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- EMDB-61466: cryo-EM structure of 5-Hydroxytryptamine 2B Receptor in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-61466
Titlecryo-EM structure of 5-Hydroxytryptamine 2B Receptor in complex with balovaptan
Map data
Sample
  • Complex: 5-Hydroxytryptamine 2B Receptor/de novo design fusion protein
    • Protein or peptide: Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,de novo design fusion protein
  • Ligand: 8-chloranyl-5-methyl-1-(4-pyridin-2-yloxycyclohexyl)-4,6-dihydro-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine
KeywordsGPCR / inactive-state / de novo protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


intestine smooth muscle contraction / 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 behavior / Serotonin receptors / serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway / G protein-coupled serotonin receptor activity ...intestine smooth muscle contraction / 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 behavior / Serotonin receptors / serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway / G protein-coupled serotonin receptor activity / serotonin receptor signaling pathway / embryonic morphogenesis / vasoconstriction / neurotransmitter receptor activity / serotonin binding / cardiac muscle hypertrophy / neural crest cell migration / neural crest cell differentiation / cGMP-mediated signaling / positive regulation of cell division / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G-protein alpha-subunit binding / heart morphogenesis / release of sequestered calcium ion into cytosol / positive regulation of endothelial cell proliferation / ERK1 and ERK2 cascade / GTPase activator activity / positive regulation of cytokine production / calcium-mediated signaling / electron transport chain / intracellular calcium ion homeostasis / chemical synaptic transmission / G alpha (q) signalling events / periplasmic space / electron transfer activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / iron ion binding / response to xenobiotic stimulus / positive regulation of cell population proliferation / synapse / heme binding / dendrite / negative regulation of apoptotic process / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
5-Hydroxytryptamine 2B receptor / 5-hydroxytryptamine receptor family / 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 / 5-hydroxytryptamine receptor 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGao K / Zhang X / Liu X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81974236 China
CitationJournal: To Be Published
Title: cryo-EM structure of 5-Hydroxytryptamine 2B Receptor in complex with balovaptan
Authors: Kaixuan G / Xin Z / Xiangyu L
History
DepositionSep 7, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61466.png

Downloads & links

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Map

FileDownload / File: emd_61466.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.)
1.1 Å/pix.
x 256 pix.
= 281.062 Å		1.1 Å/pix.
x 256 pix.
= 281.062 Å		1.1 Å/pix.
x 256 pix.
= 281.062 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.7810917 - 3.8565443
Average (Standard dev.)-0.00073989766 (±0.055128247)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.0624 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61466_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_61466_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : 5-Hydroxytryptamine 2B Receptor/de novo design fusion protein

EntireName: 5-Hydroxytryptamine 2B Receptor/de novo design fusion protein
Components
  • Complex: 5-Hydroxytryptamine 2B Receptor/de novo design fusion protein
    • Protein or peptide: Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,de novo design fusion protein
  • Ligand: 8-chloranyl-5-methyl-1-(4-pyridin-2-yloxycyclohexyl)-4,6-dihydro-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine

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Supramolecule #1: 5-Hydroxytryptamine 2B Receptor/de novo design fusion protein

SupramoleculeName: 5-Hydroxytryptamine 2B Receptor/de novo design fusion protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,Soluble c...

MacromoleculeName: Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,Soluble cytochrome b562,5-hydroxytryptamine receptor 2B,de novo design fusion protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.403453 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDAADL EDNWETLNDN LKVIEKADNA AQVKDALTKM RAAALDAQKA TPPKLEDKSP DSPEMKDFRH GFDILVGQID DALKLANEG KVKEAQAAAE QLKTTRNAYI QKYLTESIPE EMKQIVEEQG NKLHWAALLI LMVIIPTIGG NTLVILAVSL E KKLQYATN ...String:
DYKDDDAADL EDNWETLNDN LKVIEKADNA AQVKDALTKM RAAALDAQKA TPPKLEDKSP DSPEMKDFRH GFDILVGQID DALKLANEG KVKEAQAAAE QLKTTRNAYI QKYLTESIPE EMKQIVEEQG NKLHWAALLI LMVIIPTIGG NTLVILAVSL E KKLQYATN YFLMSLAVAD LLVGLFVMPI ALLTIMFEAM WPLPLVLCPA WLFLDVLFST ASIWHLCAIS VDRYIAIKKP IQ ANQYNSR ATAFIKITVV WLISIGIAIP VPIKGIETDV DNPNNITCVL TKERFGDFML FGSLAAFFTP LAIMIVTYFL TIR FRRRGA EALERAFSLE DDKEALLAAL DALAEAFADD AELTALLALL RRLLEDPDLP ADELAALRAA LTRFPEFREA LLAL LDRYL ATRDLADARD LVWALVLAIA SDPRYRPAVA AMIAFGDAEV LRAGLLRGAE ALGLPGGEAL VEEIMAEAEN EQRAS KVLG IVFFLFLLMW CPFFITNITL VLCDSCNQTT LQMLLEIFVW IGYVSSGVNP LVYTLFNKTF RDAFGRYITC NYRATK SVH HHHHH

UniProtKB: Soluble cytochrome b562, 5-hydroxytryptamine receptor 2B, 5-hydroxytryptamine receptor 2B

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Macromolecule #2: 8-chloranyl-5-methyl-1-(4-pyridin-2-yloxycyclohexyl)-4,6-dihydro-...

MacromoleculeName: 8-chloranyl-5-methyl-1-(4-pyridin-2-yloxycyclohexyl)-4,6-dihydro-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1EB7
Molecular weightTheoretical: 409.912 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

Concentration10 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TITAN THEMIS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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 / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.1 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 291656
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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