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- EMDB-38980: Cryo-EM structure of the inactive CD97 -

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Basic information

Entry
Database: EMDB / ID: EMD-38980
TitleCryo-EM structure of the inactive CD97
Map data
Sample
  • Organelle or cellular component: Adhesion G protein-coupled receptor E5
Keywordsadhension GPCR / CD97 / inactive / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsMao C / Zhao R / Dong Y / Gao M / Chen L / Zhang C / Xiao P / Guo J / Qin J / Shen D ...Mao C / Zhao R / Dong Y / Gao M / Chen L / Zhang C / Xiao P / Guo J / Qin J / Shen D / Ji S / Zang S / Zhang H / Wang W / Shen Q / Sun J / Zhang Y
Funding support China, 1 items
OrganizationGrant numberCountry
Not funded China
CitationJournal: Mol Cell / Year: 2024
Title: Conformational transitions and activation of the adhesion receptor CD97.
Authors: Chunyou Mao / Ru-Jia Zhao / Ying-Jun Dong / Mingxin Gao / Li-Nan Chen / Chao Zhang / Peng Xiao / Jia Guo / Jiao Qin / Dan-Dan Shen / Su-Yu Ji / Shao-Kun Zang / Huibing Zhang / Wei-Wei Wang / ...Authors: Chunyou Mao / Ru-Jia Zhao / Ying-Jun Dong / Mingxin Gao / Li-Nan Chen / Chao Zhang / Peng Xiao / Jia Guo / Jiao Qin / Dan-Dan Shen / Su-Yu Ji / Shao-Kun Zang / Huibing Zhang / Wei-Wei Wang / Qingya Shen / Jin-Peng Sun / Yan Zhang /
Abstract: Adhesion G protein-coupled receptors (aGPCRs) are evolutionarily ancient receptors involved in a variety of physiological and pathophysiological processes. Modulators of aGPCR, particularly ...Adhesion G protein-coupled receptors (aGPCRs) are evolutionarily ancient receptors involved in a variety of physiological and pathophysiological processes. Modulators of aGPCR, particularly antagonists, hold therapeutic promise for diseases like cancer and immune and neurological disorders. Hindered by the inactive state structural information, our understanding of antagonist development and aGPCR activation faces challenges. Here, we report the cryo-electron microscopy structures of human CD97, a prototypical aGPCR that plays crucial roles in immune system, in its inactive apo and G13-bound fully active states. Compared with other family GPCRs, CD97 adopts a compact inactive conformation with a constrained ligand pocket. Activation induces significant conformational changes for both extracellular and intracellular sides, creating larger cavities for Stachel sequence binding and G13 engagement. Integrated with functional and metadynamics analyses, our study provides significant mechanistic insights into the activation and signaling of aGPCRs, paving the way for future drug discovery efforts.
History
DepositionFeb 2, 2024-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38980.png

Downloads & links

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Map

FileDownload / File: emd_38980.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.01776592 - 0.0355062
Average (Standard dev.)0.0000034553493 (±0.00065178814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38980_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38980_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Adhesion G protein-coupled receptor E5

EntireName: Adhesion G protein-coupled receptor E5
Components
  • Organelle or cellular component: Adhesion G protein-coupled receptor E5

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Supramolecule #1: Adhesion G protein-coupled receptor E5

SupramoleculeName: Adhesion G protein-coupled receptor E5 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 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: 1.5 µm / Nominal defocus min: 0.7000000000000001 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 827823
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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