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- EMDB-72319: Zymogen ADAM17- iRhom1 Cytoplasmic Deletion (365) Complex Bound b... -

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Basic information

Entry
Database: EMDB / ID: EMD-72319
TitleZymogen ADAM17- iRhom1 Cytoplasmic Deletion (365) Complex Bound by the MEDI3622 Fab
Map data
Sample
  • Complex: mVenus chimera iRhom1 amino acid 365 cytoplasmic truncation complexed with ADAM17 bound to MEDI3622 Fab
    • Protein or peptide: MEDI3622 Fab Light Chain
    • Protein or peptide: MEDI3622 Fab Heavy Chain
    • Protein or peptide: Inactive rhomboid protein 1
    • 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
Function / homology
Function and homology information


ADAM 17 endopeptidase / regulation of mast cell apoptotic process / signal release / 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 ...ADAM 17 endopeptidase / regulation of mast cell apoptotic process / signal release / 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 / regulation of axon regeneration / metallodipeptidase activity / commissural neuron axon guidance / regulation of neuron migration / positive regulation of tumor necrosis factor-mediated signaling pathway / germinal center formation / neutrophil mediated immunity / Notch binding / wound healing, spreading of epidermal cells / positive regulation of vascular endothelial cell proliferation / negative regulation of cold-induced thermogenesis / cell adhesion mediated by integrin / CD163 mediating an anti-inflammatory response / regulation of protein secretion / growth factor binding / ERBB2-EGFR signaling pathway / amyloid precursor protein catabolic process / Signaling by EGFR / cytokine binding / Collagen degradation / membrane protein ectodomain proteolysis / negative regulation of protein secretion / 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 / positive regulation of epidermal growth factor receptor signaling pathway / spleen development / positive regulation of chemokine production / Notch signaling pathway / regulation of proteasomal protein catabolic process / B cell differentiation / Constitutive Signaling by NOTCH1 HD Domain Mutants / Activated NOTCH1 Transmits Signal to the Nucleus / PDZ domain binding / cell motility / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transforming growth factor beta receptor signaling pathway / protein processing / metalloendopeptidase activity / SH3 domain binding / integrin binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / epidermal growth factor receptor signaling pathway / metallopeptidase activity / positive regulation of tumor necrosis factor production / T cell differentiation in thymus / peptidase activity / cell migration / protein transport / negative regulation of neuron projection development / actin cytoskeleton / positive regulation of cell growth / endopeptidase activity / response to lipopolysaccharide / response to hypoxia / cell adhesion / cell population proliferation / apical plasma membrane / defense response to Gram-positive bacterium / positive regulation of cell migration / membrane raft / response to xenobiotic stimulus / endoplasmic reticulum lumen / Golgi membrane / positive regulation of cell population proliferation / endoplasmic reticulum membrane / cell surface / proteolysis / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol
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: 3.35 Å
AuthorsSeegar TM / Maciag JJ / Ungvary JN
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 (365) Complex Bound by the MEDI3622 Fab
Authors: Seegar TM / Maciag JJ / Ungvary JN
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_72319.png

Downloads & links

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Map

FileDownload / File: emd_72319.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 560 pix.
= 362.32 Å		0.65 Å/pix.
x 560 pix.
= 362.32 Å		0.65 Å/pix.
x 560 pix.
= 362.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.3577429 - 0.55277675
Average (Standard dev.)-0.00007786591 (±0.010603042)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 362.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72319_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72319_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_72319_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : mVenus chimera iRhom1 amino acid 365 cytoplasmic truncation compl...

EntireName: mVenus chimera iRhom1 amino acid 365 cytoplasmic truncation complexed with ADAM17 bound to MEDI3622 Fab
Components
  • Complex: mVenus chimera iRhom1 amino acid 365 cytoplasmic truncation complexed with ADAM17 bound to MEDI3622 Fab
    • Protein or peptide: MEDI3622 Fab Light Chain
    • Protein or peptide: MEDI3622 Fab Heavy Chain
    • Protein or peptide: Inactive rhomboid protein 1
    • 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 365 cytoplasmic truncation compl...

SupramoleculeName: mVenus chimera iRhom1 amino acid 365 cytoplasmic truncation complexed with ADAM17 bound to MEDI3622 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #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: 52.991184 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: REKRPYGLGM VGRLTNRTYR KRIDSFVKRQ IEDMDDHRPF FTYWLTFVHS LVTILAVCIY GIAPVGFSQH ETVDSVLRNR GVYENVKYV QQENFWIGPS SEALIHLGAK FSPCMRQDPQ VHSFIRSARE REKHSACCVR NDRSGCVQTS EEECSSTLAV W VKWPIHPS ...String:
REKRPYGLGM VGRLTNRTYR KRIDSFVKRQ IEDMDDHRPF FTYWLTFVHS LVTILAVCIY GIAPVGFSQH ETVDSVLRNR GVYENVKYV QQENFWIGPS SEALIHLGAK FSPCMRQDPQ VHSFIRSARE REKHSACCVR NDRSGCVQTS EEECSSTLAV W VKWPIHPS APELAGHKRQ FGSVCHQDPR VCDEPSSEDP HEWPEDITKW PICTKNSAGN HTNHPHMDCV ITGRPCCIGT KG RCEITSR EYCDFMRGYF HEEATLCSQV HCMDDVCGLL PFLNPEVPDQ FYRLWLSLFL HAGILHCLVS ICFQMTVLRD LEK LAGWHR IAIIYLLSGV TGNLASAIFL PYRAEVGPAG SQFGILACLF VELFQSWQIL ARPWRAFFKL LAVVLFLFTF GLLP WIDNF AHISGFISGL FLSFAFLPYI SFGKFDLYRK RCQIIIFQVV FLGLLAGLVV LFYVYPV

UniProtKB: Inactive rhomboid protein 1

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Macromolecule #2: MEDI3622 Fab Light Chain

MacromoleculeName: MEDI3622 Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.435687 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRSSQSIP SYLNWYQQKP GKAPKLLIYA ASRLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSTPLTFG GGTKVEI

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Macromolecule #3: MEDI3622 Fab Heavy Chain

MacromoleculeName: MEDI3622 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.86238 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLLESGGG LVQPGGSLRL SCAASGFTFS SYPMNWVRQA PGKGLEWVSY ISPFGGMTDY ATSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARD AMRGAEVDYW GQGTLVTVS

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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

Concentration8.0 mg/mL
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: 63.5 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 55059
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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