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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 8PET

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

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit alpha-1A,
D [auth C]		484Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14867
Glycosylation
Glycosylation Sites: 1
Go to GlyGen: P14867-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit beta-3B,
C [auth D],
E		490Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28472
Glycosylation
Glycosylation Sites: 2
Go to GlyGen: P28472-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody Nb25135Lama glamaMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseG [auth a],
H [auth b],
J [auth c],
L [auth d],
M [auth e]		5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth G],
K [auth H],
N [auth I]		2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PIO

Query on PIO


Download:Ideal Coordinates CCD File
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
R16

Query on R16


Download:Ideal Coordinates CCD File
AA [auth C],
O [auth A]		HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
D10

Query on D10


Download:Ideal Coordinates CCD File
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
ZN

Query on ZN


Download:Ideal Coordinates CCD File
U [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.1.2

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/L009609/1
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/15
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM135550-01
Medical Research Council (MRC, United Kingdom)United KingdomMC_EX_MR/T046279/1
National Science Foundation (NSF, United States)United States2014862

Revision History  (Full details and data files)

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