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- EMDB-48537: A8 Fab in complex with CD97 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48537
TitleA8 Fab in complex with CD97
Map data
Sample
  • Complex: A8 Fab in complex with CD97
    • Protein or peptide: Adhesion G protein-coupled receptor E5
    • Protein or peptide: Heavy chain of A8 Fab
    • Protein or peptide: Light chain of A8 Fab
KeywordsProtein complex / Antibody / Adhesion G protein-coupled receptor / IMMUNE SYSTEM
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsHattori T / Bang I / Fang M / Koide S
Funding support United States, 1 items
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 AD / Gross S / Fang M / Bang I / Roy N / Berezniuk I / Donaldson H / Groff K / Ravn-Boess N / Koide A / Placantonakis DG / Park CY / Koide S
History
DepositionJan 6, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48537.png

Downloads & links

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Map

FileDownload / File: emd_48537.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.2301944 - 1.9554895
Average (Standard dev.)0.00023228943 (±0.027171945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48537_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_48537_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 : A8 Fab in complex with CD97

EntireName: A8 Fab in complex with CD97
Components
  • Complex: A8 Fab in complex with CD97
    • Protein or peptide: Adhesion G protein-coupled receptor E5
    • Protein or peptide: Heavy chain of A8 Fab
    • Protein or peptide: Light chain of A8 Fab

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Supramolecule #1: A8 Fab in complex with CD97

SupramoleculeName: A8 Fab in complex with CD97 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 110 KDa

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Macromolecule #1: Adhesion G protein-coupled receptor E5

MacromoleculeName: Adhesion G protein-coupled receptor E5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.277082 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QDSRGCARWC PQNSSCVNAT ACRCNPGFSS FSEIITTPTE TCDDINECAT PSKVSCGKFS DCWNTEGSYD CVCSPGYEPV SGAKTFKNE SENTCQDVDE CQQNPRLCKS YGTCVNTLGS YTCQCLPGFK FIPEDPKVCT DVNECTSGQN PCHSSTHCLN N VGSYQCRC ...String:
QDSRGCARWC PQNSSCVNAT ACRCNPGFSS FSEIITTPTE TCDDINECAT PSKVSCGKFS DCWNTEGSYD CVCSPGYEPV SGAKTFKNE SENTCQDVDE CQQNPRLCKS YGTCVNTLGS YTCQCLPGFK FIPEDPKVCT DVNECTSGQN PCHSSTHCLN N VGSYQCRC RPGWQPIPGS PNGPNNTVCE DVDECSSGQH QCDSSTVCFN TVGSYSCRCR PGWKPRHGIP NNQKDTVCED MT FSTWTPP PGVHSQTLSR FFDKVQDLGR DSKTSSAEVT IQNVIKLVDE LMEAPGDVEA LAPPVRHLIA TQLLSNLEDI MRI LAKSLP KGPFTYISPS NTELTLMIQE RGDKNVTMGQ SSARMKLNWA VAAGAEDPGP AVAGILSIQN MTTLLANASL NLHS KKQAE LEEIYESSIR GVQLRRLSAV NSIFLSHNNT KELNSPILFA FSHLESSDGE AGRDPPAKDV MPGPRQELLC AFWKS DSDR GGHWATEGCQ VLGSKNGSTT CQCSHLASFA ILMAHYDVED WKLTLITRSS SSHHHHHH

UniProtKB: Adhesion G protein-coupled receptor E5

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Macromolecule #2: Heavy chain of A8 Fab

MacromoleculeName: Heavy chain of A8 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.019936 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF TISSYSIHWV RQAPGKGLEW VASISPYYGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSWYYYEQN PYWYQKEEQA LDYWGQGTLV TVFNQIKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF TISSYSIHWV RQAPGKGLEW VASISPYYGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSWYYYEQN PYWYQKEEQA LDYWGQGTLV TVFNQIKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HT

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Macromolecule #3: Light chain of A8 Fab

MacromoleculeName: Light chain of A8 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.229785 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QSVYSPVTFG QGTKVEIKRT VAAPSVFIFP PSDSQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QSVYSPVTFG QGTKVEIKRT VAAPSVFIFP PSDSQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
150.0 mMNaClsodium chloride
10.0 mMCaCl2calcium chloride
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 3.5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.53 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 89719
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
PDB IDChain

6az2

source_name: PDB, initial_model_type: experimental model

0-f1

source_name: AlphaFold, initial_model_type: in silico model
Output model

PDB-9mqr:
A8 Fab in complex with CD97

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