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- EMDB-37259: Cryo-EM structure of MC3R in complex with SHU9119 -

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Basic information

Entry
Database: EMDB / ID: EMD-37259
TitleCryo-EM structure of MC3R in complex with SHU9119
Map data
Sample
  • Complex: The complex of alpha -MSH coupled MC3R-Gas
    • Protein or peptide: Soluble cytochrome b562,Melanocortin receptor 3,GlgA glycogen synthase,Fusion protein
    • Protein or peptide: SHU9119
  • Ligand: CALCIUM ION
Keywordsalpha-MSH / MC3R / MEMBRANE PROTEIN
Function / homology
Function and homology information


homoiothermy / melanocyte-stimulating hormone receptor activity / melanocortin receptor activity / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / sodium ion homeostasis / regulation of feeding behavior / neuropeptide binding / regulation of metabolic process / locomotor rhythm / peptide hormone binding ...homoiothermy / melanocyte-stimulating hormone receptor activity / melanocortin receptor activity / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / sodium ion homeostasis / regulation of feeding behavior / 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 speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChen Q / Fu J
Funding support2 items
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, 2023-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37259.png

Downloads & links

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Map

FileDownload / File: emd_37259.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-6.6467133 - 6.96441
Average (Standard dev.)-0.0014170039 (±0.050881878)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37259_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37259_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of alpha -MSH coupled MC3R-Gas

EntireName: The complex of alpha -MSH coupled MC3R-Gas
Components
  • Complex: The complex of alpha -MSH coupled MC3R-Gas
    • Protein or peptide: Soluble cytochrome b562,Melanocortin receptor 3,GlgA glycogen synthase,Fusion protein
    • Protein or peptide: SHU9119
  • Ligand: CALCIUM ION

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Supramolecule #1: The complex of alpha -MSH coupled MC3R-Gas

SupramoleculeName: The complex of alpha -MSH coupled MC3R-Gas / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Soluble cytochrome b562,Melanocortin receptor 3,GlgA glycogen syn...

MacromoleculeName: Soluble cytochrome b562,Melanocortin receptor 3,GlgA glycogen synthase,Fusion protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 69.030398 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDKGS ADLEDNWETL NDNLKVIEKA DNAAQVKDAL TKMRAAALDA QKATPPKLED KSPDSPEMKD FRHGFDILVG QIDDALKLA NEGKVKEAQA AAEQLKTTRN AYIQKYLLVP RGSNASCCLP SVQPTLPNGS EHLQAPFFSN QSSSAFCEQV F IKPEVFLS ...String:
DYKDDDDKGS ADLEDNWETL NDNLKVIEKA DNAAQVKDAL TKMRAAALDA QKATPPKLED KSPDSPEMKD FRHGFDILVG QIDDALKLA NEGKVKEAQA AAEQLKTTRN AYIQKYLLVP RGSNASCCLP SVQPTLPNGS EHLQAPFFSN QSSSAFCEQV F IKPEVFLS LGIVSLLENI LVILAVVRNG NLHSPMYFFL CSLAVADMLV SVSNALETIM IAIVHSDYLT FEDQFIQHMD NI FDSMICI SLVASICNLL AIAVDRYVTI FYALRYHSIM TVRKALTLIV AIWVCCGVCG VVFIVYSESK MVIVCLITMF FAM MLLMGT LYVHMFLFAG IDCSFWNESY LTGSRDERKK SLLSKFGMDE GVTFMFIGRF DRGQKGVDVL LKAIEILSSK KEFQ EMRFI IIGKGDPELE GWARSLEEKH GNVKVITEML SREFVRELYG SVDFVIIPSY FEPFGLVALE AMCLGAIPIA SAVGG LRDI ITNETGILVK AGDPGELANA ILKALELSRS DLSKFRENCK KRAMSFSSCM KGAVTITILL GVFIFCWAPF FLHLVL IIT CPTNPYCICY TAHFNTYLVL IMCNSVIDPL IYAFRSLELR NTFREILCGC NGMNLG

UniProtKB: Soluble cytochrome b562, Melanocortin receptor 3, Glycogen synthase

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Macromolecule #2: SHU9119

MacromoleculeName: SHU9119 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.078269 KDa
SequenceString:
(ACE)(NLE)DH(4J2)RWK(NH2)

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 569550
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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