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- PDB-8kig: Cryo-EM structure of MC3R in complex with SHU9119 -

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Basic information

Entry
Database: PDB / ID: 8kig
TitleCryo-EM structure of MC3R in complex with SHU9119
Components
  • SHU9119
  • Soluble cytochrome b562,Melanocortin receptor 3,GlgA glycogen synthase,Fusion protein
KeywordsMEMBRANE PROTEIN / alpha-MSH / MC3R
Function / homology
Function and homology information


homoiothermy / melanocyte-stimulating hormone receptor activity / melanocortin receptor activity / regulation of feeding behavior / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / sodium ion homeostasis / neuropeptide binding / regulation of metabolic process / locomotor rhythm / peptide hormone binding ...homoiothermy / melanocyte-stimulating hormone receptor activity / melanocortin receptor activity / regulation of feeding behavior / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / sodium ion homeostasis / neuropeptide binding / regulation of metabolic process / locomotor rhythm / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of heart rate / Peptide ligand-binding receptors / circadian regulation of gene expression / electron transport chain / regulation of blood pressure / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / periplasmic space / electron transfer activity / iron ion binding / heme binding / plasma membrane / cytoplasm
Similarity search - Function
Melanocortin 3 receptor / Melanocortin receptor 3-5 / Melanocortin/ACTH receptor / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 ...Melanocortin 3 receptor / Melanocortin receptor 3-5 / Melanocortin/ACTH receptor / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Soluble cytochrome b562 / Melanocortin receptor 3 / Glycogen synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
Pyrococcus abyssi GE5 (archaea)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChen, Q. / Fu, J.
Funding support2items
OrganizationGrant numberCountry
Other governmentShenzhen Science and Technology Innovation Committee
Other privateGanghong Young Scholar Development Fund
CitationJournal: To Be Published
Title: Structure basis of ligand selectivity and signal transduction in human melanocortin-3 receptor
Authors: Jingpeng, F. / Hongli, H.
History
DepositionAug 23, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: Soluble cytochrome b562,Melanocortin receptor 3,GlgA glycogen synthase,Fusion protein
L: SHU9119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1493
Polymers70,1092
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Soluble cytochrome b562,Melanocortin receptor 3,GlgA glycogen synthase,Fusion protein / Cytochrome b-562 / MC3-R / Glycogen synthase


Mass: 69030.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi GE5 (archaea), (gene. exp.) synthetic construct (others)
Gene: cybC, MC3R, PAB2292 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P0ABE7, UniProt: P41968, UniProt: Q9V2J8
#2: Protein/peptide SHU9119


Mass: 1078.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The complex of alpha -MSH coupled MC3R-Gas / Type: COMPLEX
Details: Cryo-EM structure of the agonist a-MSH bound to the active melanocortin-3 receptor (MC3R) in complex with the heterotrimeric Gs protein at 2.9 A resolution.
Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Escherichia coli (E. coli)562
41Pyrococcus abyssi (strain GE5 / Orsay) (archaea)272844
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 569550 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0062163
ELECTRON MICROSCOPYf_angle_d0.7192942
ELECTRON MICROSCOPYf_dihedral_angle_d5.607287
ELECTRON MICROSCOPYf_chiral_restr0.045364
ELECTRON MICROSCOPYf_plane_restr0.005346

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