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- EMDB-72322: Zymogen ADAM17- iRhom1 Cytoplasmic Deletion (370) Complex Bound b... -

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Basic information

Entry
Database: EMDB / ID: EMD-72322
TitleZymogen ADAM17- iRhom1 Cytoplasmic Deletion (370) Complex Bound by the MEDI3622 Fab
Map data
Sample
  • Complex: mVenus chimera iRhom1 amino acid 370 cytoplasmic truncation complexed with ADAM17 bound to MEDI3622 Fab
    • Protein or peptide: Inactive rhomboid protein 1
    • Protein or peptide: MEDI3622 Fab Heavy Chain
    • Protein or peptide: MEDI3622 Fab Light Chain
    • Protein or peptide: Disintegrin and metalloproteinase domain-containing protein 17
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsComplex / Membrane Protein / Enzyme / ADAM / Rhomboid / SIGNALING PROTEIN
Function / homology
Function and homology information


ADAM 17 endopeptidase / regulation of mast cell apoptotic process / signal release / germinal center formation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / cellular response to high density lipoprotein particle stimulus / regulation of epidermal growth factor receptor signaling pathway / production of molecular mediator involved in inflammatory response / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / Notch receptor processing ...ADAM 17 endopeptidase / regulation of mast cell apoptotic process / signal release / germinal center formation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / cellular response to high density lipoprotein particle stimulus / regulation of epidermal growth factor receptor signaling pathway / production of molecular mediator involved in inflammatory response / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / Notch receptor processing / tumor necrosis factor binding / interleukin-6 receptor binding / positive regulation of T cell chemotaxis / TNF signaling / cytokine precursor processing / positive regulation of leukocyte chemotaxis / Release of Hh-Np from the secreting cell / Regulated proteolysis of p75NTR / metallodipeptidase activity / spleen development / commissural neuron axon guidance / positive regulation of tumor necrosis factor-mediated signaling pathway / neutrophil mediated immunity / Notch binding / positive regulation of vascular endothelial cell proliferation / wound healing, spreading of epidermal cells / negative regulation of cold-induced thermogenesis / CD163 mediating an anti-inflammatory response / cell adhesion mediated by integrin / regulation of protein secretion / amyloid precursor protein catabolic process / growth factor binding / Signaling by EGFR / positive regulation of epidermal growth factor receptor signaling pathway / cytokine binding / Collagen degradation / membrane protein ectodomain proteolysis / T cell differentiation in thymus / negative regulation of protein secretion / Notch signaling pathway / positive regulation of blood vessel endothelial cell migration / Growth hormone receptor signaling / Nuclear signaling by ERBB4 / positive regulation of G1/S transition of mitotic cell cycle / B cell differentiation / positive regulation of chemokine production / Constitutive Signaling by NOTCH1 HD Domain Mutants / cell motility / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of proteasomal protein catabolic process / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Activated NOTCH1 Transmits Signal to the Nucleus / protein processing / PDZ domain binding / metalloendopeptidase activity / SH3 domain binding / integrin binding / cell population proliferation / epidermal growth factor receptor signaling pathway / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / metallopeptidase activity / actin cytoskeleton / positive regulation of tumor necrosis factor production / peptidase activity / cell migration / positive regulation of cell growth / protein transport / response to lipopolysaccharide / endopeptidase activity / response to hypoxia / cell adhesion / defense response to Gram-positive bacterium / apical plasma membrane / response to xenobiotic stimulus / positive regulation of cell migration / membrane raft / endoplasmic reticulum lumen / Golgi membrane / positive regulation of cell population proliferation / endoplasmic reticulum membrane / cell surface / proteolysis / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Rhomboid serine protease / : / Inactive rhomboid proteins 1/2, N-terminal / ADAM17, membrane-proximal domain / Membrane-proximal domain, switch, for ADAM17 / ADAM10/ADAM17 catalytic domain / : / Metallo-peptidase family M12B Reprolysin-like / Peptidase S54, rhomboid domain / Rhomboid domain ...Rhomboid serine protease / : / Inactive rhomboid proteins 1/2, N-terminal / ADAM17, membrane-proximal domain / Membrane-proximal domain, switch, for ADAM17 / ADAM10/ADAM17 catalytic domain / : / Metallo-peptidase family M12B Reprolysin-like / Peptidase S54, rhomboid domain / Rhomboid domain / Rhomboid-like superfamily / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Disintegrin and metalloproteinase domain-containing protein 17 / Inactive rhomboid protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsUngvary JN / Maciag JJ / Seegar TCM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM146830 United States
CitationJournal: To Be Published
Title: Zymogen ADAM17- iRhom1 Cytoplasmic Deletion (370) Complex Bound by the MEDI3622 Fab
Authors: Ungvary JN / Maciag JJ / Seegar TCM
History
DepositionAug 25, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72322.png

Downloads & links

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Map

FileDownload / File: emd_72322.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 440 pix.
= 360.8 Å		0.82 Å/pix.
x 440 pix.
= 360.8 Å		0.82 Å/pix.
x 440 pix.
= 360.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.16435704 - 0.3147955
Average (Standard dev.)0.00013285484 (±0.0064998916)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 360.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72322_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72322_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_72322_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 : mVenus chimera iRhom1 amino acid 370 cytoplasmic truncation compl...

EntireName: mVenus chimera iRhom1 amino acid 370 cytoplasmic truncation complexed with ADAM17 bound to MEDI3622 Fab
Components
  • Complex: mVenus chimera iRhom1 amino acid 370 cytoplasmic truncation complexed with ADAM17 bound to MEDI3622 Fab
    • Protein or peptide: Inactive rhomboid protein 1
    • Protein or peptide: MEDI3622 Fab Heavy Chain
    • Protein or peptide: MEDI3622 Fab Light Chain
    • Protein or peptide: Disintegrin and metalloproteinase domain-containing protein 17
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: mVenus chimera iRhom1 amino acid 370 cytoplasmic truncation compl...

SupramoleculeName: mVenus chimera iRhom1 amino acid 370 cytoplasmic truncation complexed with ADAM17 bound to MEDI3622 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Inactive rhomboid protein 1

MacromoleculeName: Inactive rhomboid protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.959516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDDHRPFFTY WLTFVHSLVT ILAVCIYGIA PVGFSQHETV DSVLRNRGVY ENVKYVQQEN FWIGPSSEAL IHLGAKFSPC MRQDPQVHS FIRSAREREK HSACCVRNDR SGCVQTSEEE CSSTLAVWVK WPIHPSAPEL AGHKRQFGSV CHQDPRVCDE P SSEDPHEW ...String:
MDDHRPFFTY WLTFVHSLVT ILAVCIYGIA PVGFSQHETV DSVLRNRGVY ENVKYVQQEN FWIGPSSEAL IHLGAKFSPC MRQDPQVHS FIRSAREREK HSACCVRNDR SGCVQTSEEE CSSTLAVWVK WPIHPSAPEL AGHKRQFGSV CHQDPRVCDE P SSEDPHEW PEDITKWPIC TKNSAGNHTN HPHMDCVITG RPCCIGTKGR CEITSREYCD FMRGYFHEEA TLCSQVHCMD DV CGLLPFL NPEVPDQFYR LWLSLFLHAG ILHCLVSICF QMTVLRDLEK LAGWHRIAII YLLSGVTGNL ASAIFLPYRA EVG PAGSQF GILACLFVEL FQSWQILARP WRAFFKLLAV VLFLFTFGLL PWIDNFAHIS GFISGLFLSF AFLPYISFGK FDLY RKRCQ IIIFQVVFLG LLAGLVVLFY VYPV

UniProtKB: Inactive rhomboid protein 1

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Macromolecule #2: MEDI3622 Fab Heavy Chain

MacromoleculeName: MEDI3622 Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.324887 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRSSQSIP SYLNWYQQKP GKAPKLLIYA ASRLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSTPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCRSSQSIP SYLNWYQQKP GKAPKLLIYA ASRLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSTPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #3: MEDI3622 Fab Light Chain

MacromoleculeName: MEDI3622 Fab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.90065 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLLESGGG LVQPGGSLRL SCAASGFTFS SYPMNWVRQA PGKGLEWVSY ISPFGGMTDY ATSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARD AMRGAEVDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String:
EVQLLESGGG LVQPGGSLRL SCAASGFTFS SYPMNWVRQA PGKGLEWVSY ISPFGGMTDY ATSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARD AMRGAEVDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKR

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Macromolecule #4: Disintegrin and metalloproteinase domain-containing protein 17

MacromoleculeName: Disintegrin and metalloproteinase domain-containing protein 17
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: ADAM 17 endopeptidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.130922 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PHQRLEKLDS LLSDYDILSL SNIQQHSVRK RDLQTSTHVE TLLTFSALKR HFKLYLTSST ERFSQNFKVV VVDGKNESEY TVKWQDFFT GHVVGEPDSR VLAHIRDDDV IIRINTDGAE YNIEPLWRFV NDTKDKRMLV YKSEDIKNVS RLQSPKVCGY L KVDNEELL ...String:
PHQRLEKLDS LLSDYDILSL SNIQQHSVRK RDLQTSTHVE TLLTFSALKR HFKLYLTSST ERFSQNFKVV VVDGKNESEY TVKWQDFFT GHVVGEPDSR VLAHIRDDDV IIRINTDGAE YNIEPLWRFV NDTKDKRMLV YKSEDIKNVS RLQSPKVCGY L KVDNEELL PKGLVDREPP EELVHRVKRR ADPDPMKNTC KLLVVADHRF YRYMGRGEES TTTNYLIELI DRVDDIYRNT SW DNAGFKG YGIQIEQIRI LKSPQEVKPG EKHYNMAKSY PNEEKDAWDV KMLLEQFSFD IAEEASKVCL AHLFTYQDFD MGT LGLAYV GSPRANSHGG VCPKAYYSPV GKKNIYLNSG LTSTKNYGKT ILTKEADLVT THALGHNFGA EHDPDGLAEC APNE DQGGK YVMYPIAVSG DHENNKMFSN CSKQSIYKTI ESKAQECFQE RSNKVCGNSR VDEGEECDPG IMYLNNDTCC NSDCT LKEG VQCSDRNSPC CKNCQFETAQ KKCQEAINAT CKGVSYCTGN SSECPPPGNA EDDTVCLDLG KCKDGKCIPF CEREQQ LES CACNETDNSC KVCCRDLSGR CVPYVDAEQK NLFLRKGKPC TVGFCDMNGK CEKRVQDVIE RFWDFIDQLS INTFGKF LA DNIVGSVLVF SLIFWIPFSI LVHCVDKKL

UniProtKB: Disintegrin and metalloproteinase domain-containing protein 17

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 6 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 56.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.4 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: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 34630
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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