6WIV

Structure of human GABA(B) receptor in an inactive state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of human GABABreceptor in an inactive state.

Park, J.Fu, Z.Frangaj, A.Liu, J.Mosyak, L.Shen, T.Slavkovich, V.N.Ray, K.M.Taura, J.Cao, B.Geng, Y.Zuo, H.Kou, Y.Grassucci, R.Chen, S.Liu, Z.Lin, X.Williams, J.P.Rice, W.J.Eng, E.T.Huang, R.K.Soni, R.K.Kloss, B.Yu, Z.Javitch, J.A.Hendrickson, W.A.Slesinger, P.A.Quick, M.Graziano, J.Yu, H.Fiehn, O.Clarke, O.B.Frank, J.Fan, Q.R.

(2020) Nature 584: 304-309

  • DOI: 10.1038/s41586-020-2452-0
  • Primary Citation of Related Structures:  
    6WIV

  • PubMed Abstract: 
  • The human GABA B receptor-a member of the class C family of G-protein-coupled receptors (GPCRs)-mediates inhibitory neurotransmission and has been implicated in epilepsy, pain and addiction 1 . A unique GPCR that is known to require heterodimerization for function 2-6 , the GABA B receptor has two subunits, GABA B1 and GABA B2 , that are structurally homologous but perform distinct and complementary functions ...

    The human GABA B receptor-a member of the class C family of G-protein-coupled receptors (GPCRs)-mediates inhibitory neurotransmission and has been implicated in epilepsy, pain and addiction 1 . A unique GPCR that is known to require heterodimerization for function 2-6 , the GABA B receptor has two subunits, GABA B1 and GABA B2 , that are structurally homologous but perform distinct and complementary functions. GABA B1 recognizes orthosteric ligands 7,8 , while GABA B2 couples with G proteins 9-14 . Each subunit is characterized by an extracellular Venus flytrap (VFT) module, a descending peptide linker, a seven-helix transmembrane domain and a cytoplasmic tail 15 . Although the VFT heterodimer structure has been resolved 16 , the structure of the full-length receptor and its transmembrane signalling mechanism remain unknown. Here we present a near full-length structure of the GABA B receptor, captured in an inactive state by cryo-electron microscopy. Our structure reveals several ligands that preassociate with the receptor, including two large endogenous phospholipids that are embedded within the transmembrane domains to maintain receptor integrity and modulate receptor function. We also identify a previously unknown heterodimer interface between transmembrane helices 3 and 5 of both subunits, which serves as a signature of the inactive conformation. A unique 'intersubunit latch' within this transmembrane interface maintains the inactive state, and its disruption leads to constitutive receptor activity.


    Organizational Affiliation

    Department of Pathology and Cell Biology, Columbia University, New York, NY, USA. qf13@cumc.columbia.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-aminobutyric acid type B receptor subunit 1A810Homo sapiensMutation(s): 0 
Gene Names: GABBR1GPRC3A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBS5 (Homo sapiens)
Explore Q9UBS5 
Go to UniProtKB:  Q9UBS5
PHAROS:  Q9UBS5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-aminobutyric acid type B receptor subunit 2B827Homo sapiensMutation(s): 0 
Gene Names: GABBR2GPR51GPRC3B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O75899 (Homo sapiens)
Explore O75899 
Go to UniProtKB:  O75899
PHAROS:  O75899
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U3D (Subject of Investigation/LOI)
Query on U3D

Download Ideal Coordinates CCD File 
M [auth B][(2R)-3-[(Z)-icos-11-enoyl]oxy-2-[(Z)-octadec-9-enoyl]oxypropyl] 2-(trimethylazaniumyl)ethyl phosphate
C46 H88 N O8 P
QLEJPADMSQQACL-WWUFLCHTSA-N
 Ligand Interaction
U3G (Subject of Investigation/LOI)
Query on U3G

Download Ideal Coordinates CCD File 
G [auth A](2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-{[(9Z)-octadec-9-enoyl]oxy}propyl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate
C43 H76 N O8 P
VFUVYNGTMNUBMF-ZRVIQYDLSA-N
 Ligand Interaction
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
H [auth A] , I [auth A] , J [auth A] , K [auth A] , N [auth B] , O [auth B] , P [auth B] , Q [auth B] , 
H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], L [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM088454
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM125801
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU2CES030158
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM116799
National Institutes of Health/Office of the DirectorUnited StatesR01GM107462
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103310

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2020-08-26
    Changes: Database references, Structure summary