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- EMDB-64140: Cryo-EM structure of 5-HT2CR. -

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Basic information

Entry
Database: EMDB / ID: EMD-64140
TitleCryo-EM structure of 5-HT2CR.
Map data
Sample
  • Complex: Complex of receptor with BRIL, anti-BRIL Fab and anti-Fab nanobody
    • Protein or peptide: 5-hydroxytryptamine receptor 2C
  • Ligand: SB-242084
Keywords5HTR / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of corticotropin-releasing hormone secretion / regulation of appetite / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / Gq/11-coupled serotonin receptor activity / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / regulation of nervous system process / phospholipase C-activating serotonin receptor signaling pathway / serotonin receptor activity ...regulation of corticotropin-releasing hormone secretion / regulation of appetite / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / Gq/11-coupled serotonin receptor activity / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / regulation of nervous system process / phospholipase C-activating serotonin receptor signaling pathway / serotonin receptor activity / Serotonin receptors / G protein-coupled serotonin receptor activity / serotonin receptor signaling pathway / neurotransmitter receptor activity / serotonin binding / feeding behavior / : / positive regulation of fat cell differentiation / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / behavioral fear response / release of sequestered calcium ion into cytosol / positive regulation of calcium-mediated signaling / locomotory behavior / intracellular calcium ion homeostasis / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / chemical synaptic transmission / positive regulation of ERK1 and ERK2 cascade / synapse / dendrite / identical protein binding / plasma membrane
Similarity search - Function
5-Hydroxytryptamine 2C receptor / 5-hydroxytryptamine receptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
5-hydroxytryptamine receptor 2C
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsParajulee A / Kim K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of membrane protein
Authors: Parajulee A / Kim K
History
DepositionApr 12, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64140.png

Downloads & links

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Map

FileDownload / File: emd_64140.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 400 pix.
= 259.6 Å		0.65 Å/pix.
x 400 pix.
= 259.6 Å		0.65 Å/pix.
x 400 pix.
= 259.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.649 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.09644437 - 0.23701592
Average (Standard dev.)-0.00010672713 (±0.002990074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 259.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64140_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_64140_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 : Complex of receptor with BRIL, anti-BRIL Fab and anti-Fab nanobody

EntireName: Complex of receptor with BRIL, anti-BRIL Fab and anti-Fab nanobody
Components
  • Complex: Complex of receptor with BRIL, anti-BRIL Fab and anti-Fab nanobody
    • Protein or peptide: 5-hydroxytryptamine receptor 2C
  • Ligand: SB-242084

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Supramolecule #1: Complex of receptor with BRIL, anti-BRIL Fab and anti-Fab nanobody

SupramoleculeName: Complex of receptor with BRIL, anti-BRIL Fab and anti-Fab nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: 5-hydroxytryptamine receptor 2C

MacromoleculeName: 5-hydroxytryptamine receptor 2C / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.915184 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLTIIALSYI FCLVFADYKD DDDGAPTSDG GRFKFPDGVQ NWPALSIVII IIMTIGGNIL VIMAVSMEKK LHNATNYFLM SLAIADMLV GLLVMPLSLL AILYDYVWPL PRYLCPVWIS LDVLFSTASI MHLCAISLDR YVAIRNPIEH SRFNSRTKAI M KIAIVWAI ...String:
MLTIIALSYI FCLVFADYKD DDDGAPTSDG GRFKFPDGVQ NWPALSIVII IIMTIGGNIL VIMAVSMEKK LHNATNYFLM SLAIADMLV GLLVMPLSLL AILYDYVWPL PRYLCPVWIS LDVLFSTASI MHLCAISLDR YVAIRNPIEH SRFNSRTKAI M KIAIVWAI SIGVSVPIPV IGLRDEEKVF VNNTTCVLND PNFVLIGSFV AFFIPLTIMV ITYCLTIYVL RRQALMLLHG HT EEPPGLS LDFLKCCKRN TAEEENSANP NQDQNARRRK KKERRPRGTM QAINNERKAS KVLGIVFFVF LIMWCPFFIT NIL SVLCEK SCNQKLMEKL LNVFVWIGYV CSGINPLVYT LFNKIYRRAF SNYLRCNYKV EKKPGRPLEV LFQGPHHHHH HHHH H

UniProtKB: 5-hydroxytryptamine receptor 2C

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Macromolecule #2: SB-242084

MacromoleculeName: SB-242084 / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1L83
Molecular weightTheoretical: 394.854 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

Concentration8 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 13717 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1864086
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 402295
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

6bqh


Chain - Chain ID: A / Chain - Residue range: 46-387 / Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF Chimera (ver. 1.17.3)
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9ugl:
Cryo-EM structure of 5-HT2CR.

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