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- EMDB-68739: local refinement of 5HT2BR-fab heterotrimer in complex with a nov... -

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Basic information

Entry
Database: EMDB / ID: EMD-68739
Titlelocal refinement of 5HT2BR-fab heterotrimer in complex with a novel antagonist IHCH-2330
Map data
Sample
  • Complex: local refinemnent of 5-HT2B receptor bound to IHCH-2330 in complex with a fab (P2C2) obtained by cryo-electron microscopy (cryoEM)
    • Protein or peptide: 5-hydroxytryptamine receptor 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 3-[2-[2-[2,5-dimethoxy-4-(trifluoromethyl)phenyl]ethyl-methyl-amino]ethyl]-2-methyl-pyrido[1,2-a]pyrimidin-4-one
KeywordsGPCR / serotonin receptor / MEMBRANE PROTEIN / 5HT2BR
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsTang L / Ji X / Cheng J / Wang S
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Chinese Academy of Sciences China
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Mechanistic Basis for 5-HT2AR Over 5-HT2BR Activation
Authors: Tang L / Ji X / Wang Y / Cao D / Li H / He L / Cheng J / Wang S
History
DepositionJan 26, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68739.png

Downloads & links

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Map

FileDownload / File: emd_68739.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 260 pix.
= 299.52 Å		1.15 Å/pix.
x 260 pix.
= 299.52 Å		1.15 Å/pix.
x 260 pix.
= 299.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.152 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-2.9277332 - 3.110762
Average (Standard dev.)-0.00026752852 (±0.03237552)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 299.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_68739_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_68739_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 : local refinemnent of 5-HT2B receptor bound to IHCH-2330 in comple...

EntireName: local refinemnent of 5-HT2B receptor bound to IHCH-2330 in complex with a fab (P2C2) obtained by cryo-electron microscopy (cryoEM)
Components
  • Complex: local refinemnent of 5-HT2B receptor bound to IHCH-2330 in complex with a fab (P2C2) obtained by cryo-electron microscopy (cryoEM)
    • Protein or peptide: 5-hydroxytryptamine receptor 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 3-[2-[2-[2,5-dimethoxy-4-(trifluoromethyl)phenyl]ethyl-methyl-amino]ethyl]-2-methyl-pyrido[1,2-a]pyrimidin-4-one

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Supramolecule #1: local refinemnent of 5-HT2B receptor bound to IHCH-2330 in comple...

SupramoleculeName: local refinemnent of 5-HT2B receptor bound to IHCH-2330 in complex with a fab (P2C2) obtained by cryo-electron microscopy (cryoEM)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 5-hydroxytryptamine receptor 2B

MacromoleculeName: 5-hydroxytryptamine receptor 2B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.518674 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: WAALLILMVI IPTIGGNTLV ILAVSLEKKL QYATNYFLMS LAVADLLVGL FVMPIALLTI MFEAMWPLPL VLCPAWLFLD VLFSTASIW HLCAISVDRY IAIKKPIQAN QYNSRATAFI KITVVWLISI GIAIPVPIKG IETDVDNPNN ITCVLTKERF G DFMLFGSL ...String:
WAALLILMVI IPTIGGNTLV ILAVSLEKKL QYATNYFLMS LAVADLLVGL FVMPIALLTI MFEAMWPLPL VLCPAWLFLD VLFSTASIW HLCAISVDRY IAIKKPIQAN QYNSRATAFI KITVVWLISI GIAIPVPIKG IETDVDNPNN ITCVLTKERF G DFMLFGSL AAFFTPLAIM IVTYFLTIHA LQKKRLLSGS RQTISNEQRA SKVLGIVFFL FLLMWCPFFI TNITLVLCDS CN QTTLQML LEIFVWIGYV SSGVNPLVYT LFNKTFRDAF GRY

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #3: 3-[2-[2-[2,5-dimethoxy-4-(trifluoromethyl)phenyl]ethyl-methyl-ami...

MacromoleculeName: 3-[2-[2-[2,5-dimethoxy-4-(trifluoromethyl)phenyl]ethyl-methyl-amino]ethyl]-2-methyl-pyrido[1,2-a]pyrimidin-4-one
type: ligand / ID: 3 / Number of copies: 1 / Formula: A1EXY
Molecular weightTheoretical: 449.466 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ran

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: CCP4 package / Number images used: 457517
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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