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- EMDB-35514: Cryo-EM structure of the inactive CD97 -

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Basic information

Entry
Database: EMDB / ID: EMD-35514
TitleCryo-EM structure of the inactive CD97
Map data
Sample
  • Organelle or cellular component: Adhesion G protein-coupled receptor E5
    • Protein or peptide: Adhesion G protein-coupled receptor E5,Soluble cytochrome b562,Adhesion G protein-coupled receptor E5 subunit beta
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsadhension GPCR / CD97 / inactive / MEMBRANE PROTEIN
Function / homology
Function and homology information


Class B/2 (Secretin family receptors) / secretory granule membrane / G protein-coupled receptor activity / electron transport chain / adenylate cyclase-activating G protein-coupled receptor signaling pathway / transmembrane signaling receptor activity / cell-cell signaling / periplasmic space / electron transfer activity / cell surface receptor signaling pathway ...Class B/2 (Secretin family receptors) / secretory granule membrane / G protein-coupled receptor activity / electron transport chain / adenylate cyclase-activating G protein-coupled receptor signaling pathway / transmembrane signaling receptor activity / cell-cell signaling / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / cell adhesion / inflammatory response / immune response / iron ion binding / G protein-coupled receptor signaling pathway / focal adhesion / calcium ion binding / heme binding / Neutrophil degranulation / extracellular exosome / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, ADGRE2/ADGRE5 / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / : / Calcium-binding EGF domain / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site ...GPCR, family 2, ADGRE2/ADGRE5 / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / : / Calcium-binding EGF domain / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Cytochrome b562 / Cytochrome b562 / EGF-type aspartate/asparagine hydroxylation site / Cytochrome c/b562 / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain
Similarity search - Domain/homology
Soluble cytochrome b562 / Adhesion G protein-coupled receptor E5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 P / 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 28, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35514.png

Downloads & links

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Map

FileDownload / File: emd_35514.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.)
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.0006579501 - 1.3627725
Average (Standard dev.)0.0004965271 (±0.012521489)
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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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
    • Protein or peptide: Adhesion G protein-coupled receptor E5,Soluble cytochrome b562,Adhesion G protein-coupled receptor E5 subunit beta
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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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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Macromolecule #1: Adhesion G protein-coupled receptor E5,Soluble cytochrome b562,Ad...

MacromoleculeName: Adhesion G protein-coupled receptor E5,Soluble cytochrome b562,Adhesion G protein-coupled receptor E5 subunit beta
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.551656 KDa
Recombinant expressionOrganism: Fusarium sinicum (fungus)
SequenceString: EDMTFSTWTP PPGVHSQTLS RFFDKVQDLG RDSKTSSAEV TIQNVIKLVD ELMEAPGDVE ALAPPVRHLI ATQLLSNLED IMRILAKSL PKGPFTYISP SNTELTLMIQ ERGDKNVTMG QSSARMKLNW AVAAGAEDPG PAVAGILSIQ NMTTLLANAS L NLHSKKQA ...String:
EDMTFSTWTP PPGVHSQTLS RFFDKVQDLG RDSKTSSAEV TIQNVIKLVD ELMEAPGDVE ALAPPVRHLI ATQLLSNLED IMRILAKSL PKGPFTYISP SNTELTLMIQ ERGDKNVTMG QSSARMKLNW AVAAGAEDPG PAVAGILSIQ NMTTLLANAS L NLHSKKQA ELEEIYESSI RGVQLRRLSA VNSIFLSHNN TKELNSPILF AFSHLESSDG EAGRDPPAKD VMPGPRQELL CA FWKSDSD RGGHWATEGC QVLGSKNGST TCQCSSLSSF AILMAHYDVE DWKLTLITRV GLALSLFCLL LCILTFLLVR PIQ GSRTTI HLHLCICLFV GSTIFLAGIE NEGGQVGLRC RLVAGLLHYC FLAAFCWMSL EGLELYFLVV RVFQGQGLST RWLC LIGYG VPLLIVGVSA AIYSKGYGRP RYCWLDFEQG FLWSFLGPVT FIILCNAVIF VTTVWKLTQL AADLEDNWET LNDNL KVIE KADNAAQVKD ALTKMRAAAL DAQKATPPKL EDKSPDSPEM KDFRHGFDIL VGQIDDALKL ANEGKVKEAQ AAAEQL KTT RNAYIQKYLE RARSTLQKAR ALTITAIAQL FLLGCTWVFG LFIFDDRSLV LTYVFTILNC LQGAFLYLLH CLLNKKV RE EYRKWACLVA GGS

UniProtKB: Adhesion G protein-coupled receptor E5, Soluble cytochrome b562, Adhesion G protein-coupled receptor E5

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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: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 540042
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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