7DD5 | pdb_00007dd5

Structure of Calcium-Sensing Receptor in complex with NPS-2143

PDB DOI: https://doi.org/10.2210/pdb7DD5/pdb
EM Map EMD-30644: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Gallus gallus
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2020-10-27 Released: 2021-06-16
Deposition Author(s): Wen, T.L., Yang, X., Shen, Y.Q.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for activation and allosteric modulation of full-length calcium-sensing receptor.

Wen, T., Wang, Z., Chen, X., Ren, Y., Lu, X., Xing, Y., Lu, J., Chang, S., Zhang, X., Shen, Y., Yang, X.

(2021) Sci Adv 7

PubMed: 34088669 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abg1483
Primary Citation Related Structures:
7DD5, 7DD6, 7DD7

PubMed Abstract:
Calcium-sensing receptor (CaSR) is a class C G protein-coupled receptor (GPCR) that plays an important role in calcium homeostasis and parathyroid hormone secretion. Here, we present multiple cryo-electron microscopy structures of full-length CaSR in distinct ligand-bound states. Ligands (Ca ²⁺ and l-tryptophan) bind to the extracellular domain of CaSR and induce large-scale conformational changes, leading to the closure of two heptahelical transmembrane domains (7TMDs) for activation. The positive modulator (evocalcet) and the negative allosteric modulator (NPS-2143) occupy the similar binding pocket in 7TMD. The binding of NPS-2143 causes a considerable rearrangement of two 7TMDs, forming an inactivated TM6/TM6 interface. Moreover, a total of 305 disease-causing missense mutations of CaSR have been mapped to the structure in the active state, creating hotspot maps of five clinical endocrine disorders. Our results provide a structural framework for understanding the activation, allosteric modulation mechanism, and disease therapy for class C GPCRs.

Organizational Affiliation

State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China.

Macromolecule Content

Total Structure Weight: 243.19 kDa
Atom Count: 12,810
Modeled Residue Count: 1,597
Deposited Residue Count: 2,138
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-Sensing Receptor	A, B	1,069	Gallus gallus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A8I3AZV5 (Gallus gallus) Explore A0A8I3AZV5 Go to UniProtKB: A0A8I3AZV5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8I3AZV5
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YP1 Query on YP1 Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain X [auth B] MOL2 format, chain O [auth A] MOL2 format, chain X [auth B] mmCIF format, chain O [auth A] mmCIF format, chain X [auth B]	O [auth A], X [auth B]	2-chloro-6-[(2R)-2-hydroxy-3-{[2-methyl-1-(naphthalen-2-yl)propan-2-yl]amino}propoxy]benzonitrile C₂₄ H₂₅ Cl N₂ O₂ PZUJQWHTIRWCID-HXUWFJFHSA-N		Interactions Focus chain O [auth A] Focus chain X [auth B] Interactions & Density Focus chain O [auth A] Focus chain X [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	K [auth A] L [auth A] M [auth A] T [auth B] U [auth B] K [auth A], L [auth A], M [auth A], T [auth B], U [auth B], V [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
TRP Query on TRP Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain W [auth B] MOL2 format, chain N [auth A] MOL2 format, chain W [auth B] mmCIF format, chain N [auth A] mmCIF format, chain W [auth B]	N [auth A], W [auth B]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain N [auth A] Focus chain W [auth B] Interactions & Density Focus chain N [auth A] Focus chain W [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	H [auth A] I [auth A] J [auth A] P [auth A] R [auth B] H [auth A], I [auth A], J [auth A], P [auth A], R [auth B], S [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain S [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Q [auth B] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain G [auth A] mmCIF format, chain Q [auth B]	G [auth A], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-06-16

Deposition Author(s):

Wen, T.L.

Yang, X.

Shen, Y.Q.

Revision History (Full details and data files)

Version 1.0: 2021-06-16
Type: Initial release
Version 1.1: 2021-06-23
Changes: Database references
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Structure summary