8PET | pdb_00008pet

Cryo-EM structure of the full-length human alpha1beta3 GABA(A) receptor (babba arrangement) in complex with nanobody Nb25, expressed with a 5-fold excess of beta3 over alpha1

PDB DOI: https://doi.org/10.2210/pdb8PET/pdb
EM Map EMD-17636: EMDB EMDataResource

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

Deposited: 2023-06-14 Released: 2025-07-02
Deposition Author(s): Sente, A., Malinauskas, T., Naydenova, K., Hardwick, S.W., Chirgadze, D.Y., Aricescu, A.R.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Subunit abundance shapes GABAA receptor stoichiometry

Sente, A., Malinauskas, T., Naydenova, K., Hardwick, S.W., Chirgadze, D.Y., Aricescu, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 300.54 kDa
Atom Count: 15,451
Modeled Residue Count: 1,802
Deposited Residue Count: 2,573
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 alpha-1	A, D [auth C]	484	Homo sapiens	Mutation(s): 0 Gene Names: GABRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P14867 (Homo sapiens) Explore P14867 Go to UniProtKB: P14867
PHAROS: P14867 GTEx: ENSG00000022355
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14867
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain D [auth C]	Go to GlyGen: P14867-1
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 beta-3	B, C [auth D], E	490	Homo sapiens	Mutation(s): 0 Gene Names: GABRB3
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
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B Focus chain C [auth D] Focus chain E	Go to GlyGen: P28472-1
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	135	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
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	G [auth a], H [auth b], J [auth c], L [auth d], M [auth e]	5		N-Glycosylation	Interactions Focus chain G [auth a] Focus chain H [auth b] Focus chain J [auth c] Focus chain L [auth d] Focus chain M [auth e] Interactions & Density Focus chain G [auth a] Focus chain H [auth b] Focus chain J [auth c] Focus chain L [auth d] Focus chain M [auth e]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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	I [auth G], K [auth H], N [auth I]	2		N-Glycosylation	Interactions Focus chain I [auth G] Focus chain K [auth H] Focus chain N [auth I] Interactions & Density Focus chain I [auth G] Focus chain K [auth H] Focus chain N [auth I]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PIO Query on PIO Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain BA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain BA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain BA [auth C]	BA [auth C], P [auth A]	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate C₂₅ H₄₉ O₁₉ P₃ XLNCEHRXXWQMPK-MJUMVPIBSA-N		Interactions Focus chain BA [auth C] Focus chain P [auth A] Interactions & Density Focus chain BA [auth C] Focus chain P [auth A]
R16 Query on R16 Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain AA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain AA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain AA [auth C]	AA [auth C], O [auth A]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain O [auth A] Interactions & Density Focus chain AA [auth C] Focus chain O [auth A]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain EA [auth E] SDF format, chain DA [auth E] SDF format, chain CA [auth E] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth E] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth E]	CA [auth E] DA [auth E] EA [auth E] Q [auth B] R [auth B] CA [auth E], DA [auth E], EA [auth E], Q [auth B], R [auth B], S [auth B], T [auth B], V [auth D], W [auth D], X [auth D], Y [auth D], Z [auth D]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain U [auth B] MOL2 format, chain U [auth B] mmCIF format, chain U [auth B]	U [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.1.2

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-02

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 States	1R01GM135550-01
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_EX_MR/T046279/1
National Science Foundation (NSF, United States)	United States	2014862

Revision History (Full details and data files)

Version 1.0: 2025-07-02
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 8PET | pdb_00008pet

Cryo-EM structure of the full-length human alpha1beta3 GABA(A) receptor (babba arrangement) in complex with nanobody Nb25, expressed with a 5-fold excess of beta3 over alpha1

Subunit abundance shapes GABAA receptor stoichiometry

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 3

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

8PET | pdb_00008pet