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- PDB-9mqr: A8 Fab in complex with CD97 -

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Basic information

Entry
Database: PDB / ID: 9mqr
TitleA8 Fab in complex with CD97
Components
  • Adhesion G protein-coupled receptor E5
  • Heavy chain of A8 Fab
  • Light chain of A8 Fab
KeywordsIMMUNE SYSTEM / Protein complex / Antibody / Adhesion G protein-coupled receptor
Function / homology
Function and homology information


Class B/2 (Secretin family receptors) / secretory granule membrane / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / transmembrane signaling receptor activity / cell-cell signaling / cell surface receptor signaling pathway / cell adhesion / immune response / G protein-coupled receptor signaling pathway ...Class B/2 (Secretin family receptors) / secretory granule membrane / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / transmembrane signaling receptor activity / cell-cell signaling / cell surface receptor signaling pathway / cell adhesion / immune response / G protein-coupled receptor signaling pathway / inflammatory response / focal adhesion / calcium ion 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, 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. / EGF-type aspartate/asparagine hydroxylation site / 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
Adhesion G protein-coupled receptor E5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsHattori, T. / Bang, I. / Fang, M. / Koide, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA251669 United States
CitationJournal: Biorxiv / Year: 2025
Title: Engineering Antibody-Drug Conjugates targeting an Adhesion GPCR, CD97
Authors: Hattori, T. / Wang, M. / Corrado, A.D. / Gross, S. / Fang, M. / Bang, I. / Roy, N. / Berezniuk, I. / Donaldson, H. / Groff, K. / Ravn-Boess, N. / Koide, A. / Placantonakis, D.G. / Park, C.Y. / Koide, S.
History
DepositionJan 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adhesion G protein-coupled receptor E5
D: Heavy chain of A8 Fab
E: Light chain of A8 Fab


Theoretical massNumber of molelcules
Total (without water)108,5273
Polymers108,5273
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The binding of A8 Fab (chains D and E) to CD97 (chain A) was confirmed by gel filtration and the immunoprecipitation-based binding assay.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Adhesion G protein-coupled receptor E5 / Leukocyte antigen CD97


Mass: 59277.082 Da / Num. of mol.: 1 / Mutation: S531A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADGRE5, CD97 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P48960
#2: Antibody Heavy chain of A8 Fab


Mass: 26019.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Light chain of A8 Fab


Mass: 23229.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: A8 Fab in complex with CD97 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.11 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris(hydroxymethyl)aminomethane hydrochlorideTris-HCl1
2150 mMsodium chlorideNaCl1
310 mMcalcium chlorideCaCl21
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 48.53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89719 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16AZ2

6az2

16AZ21PDBexperimental model
21AF-P48960-F12AlphaFoldin silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0043809
ELECTRON MICROSCOPYf_angle_d0.5025167
ELECTRON MICROSCOPYf_dihedral_angle_d4.224517
ELECTRON MICROSCOPYf_chiral_restr0.043581
ELECTRON MICROSCOPYf_plane_restr0.004656

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