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 9AVG | pdb_00009avg

Structure of human calcium-sensing receptor in complex with chimeric Gs (miniGis) protein in nanodiscs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9AVG

This is version 1.3 of the entry. See complete history. 

Literature

Promiscuous G-protein activation by the calcium-sensing receptor.

Zuo, H., Park, J., Frangaj, A., Ye, J., Lu, G., Manning, J.J., Asher, W.B., Lu, Z., Hu, G.B., Wang, L., Mendez, J., Eng, E., Zhang, Z., Lin, X., Grassucci, R., Hendrickson, W.A., Clarke, O.B., Javitch, J.A., Conigrave, A.D., Fan, Q.R.

(2024) Nature 629: 481-488

  • DOI: https://doi.org/10.1038/s41586-024-07331-1
  • Primary Citation Related Structures: 
    9ASB, 9AVG, 9AVL, 9AXF, 9AYF

  • PubMed Abstract: 

    The human calcium-sensing receptor (CaSR) detects fluctuations in the extracellular Ca 2+ concentration and maintains Ca 2+ homeostasis 1,2 . It also mediates diverse cellular processes not associated with Ca 2+ balance 3-5 . The functional pleiotropy of CaSR arises in part from its ability to signal through several G-protein subtypes 6 . We determined structures of CaSR in complex with G proteins from three different subfamilies: G q , G i and G s . We found that the homodimeric CaSR of each complex couples to a single G protein through a common mode. This involves the C-terminal helix of each Gα subunit binding to a shallow pocket that is formed in one CaSR subunit by all three intracellular loops (ICL1-ICL3), an extended transmembrane helix 3 and an ordered C-terminal region. G-protein binding expands the transmembrane dimer interface, which is further stabilized by phospholipid. The restraint imposed by the receptor dimer, in combination with ICL2, enables G-protein activation by facilitating conformational transition of Gα. We identified a single Gα residue that determines G q and G s versus G i selectivity. The length and flexibility of ICL2 allows CaSR to bind all three Gα subtypes, thereby conferring capacity for promiscuous G-protein coupling.


  • Organizational Affiliation: 
    • Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, USA.

Macromolecule Content 

  • Total Structure Weight: 285.94 kDa 
  • Atom Count: 17,498 
  • Modeled Residue Count: 2,208 
  • Deposited Residue Count: 2,487 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 1 of Extracellular calcium-sensing receptorA [auth Q],
B [auth R]
911Homo sapiensMutation(s): 0 
Gene Names: CASR, GPRC2A, PCAR1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P41180 (Homo sapiens)
Explore P41180 
Go to UniProtKB:  P41180
PHAROS:  P41180
GTEx:  ENSG00000036828 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41180
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P41180-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Chimeric mini guanine nucleotide-binding protein G(i)(s) subunit alphaC [auth A]246Homo sapiensMutation(s): 21 
Gene Names: GNAI1, GNAS
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP63092P63096
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1D [auth B]348Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62873
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59768
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth C],
G [auth D],
H [auth E],
I [auth F]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AF7

Query on A1AF7



Download:Ideal Coordinates CCD File
BA [auth R](19R,22S,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9Z)-octadec-9-enoate
C40 H77 O10 P
PAZGBAOHGQRCBP-LLSCNKDYSA-N
Y01

Query on Y01



Download:Ideal Coordinates CCD File
S [auth Q]CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
9IG

Query on 9IG



Download:Ideal Coordinates CCD File
AA [auth R],
R [auth Q]
3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine
C18 H22 Cl N O
ZVQUCWXZCKWZBP-CQSZACIVSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
J [auth Q],
K [auth Q],
L [auth Q],
T [auth R],
U [auth R]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
TCR

Query on TCR



Download:Ideal Coordinates CCD File
M [auth Q],
V [auth R]
CYCLOMETHYLTRYPTOPHAN
C12 H12 N2 O2
FSNCEEGOMTYXKY-JTQLQIEISA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
N [auth Q],
W [auth R]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA

Query on CA



Download:Ideal Coordinates CCD File
O [auth Q]
P [auth Q]
Q
X [auth R]
Y [auth R]
O [auth Q],
P [auth Q],
Q,
X [auth R],
Y [auth R],
Z [auth R]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9IG BindingDB:  9AVG EC50: min: 80, max: 194 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.2
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 Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM141871

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Data collection, Structure summary