://doi.org/10.2210/pdb6PV8/pdb
EM Map EMD-20488: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Escherichia coli O11, Mus musculus
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2019-07-19 Released: 2019-09-11
Deposition Author(s): Gharpure, A., Teng, J., Zhuang, Y., Noviello, C.M., Walsh, R.M., Cabuco, R., Howard, R.J., Zaveri, N.T., Lindahl, E., Hibbs, R.E.
Funding Organization(s): Welch Foundation, National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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.

Macromolecule Content

Total Structure Weight: 411.78 kDa
Atom Count: 20,051
Modelled Residue Count: 2,379
Deposited Residue Count: 3,528
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion protein of Neuronal acetylcholine receptor subunit alpha-3 and Soluble cytochrome b562	A, D	525	Homo sapiens, Escherichia coli O11	Mutation(s): 0 Gene Names: CHRNA3, NACHRA3, CWJ32_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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32297
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion protein of Neuronal acetylcholine receptor subunit beta-4 and Soluble cytochrome b562	B, C, E	538	Homo sapiens, Escherichia coli O11	Mutation(s): 0 Gene Names: CHRNB4, CWJ32_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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30926
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG2b Fab heavy chain	F, H	219	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Kappa Fab light chain	G, I	213	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, P	2		N-Glycosylation	Interactions Focus chain J Focus chain P Interactions & Density Focus chain J Focus chain P
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	5		N-Glycosylation	Interactions Focus chain K Focus chain M Focus chain O Focus chain Q Focus chain S Interactions & Density Focus chain K Focus chain M Focus chain O Focus chain Q Focus chain S
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	3		N-Glycosylation	Interactions Focus chain L Focus chain N Focus chain R Interactions & Density Focus chain L Focus chain N Focus chain R
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	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		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain U [auth A] Focus chain V [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain U [auth A] Focus chain V [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
P1M (Subject of Investigation/LOI) Query on P1M Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain T [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain T [auth A]	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		Interactions Focus chain FA [auth D] Focus chain T [auth A] Interactions & Density Focus chain FA [auth D] Focus chain T [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	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		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain W [auth B] Focus chain X [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth B] MOL2 format, chain AA [auth B]	AA [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Interactions & Density Focus chain AA [auth B]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-09-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Welch Foundation	United States	I-1812
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	T32DA07290
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008203
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	DA037492
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	DA042072
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS095899

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