6CNJ

Structure of the 2alpha3beta stiochiometry of the human Alpha4Beta2 nicotinic receptor

PDB DOI: https://doi.org/10.2210/pdb6CNJ/pdb
EM Map EMD-7535: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens, Mus musculus
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2018-03-08 Released: 2018-05-02
Deposition Author(s): Walsh Jr, R.M., Roh, S.H., Gharpure, A., Morales-Perez, C.L., Teng, J., Hibbs, R.E.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 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: 470.11 kDa
Atom Count: 25,343
Modelled Residue Count: 3,122
Deposited Residue Count: 4,081
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuronal acetylcholine receptor subunit alpha-4	A, D	386	Homo sapiens	Mutation(s): 0 Gene Names: CHRNA4, NACRA4 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P43681 (Homo sapiens) Explore P43681 Go to UniProtKB: P43681
PHAROS: P43681 GTEx: ENSG00000101204
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43681
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuronal acetylcholine receptor subunit beta-2	B, C, E	403	Homo sapiens	Mutation(s): 0 Gene Names: CHRNB2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P17787 (Homo sapiens) Explore P17787 Go to UniProtKB: P17787
PHAROS: P17787 GTEx: ENSG00000160716
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17787
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG1 Kappa Light Chain	F, H, J	238	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
IgG1 Heavy Chain	G, I, K	462	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
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L, M, N	3		N-Glycosylation	Interactions Focus chain L Focus chain M Focus chain N Interactions & Density Focus chain L Focus chain M Focus chain N
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 AA [auth D] SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D]	AA [auth D] BA [auth E] CA [auth E] Q [auth A] R [auth A] AA [auth D], BA [auth E], CA [auth E], Q [auth A], R [auth A], T [auth B], U [auth B], V [auth C], W [auth C], Z [auth D]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain X [auth D] MOL2 format, chain O [auth A] MOL2 format, chain X [auth D]	O [auth A], X [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain O [auth A] Focus chain X [auth D] Interactions & Density Focus chain O [auth A] Focus chain X [auth D]
NCT Query on NCT Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Y [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Y [auth D]	P [auth A], Y [auth D]	(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE C₁₀ H₁₄ N₂ SNICXCGAKADSCV-JTQLQIEISA-N		Interactions Focus chain P [auth A] Focus chain Y [auth D] Interactions & Density Focus chain P [auth A] Focus chain Y [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A]	S [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Interactions & Density Focus chain S [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
NCT	BindingDB: 6CNJ	Ki: min: 0.05, max: 150 (nM) from 77 assay(s)
		IC50: min: 1.2, max: 430 (nM) from 9 assay(s)
		EC50: min: 1, max: 1.00e+4 (nM) from 25 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.1
MODEL REFINEMENT	PHENIX	1.13-2988

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS095899
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

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 1.1: 2018-05-09
Changes: Data collection, Structure summary
Version 1.2: 2018-05-16
Changes: Data collection, Database references
Version 1.3: 2018-05-30
Changes: Data collection, Database references
Version 1.4: 2018-07-18
Changes: Data collection
Version 1.5: 2019-01-30
Changes: Data collection
Version 1.6: 2019-12-11
Changes: Author supporting evidence
Version 1.7: 2019-12-18
Changes: Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary