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- EMDB-39429: Cryo-EM structure of SNAP-94847-bound MCHR1, S1 state -

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Basic information

Entry
Database: EMDB / ID: EMD-39429
TitleCryo-EM structure of SNAP-94847-bound MCHR1, S1 state
Map data
Sample
  • Complex: SNAP-94847-MCHR1-Fab1B3-glue complex
    • Protein or peptide: Antibody 1B3 Fab heavy chain
    • Protein or peptide: Antibody 1B3 Fab light chain
    • Protein or peptide: Glue molecule 4-9
    • Protein or peptide: Melanin-concentrating hormone receptor 1,Soluble cytochrome b562
  • Ligand: ~{N}-[3-[1-[[4-[3,4-bis(fluoranyl)phenoxy]phenyl]methyl]piperidin-4-yl]-4-methyl-phenyl]-2-methyl-propanamide
KeywordsGPCR / SIGNALING PROTEIN
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 speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsYe X / Liu G / Li X / Liu H / Gong W
Funding support China, 2 items
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, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateJan 8, 2025-
Current statusJan 8, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39429.png

Downloads & links

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Map

FileDownload / File: emd_39429.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-4.292536 - 5.822864
Average (Standard dev.)0.0005807225 (±0.09143674)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39429_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39429_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 : SNAP-94847-MCHR1-Fab1B3-glue complex

EntireName: SNAP-94847-MCHR1-Fab1B3-glue complex
Components
  • Complex: SNAP-94847-MCHR1-Fab1B3-glue complex
    • Protein or peptide: Antibody 1B3 Fab heavy chain
    • Protein or peptide: Antibody 1B3 Fab light chain
    • Protein or peptide: Glue molecule 4-9
    • Protein or peptide: Melanin-concentrating hormone receptor 1,Soluble cytochrome b562
  • Ligand: ~{N}-[3-[1-[[4-[3,4-bis(fluoranyl)phenoxy]phenyl]methyl]piperidin-4-yl]-4-methyl-phenyl]-2-methyl-propanamide

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Supramolecule #1: SNAP-94847-MCHR1-Fab1B3-glue complex

SupramoleculeName: SNAP-94847-MCHR1-Fab1B3-glue complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Antibody 1B3 Fab heavy chain

MacromoleculeName: Antibody 1B3 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.540424 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NIYYSSMHWV RQAPGKGLEW VASISPYSGS TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARPWYPWSYW SGLDYWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NIYYSSMHWV RQAPGKGLEW VASISPYSGS TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARPWYPWSYW SGLDYWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC GSLEHHHHHH

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Macromolecule #2: Antibody 1B3 Fab light chain

MacromoleculeName: Antibody 1B3 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.796396 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QPWSWGSALI TFGQGTKVEI KRTVAAPSVF IFPPSDSQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QPWSWGSALI TFGQGTKVEI KRTVAAPSVF IFPPSDSQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGECG GS

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Macromolecule #3: Glue molecule 4-9

MacromoleculeName: Glue molecule 4-9 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 30.972234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EIAALEKEIA ALEKEIAALE KGSGSQVQLQ ESGGGLVQPG GSLRLSCAAS GRTISRYAMS WFRQAPGKER EFVAVARRSG DGAFYADSV QGRFTVSRDD AKNTVYLQMN SLKPEDTAVY YCAIDSDTFY SGSYDYWGQG TQVTVSSGAS GSASSGEVQL Q ESGGGLVQ ...String:
EIAALEKEIA ALEKEIAALE KGSGSQVQLQ ESGGGLVQPG GSLRLSCAAS GRTISRYAMS WFRQAPGKER EFVAVARRSG DGAFYADSV QGRFTVSRDD AKNTVYLQMN SLKPEDTAVY YCAIDSDTFY SGSYDYWGQG TQVTVSSGAS GSASSGEVQL Q ESGGGLVQ PGGSLRLSCT ASGVTISALN AMAMGWYRQA PGERRVMVAA VSERGNAMYR ESVQGRFTVT RDFTNKMVSL QM DNLKPED TAVYYCHVLE DRVDSFHDYW GQGTQVTVSS LEHHHHHH

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Macromolecule #4: Melanin-concentrating hormone receptor 1,Soluble cytochrome b562

MacromoleculeName: Melanin-concentrating hormone receptor 1,Soluble cytochrome b562
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.594367 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDMGQ PGNGSAFLLA PNGSHAPDHD VTQQRDEENL YFQGVDMSVG AMKKGVGRAV GLGGGSGCQA TEEDPLPNCG ACAPGQGGR RWRLPQPAWV EGSSARLWEQ ATGTGWMDLE ASLLPTGPNA SNTSDGPDNL TSAGSPPRTG SISYINIIMP S VFGTICLL ...String:
DYKDDDDMGQ PGNGSAFLLA PNGSHAPDHD VTQQRDEENL YFQGVDMSVG AMKKGVGRAV GLGGGSGCQA TEEDPLPNCG ACAPGQGGR RWRLPQPAWV EGSSARLWEQ ATGTGWMDLE ASLLPTGPNA SNTSDGPDNL TSAGSPPRTG SISYINIIMP S VFGTICLL GIIGNSTVIF AVVKKSKLHW CNNVPDIFII NLSVVDLLFL LGMPFMIHQL MGNGVWHFGE TMCTLITAMD AN SQFTSTY ILTAMAIDRY LATVHPISST KFRKPSVATL VICLLWALSF ISITPVWLYA RLIPFPGGAV GCGIRLPNPD TDL YWFTLY QFFLAFALPF VVITAAYVRI LQRMKRQLAD LEDNWETLND NLKVIEKADN AAQVKDALTK MRAAALDAQK ASGS GSPEM KDFRHGFDIL VGQIDDALKL ANEGKVKEAQ AAAEQLKTTR NAYIQKYLLI RLRTKRVTRT AIAICLVFFV CWAPY YVLQ LTQLSISRPT LTFVYLYNAA ISLGYANSCL NPFVYIVLCE TFRKRLVLSV KIAALKEKIA ALKEKIAALK EAEEKR ASR LEEELRRRLT EAAAHHHHHH HH

UniProtKB: Melanin-concentrating hormone receptor 1, Melanin-concentrating hormone receptor 1, Soluble cytochrome b562, Soluble cytochrome b562, Melanin-concentrating hormone receptor 1

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Macromolecule #5: ~{N}-[3-[1-[[4-[3,4-bis(fluoranyl)phenoxy]phenyl]methyl]piperidin...

MacromoleculeName: ~{N}-[3-[1-[[4-[3,4-bis(fluoranyl)phenoxy]phenyl]methyl]piperidin-4-yl]-4-methyl-phenyl]-2-methyl-propanamide
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1D6T
Molecular weightTheoretical: 478.573 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: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 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: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 305549
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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