8WPG | pdb_00008wpg

Human calcium-sensing receptor bound with cinacalcet in detergent

PDB DOI: https://doi.org/10.2210/pdb8WPG/pdb
EM Map EMD-37716: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2023-10-10 Released: 2023-11-22
Deposition Author(s): Ling, S.L., Meng, X.Y., Tian, C.L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 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 insights into asymmetric activation of the calcium-sensing receptor-G q complex.

Ling, S., Meng, X., Zhang, Y., Xia, Z., Zhou, Y., Yang, F., Shi, P., Shi, C., Tian, C.

(2024) Cell Res 34: 169-172

PubMed: 37919470 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-023-00892-2
Primary Citation of Related Structures:
8WPG, 8WPU

Organizational Affiliation

Department of Endocrinology, Institute of Endocrine and Metabolic Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, Anhui Engineering Laboratory of Peptide Drug, Anhui Laboratory of Advanced Photonic Science and Technology, University of Science and Technology of China, Hefei, Anhui, China. lsl924@ustc.edu.cn.

Macromolecule Content

Total Structure Weight: 208.36 kDa
Atom Count: 12,443
Modeled Residue Count: 1,606
Deposited Residue Count: 1,806
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular calcium-sensing receptor	A [auth B], B [auth A]	903	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41180
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A [auth B] Focus chain B [auth A]	Go to GlyGen: P41180-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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
YP4 (Subject of Investigation/LOI) Query on YP4 Download Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain O [auth B] MOL2 format, chain U [auth A] MOL2 format, chain O [auth B] mmCIF format, chain U [auth A] mmCIF format, chain O [auth B]	O [auth B], U [auth A]	N-[(1R)-1-(naphthalen-1-yl)ethyl]-3-[3-(trifluoromethyl)phenyl]propan-1-amine C₂₂ H₂₂ F₃ N VDHAWDNDOKGFTD-MRXNPFEDSA-N		Interactions Focus chain O [auth B] Focus chain U [auth A] Interactions & Density Focus chain O [auth B] Focus chain U [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	G [auth B], H [auth B], I [auth B], P [auth A], Q [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain P [auth A] Focus chain Q [auth A]
TRP Query on TRP Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain J [auth B] MOL2 format, chain R [auth A] MOL2 format, chain J [auth B] mmCIF format, chain R [auth A] mmCIF format, chain J [auth B]	J [auth B], R [auth A]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain J [auth B] Focus chain R [auth A] Interactions & Density Focus chain J [auth B] Focus chain R [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain N [auth B] MOL2 format, chain T [auth A] MOL2 format, chain N [auth B] mmCIF format, chain T [auth A] mmCIF format, chain N [auth B]	N [auth B], T [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain N [auth B] Focus chain T [auth A] Interactions & Density Focus chain N [auth B] Focus chain T [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] MOL2 format, chain S [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] mmCIF format, chain S [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B]	K [auth B], L [auth B], M [auth B], S [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth A] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
YP4	BindingDB: 8WPG	EC50: min: 19.95, max: 180 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-22

Deposition Author(s):

Ling, S.L.

Meng, X.Y.

Tian, C.L.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21825703
National Natural Science Foundation of China (NSFC)	China	31971152
National Natural Science Foundation of China (NSFC)	China	22307113