7QND

Cryo-EM structure of human full-length extrasynaptic beta3delta GABA(A)R in complex with THIP (gaboxadol), histamine and nanobody Nb25

PDB DOI: https://doi.org/10.2210/pdb7QND/pdb
EM Map EMD-14075: EMDB EMDataResource

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

Deposited: 2021-12-20 Released: 2022-04-13
Deposition Author(s): Sente, A., Desai, R., Naydenova, K., Malinauskas, T., Jounaidi, Y., Miehling, J., Zhou, X., Masiulis, S., Hardwick, S.W., Chirgadze, D.Y., Miller, K.W., Aricescu, A.R.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 315.22 kDa
Atom Count: 16,810
Modelled Residue Count: 1,995
Deposited Residue Count: 2,727
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit beta-3	A, B, C, D	473	Homo sapiens	Mutation(s): 0 Gene Names: GABRB3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P28472 (Homo sapiens) Explore P28472 Go to UniProtKB: P28472
PHAROS: P28472 GTEx: ENSG00000166206
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28472
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit delta	E	472	Homo sapiens	Mutation(s): 0 Gene Names: GABRD Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O14764 (Homo sapiens) Explore O14764 Go to UniProtKB: O14764
PHAROS: O14764 GTEx: ENSG00000187730
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14764
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody Nb25	F [auth K], G [auth L], H [auth M]	121	Lama glama	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: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth a], K [auth b], M [auth c], O [auth d]	2		N-Glycosylation	Interactions Focus chain I [auth a] Focus chain K [auth b] Focus chain M [auth c] Focus chain O [auth d] Interactions & Density Focus chain I [auth a] Focus chain K [auth b] Focus chain M [auth c] Focus chain O [auth d]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
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	J [auth F], L [auth G], N [auth H], P [auth I]	5		N-Glycosylation	Interactions Focus chain J [auth F] Focus chain L [auth G] Focus chain N [auth H] Focus chain P [auth I] Interactions & Density Focus chain J [auth F] Focus chain L [auth G] Focus chain N [auth H] Focus chain P [auth I]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain U [auth E] MOL2 format, chain U [auth E]	U [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain U [auth E] Interactions & Density Focus chain U [auth E]
EI7 (Subject of Investigation/LOI) Query on EI7 Download Ideal Coordinates CCD File SDF format, chain T [auth E] MOL2 format, chain T [auth E]	T [auth E]	4,5,6,7-tetrahydro-[1,2]oxazolo[5,4-c]pyridin-3-one C₆ H₈ N₂ O₂ ZXRVKCBLGJOCEE-UHFFFAOYSA-N		Interactions Focus chain T [auth E] Interactions & Density Focus chain T [auth E]
HSM (Subject of Investigation/LOI) Query on HSM Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C]	Q [auth B], R [auth C], S [auth C]	HISTAMINE C₅ H₉ N₃ NTYJJOPFIAHURM-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	REFMAC	5
MODEL REFINEMENT	PHENIX	1.19.2
RECONSTRUCTION	RELION	3.1

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2022-04-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/L009609/1
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UP_1201/15
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United Kingdom	1R01-GM135550
Wellcome Trust	United Kingdom	206171/Z/17/Z
Wellcome Trust	United Kingdom	202905/Z/16/Z