8YNS | pdb_00008yns

Cryo-EM structure of SNAP-94847-bound MCHR1, S1 state

PDB DOI: https://doi.org/10.2210/pdb8YNS/pdb
EM Map EMD-39429: EMDB EMDataResource

Classification: SIGNALING PROTEIN
Organism(s): synthetic construct, Homo sapiens, Escherichia coli, Escherichia coli CFT073
Expression System: Escherichia coli, Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-03-11 Released: 2024-12-18
Deposition Author(s): Ye, X., Liu, G., Li, X., Liu, H., Gong, W.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.33 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 physiological activation and antagonism of melanin-concentrating hormone receptor MCHR1.

Ye, X., Liu, G., Li, X., He, B., Tao, Y., Guan, J., Mu, Y., Liu, H., Gong, W.

(2024) Cell Discov 10: 124-124

PubMed: 39616153 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41421-024-00754-0
Primary Citation Related Structures:
8WWK, 8WWL, 8WWM, 8WWN, 8YNS, 8YNT

Organizational Affiliation

Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.

Macromolecule Content

Total Structure Weight: 145.38 kDa
Atom Count: 7,296
Modeled Residue Count: 958
Deposited Residue Count: 1,328
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody 1B3 Fab heavy chain	A [auth H]	238	synthetic construct	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody 1B3 Fab light chain	B [auth L]	220	synthetic construct	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glue molecule 4-9	C [auth N]	285	synthetic construct	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Melanin-concentrating hormone receptor 1,Soluble cytochrome b562	D [auth R]	585	Homo sapiens, Escherichia coli, Escherichia coli CFT073	Mutation(s): 0 Gene Names: GPR24, MCHR1, SLC1, cybC, c5335
UniProt & NIH Common Fund Data Resources
Find proteins for A0A2R9AFP0 (Pan paniscus) Explore A0A2R9AFP0 Go to UniProtKB: A0A2R9AFP0
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Find proteins for Q99705 (Homo sapiens) Explore Q99705 Go to UniProtKB: Q99705
PHAROS: Q99705 GTEx: ENSG00000128285
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P0ABE7 A0A2R9AFP0 Q99705
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D6T (Subject of Investigation/LOI) Query on A1D6T Download:Ideal Coordinates CCD File SDF format, chain E [auth R] MOL2 format, chain E [auth R] mmCIF format, chain E [auth R]	E [auth R]	~{N}-[3-[1-[[4-[3,4-bis(fluoranyl)phenoxy]phenyl]methyl]piperidin-4-yl]-4-methyl-phenyl]-2-methyl-propanamide C₂₉ H₃₂ F₂ N₂ O₂ VMLZFUVIKCGATC-UHFFFAOYSA-N		Interactions Focus chain E [auth R] Interactions & Density Focus chain E [auth R]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.33 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

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2019YFA0904100
National Natural Science Foundation of China (NSFC)	China	T2221005

Revision History (Full details and data files)

Version 1.0: 2024-12-18
Type: Initial release
Version 1.1: 2025-01-08
Changes: Data collection, Database references, Source and taxonomy, Structure summary