7SIL

Structure of positive allosteric modulator-bound active human calcium-sensing receptor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Symmetric activation and modulation of the human calcium-sensing receptor.

Park, J.Zuo, H.Frangaj, A.Fu, Z.Yen, L.Y.Zhang, Z.Mosyak, L.Slavkovich, V.N.Liu, J.Ray, K.M.Cao, B.Vallese, F.Geng, Y.Chen, S.Grassucci, R.Dandey, V.P.Tan, Y.Z.Eng, E.Lee, Y.Kloss, B.Liu, Z.Hendrickson, W.A.Potter, C.S.Carragher, B.Graziano, J.Conigrave, A.D.Frank, J.Clarke, O.B.Fan, Q.R.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2115849118
  • Primary Citation of Related Structures:  
    7SIL, 7SIM, 7SIN

  • PubMed Abstract: 

    The human extracellular calcium-sensing (CaS) receptor controls plasma Ca 2+ levels and contributes to nutrient-dependent maintenance and metabolism of diverse organs. Allosteric modulation of the CaS receptor corrects disorders of calcium homeostasis. Here, we report the cryogenic-electron microscopy reconstructions of a near-full-length CaS receptor in the absence and presence of allosteric modulators. Activation of the homodimeric CaS receptor requires a break in the transmembrane 6 (TM6) helix of each subunit, which facilitates the formation of a TM6-mediated homodimer interface and expansion of homodimer interactions. This transformation in TM6 occurs without a positive allosteric modulator. Two modulators with opposite functional roles bind to overlapping sites within the transmembrane domain through common interactions, acting to stabilize distinct rotamer conformations of key residues on the TM6 helix. The positive modulator reinforces TM6 distortion and maximizes subunit contact to enhance receptor activity, while the negative modulator strengthens an intact TM6 to dampen receptor function. In both active and inactive states, the receptor displays symmetrical transmembrane conformations that are consistent with its homodimeric assembly.


  • Organizational Affiliation

    Department of Pharmacology, Columbia University, New York, NY 10032.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 1 of Extracellular calcium-sensing receptor
A, B
878Homo sapiensMutation(s): 0 
Gene Names: CASRGPRC2APCAR1
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: 5Go to GlyGen: P41180-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
EA [auth B]
FA [auth B]
GA [auth B]
HA [auth B]
Q [auth A]
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
9IG (Subject of Investigation/LOI)
Query on 9IG

Download Ideal Coordinates CCD File 
DA [auth B],
P [auth A]
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 
G [auth A]
H [auth A]
I [auth A]
U [auth B]
V [auth B]
G [auth A],
H [auth A],
I [auth A],
U [auth B],
V [auth B],
W [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
TCR (Subject of Investigation/LOI)
Query on TCR

Download Ideal Coordinates CCD File 
J [auth A],
X [auth B]
CYCLOMETHYLTRYPTOPHAN
C12 H12 N2 O2
FSNCEEGOMTYXKY-JTQLQIEISA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
K [auth A],
Y [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
L [auth A]
M [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
Z [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9IG BindingDB:  7SIL EC50: min: 80, max: 194 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.14
RECONSTRUCTIONcryoSPARC3.0

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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM29169
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM116799
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM107462
Simons FoundationUnited StatesSF349247
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Refinement description, Structure summary