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- PDB-8yns: Cryo-EM structure of SNAP-94847-bound MCHR1, S1 state -

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Basic information

Entry
Database: PDB / ID: 8yns
TitleCryo-EM structure of SNAP-94847-bound MCHR1, S1 state
Components
  • Antibody 1B3 Fab heavy chain
  • Antibody 1B3 Fab light chain
  • Glue molecule 4-9
  • Melanin-concentrating hormone receptor 1,Soluble cytochrome b562
KeywordsSIGNALING PROTEIN / GPCR
Function / homology
Function and homology information


melanin-concentrating hormone receptor activity / neuropeptide receptor activity / hormone binding / BBSome-mediated cargo-targeting to cilium / positive regulation of calcium ion transport / neuropeptide binding / feeding behavior / non-motile cilium / ciliary membrane / neuropeptide signaling pathway ...melanin-concentrating hormone receptor activity / neuropeptide receptor activity / hormone binding / BBSome-mediated cargo-targeting to cilium / positive regulation of calcium ion transport / neuropeptide binding / feeding behavior / non-motile cilium / ciliary membrane / neuropeptide signaling pathway / Peptide ligand-binding receptors / generation of precursor metabolites and energy / electron transport chain / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / G alpha (q) signalling events / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / neuron projection / cilium / G protein-coupled receptor signaling pathway / iron ion binding / signaling receptor binding / heme binding / plasma membrane
Similarity search - Function
Melanin-concentrating hormone receptor 1 / Melanin-concentrating hormone receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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 / Melanin-concentrating hormone receptor 1 / Soluble cytochrome b562 / Melanin-concentrating hormone receptor 1
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
Escherichia coli (E. coli)
Escherichia coli O6:H1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsYe, X. / Liu, G. / Li, X. / Liu, H. / Gong, W.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0904100 China
National Natural Science Foundation of China (NSFC)T2221005 China
CitationJournal: Cell Discov / Year: 2024
Title: Structural insights into physiological activation and antagonism of melanin-concentrating hormone receptor MCHR1.
Authors: Xiaofan Ye / Guibing Liu / Xiu Li / Binbin He / Yuyong Tao / Jiasheng Guan / Yuguang Mu / Haiping Liu / Weimin Gong /
History
DepositionMar 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: em_admin / entity ...em_admin / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _em_admin.last_update / _entity.pdbx_description / _entity_name_com.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Antibody 1B3 Fab heavy chain
L: Antibody 1B3 Fab light chain
N: Glue molecule 4-9
R: Melanin-concentrating hormone receptor 1,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,3825
Polymers144,9034
Non-polymers4791
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: Antibody Antibody 1B3 Fab heavy chain


Mass: 25540.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Antibody Antibody 1B3 Fab light chain


Mass: 23796.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Antibody Glue molecule 4-9


Mass: 30972.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Protein Melanin-concentrating hormone receptor 1,Soluble cytochrome b562 / G-protein coupled receptor 24 / MCH-1R / MCH receptor 1 / MCH-R1 / MCHR-1 / G-protein coupled ...G-protein coupled receptor 24 / MCH-1R / MCH receptor 1 / MCH-R1 / MCHR-1 / G-protein coupled receptor 24 / MCH-1R / MCH1R / MCHR / SLC-1 / Somatostatin receptor-like protein / Cytochrome b-562


Mass: 64594.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria)
Gene: GPR24, MCHR1, GPR24, SLC1, cybC, cybC, c5335 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q5IFH6, UniProt: Q99705, UniProt: P0ABE7, UniProt: Q8CVG7
#5: Chemical ChemComp-A1D6T / ~{N}-[3-[1-[[4-[3,4-bis(fluoranyl)phenoxy]phenyl]methyl]piperidin-4-yl]-4-methyl-phenyl]-2-methyl-propanamide / SNAP-94847


Mass: 478.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32F2N2O2 / 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: SNAP-94847-MCHR1-Fab1B3-glue complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
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: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 55 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: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 305549 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027469
ELECTRON MICROSCOPYf_angle_d0.39310181
ELECTRON MICROSCOPYf_dihedral_angle_d9.8592608
ELECTRON MICROSCOPYf_chiral_restr0.0381166
ELECTRON MICROSCOPYf_plane_restr0.0031283

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