8KIG | pdb_00008kig

Cryo-EM structure of MC3R in complex with SHU9119

PDB DOI: https://doi.org/10.2210/pdb8KIG/pdb
EM Map EMD-37259: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli, Homo sapiens, Pyrococcus abyssi GE5, synthetic construct
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-08-23 Released: 2025-02-26
Deposition Author(s): Chen, Q., Fu, J.
Funding Organization(s): Other government, Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8KIG

This is version 1.0 of the entry. See complete history.

Literature

Structure basis of ligand selectivity and signal transduction in human melanocortin-3 receptor

Jingpeng, F., Hongli, H.

To be published.

Macromolecule Content

Total Structure Weight: 70.15 kDa
Atom Count: 2,104
Modeled Residue Count: 267
Deposited Residue Count: 628
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,Melanocortin receptor 3,GlgA glycogen synthase,Fusion protein	A [auth R]	619	Escherichia coli, Homo sapiens, Pyrococcus abyssi GE5, synthetic construct This entity is chimeric	Mutation(s): 0 Gene Names: cybC, MC3R, PAB2292 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P41968 (Homo sapiens) Explore P41968 Go to UniProtKB: P41968
PHAROS: P41968 GTEx: ENSG00000124089
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41968
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SHU9119	B [auth L]	9	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth R] MOL2 format, chain C [auth R] mmCIF format, chain C [auth R]	C [auth R]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth R] Interactions & Density Focus chain C [auth R]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4J2 Query on 4J2	B [auth L]	D-PEPTIDE LINKING	C₁₃ H₁₃ N O₂		--
NLE Query on NLE	B [auth L]	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		Shenzhen Science and Technology Innovation Committee
Other private		Ganghong Young Scholar Development Fund

Revision History (Full details and data files)

Version 1.0: 2025-02-26
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.