8WPU

Human calcium-sensing receptor(CaSR) bound to cinacalcet in complex with Gq protein

PDB DOI: https://doi.org/10.2210/pdb8WPU/pdb
EM Map EMD-37724: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Rattus norvegicus
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes PDBTMmpstruc

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: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 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: 354.72 kDa
Atom Count: 18,794
Modelled Residue Count: 2,453
Deposited Residue Count: 3,142
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular calcium-sensing receptor,calcium-sensing receptor	A [auth B], B [auth A]	1,076	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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
G subunit q (Gi2-mini-Gq chimeric)	C [auth G]	246	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P04899 (Homo sapiens) Explore P04899 Go to UniProtKB: P04899
PHAROS: P04899 GTEx: ENSG00000114353
Find proteins for P63092 (Homo sapiens) Explore P63092 Go to UniProtKB: P63092
PHAROS: P63092 GTEx: ENSG00000087460
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P63092P04899
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D [auth C]	376	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	E [auth D]	71	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ScFv16	F [auth E]	297	Rattus norvegicus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth F], H	2		N-Glycosylation	Interactions Focus chain G [auth F] Focus chain H Interactions & Density Focus chain G [auth F] Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B]	R [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
YP4 (Subject of Investigation/LOI) Query on YP4 Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain M [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain M [auth B]	BA [auth A], M [auth B]	N-[(1R)-1-(naphthalen-1-yl)ethyl]-3-[3-(trifluoromethyl)phenyl]propan-1-amine C₂₂ H₂₂ F₃ N VDHAWDNDOKGFTD-MRXNPFEDSA-N		Interactions Focus chain BA [auth A] Focus chain M [auth B] Interactions & Density Focus chain BA [auth A] Focus chain M [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A]	I [auth B] J [auth B] K [auth B] L [auth B] T [auth A] I [auth B], J [auth B], K [auth B], L [auth B], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A]
TRP Query on TRP Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain Y [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Y [auth A]	N [auth B], Y [auth A]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain N [auth B] Focus chain Y [auth A] Interactions & Density Focus chain N [auth B] Focus chain Y [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain Q [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain Q [auth B]	AA [auth A], Q [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth A] Focus chain Q [auth B] Interactions & Density Focus chain AA [auth A] Focus chain Q [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain S [auth A] SDF format, chain P [auth B] SDF format, chain Z [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth A]	O [auth B], P [auth B], S [auth A], Z [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth A] Focus chain Z [auth A] Interactions & Density Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 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

Revision History (Full details and data files)

Version 1.0: 2023-11-22
Type: Initial release
Version 1.1: 2024-02-21
Changes: Database references

Prepare Data

Validate Data

Deposit Data

Help and Resources

8WPU

Human calcium-sensing receptor(CaSR) bound to cinacalcet in complex with Gq protein

Structural insights into asymmetric activation of the calcium-sensing receptor-G q complex.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 5

Entity Groups

Sequence Annotations

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Entity ID: 6

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)