8DN3 | pdb_00008dn3

Cryo-EM structure of human Glycine Receptor alpha1-beta heteromer, apo state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8DN3

This is version 1.3 of the entry. See complete history

Literature

Asymmetric gating of a human hetero-pentameric glycine receptor.

Liu, X.Wang, W.

(2023) Nat Commun 14: 6377-6377

  • DOI: https://doi.org/10.1038/s41467-023-42051-6
  • Primary Citation Related Structures: 
    8DN2, 8DN3, 8DN4, 8DN5

  • PubMed Abstract: 

    Hetero-pentameric Cys-loop receptors constitute a major type of neurotransmitter receptors that enable signal transmission and processing in the nervous system. Despite intense investigations into their working mechanism and pharmaceutical potentials, how neurotransmitters activate these receptors remains unclear due to the lack of high-resolution structural information in the activated open state. Here we report near-atomic resolution structures resolved in digitonin consistent with all principle functional states of the human α1β GlyR, which is a major Cys-loop receptor that mediates inhibitory neurotransmission in the central nervous system of adults. Glycine binding induces cooperative and symmetric structural rearrangements in the neurotransmitter-binding extracellular domain but asymmetrical pore dilation in the transmembrane domain. Symmetric response in the extracellular domain is consistent with electrophysiological data showing cooperative glycine activation and contribution from both α1 and β subunits. A set of functionally essential but differentially charged amino acid residues in the transmembrane domain of the α1 and β subunits explains asymmetric activation. These findings provide a foundation for understanding how the gating of the Cys-loop receptor family members diverges to accommodate specific physiological environments.


  • Organizational Affiliation
    • Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Macromolecule Content 

  • Total Structure Weight: 253.52 kDa 
  • Atom Count: 14,315 
  • Modeled Residue Count: 1,699 
  • Deposited Residue Count: 2,148 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycine receptor subunit alpha-1A [auth D],
B [auth A],
C [auth B],
D [auth C]
367Homo sapiensMutation(s): 0 
Gene Names: GLRA1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P23415 (Homo sapiens)
Explore P23415 
Go to UniProtKB:  P23415
PHAROS:  P23415
GTEx:  ENSG00000145888 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23415
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P23415-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycine receptor subunit beta,Green fluorescent protein,Glycine receptor beta680Homo sapiensAequorea victoriaMutation(s): 0 
Gene Names: GLRBGFP
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for A0A2K6CAQ3 (Macaca nemestrina)
Explore A0A2K6CAQ3 
Go to UniProtKB:  A0A2K6CAQ3
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Find proteins for P48167 (Homo sapiens)
Explore P48167 
Go to UniProtKB:  P48167
PHAROS:  P48167
GTEx:  ENSG00000109738 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42212P48167A0A2K6CAQ3
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P48167-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
EA [auth B],
EB [auth E],
F [auth D],
QA [auth C],
S [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
UND

Query on UND



Download:Ideal Coordinates CCD File
AA [auth A]
GB [auth E]
H [auth D]
I [auth D]
LB [auth E]
AA [auth A],
GB [auth E],
H [auth D],
I [auth D],
LB [auth E],
P [auth D],
Q [auth D],
SA [auth C],
T [auth A],
U [auth A],
WA [auth C],
XA [auth C]
UNDECANE
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
D10

Query on D10



Download:Ideal Coordinates CCD File
UA [auth C]DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
DD9

Query on DD9



Download:Ideal Coordinates CCD File
AB [auth C]
CA [auth A]
HA [auth B]
HB [auth E]
IA [auth B]
AB [auth C],
CA [auth A],
HA [auth B],
HB [auth E],
IA [auth B],
IB [auth E],
J [auth D],
KA [auth B],
MA [auth B],
NA [auth B],
OA [auth C],
Z [auth A],
ZA [auth C]
nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
HP6

Query on HP6



Download:Ideal Coordinates CCD File
BB [auth E]
DB [auth E]
M [auth D]
N [auth D]
PA [auth C]
BB [auth E],
DB [auth E],
M [auth D],
N [auth D],
PA [auth C],
V [auth A],
W [auth A],
YA [auth C]
HEPTANE
C7 H16
IMNFDUFMRHMDMM-UHFFFAOYSA-N
HEX

Query on HEX



Download:Ideal Coordinates CCD File
BA [auth A]
CB [auth E]
DA [auth A]
FA [auth B]
G [auth D]
BA [auth A],
CB [auth E],
DA [auth A],
FA [auth B],
G [auth D],
GA [auth B],
JA [auth B],
JB [auth E],
L [auth D],
R [auth D],
RA [auth C],
TA [auth C],
VA [auth C],
X [auth A],
Y [auth A]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
NBU

Query on NBU



Download:Ideal Coordinates CCD File
FB [auth E],
K [auth D],
KB [auth E],
LA [auth B],
O [auth D]
N-BUTANE
C4 H10
IJDNQMDRQITEOD-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
MB [auth E],
NB [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1R35GM146860

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Database references
  • Version 1.2: 2023-11-01
    Changes: Database references, Structure summary
  • Version 1.3: 2024-11-20
    Changes: Data collection, Structure summary