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- EMDB-40629: Structure of mature human ADAM17/iRhom2 sheddase complex in compl... -
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Basic information
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Title | Structure of mature human ADAM17/iRhom2 sheddase complex in complex with ADAM17 prodomain | |||||||||
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![]() | Membrane protein complex / MEMBRANE PROTEIN / MEMBRANE PROTEIN-HYDROLASE complex | |||||||||
Function / homology | ![]() ADAM 17 endopeptidase / regulation of mast cell apoptotic process / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / regulation of epidermal growth factor receptor signaling pathway / cellular response to high density lipoprotein particle stimulus / positive regulation of epidermal growth factor-activated receptor activity / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / Notch receptor processing / interleukin-6 receptor binding / tumor necrosis factor binding ...ADAM 17 endopeptidase / regulation of mast cell apoptotic process / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / regulation of epidermal growth factor receptor signaling pathway / cellular response to high density lipoprotein particle stimulus / positive regulation of epidermal growth factor-activated receptor activity / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / Notch receptor processing / interleukin-6 receptor binding / tumor necrosis factor binding / protein transporter activity / positive regulation of T cell chemotaxis / TNF signaling / germinal center formation / Regulated proteolysis of p75NTR / Release of Hh-Np from the secreting cell / commissural neuron axon guidance / positive regulation of tumor necrosis factor-mediated signaling pathway / neutrophil mediated immunity / wound healing, spreading of epidermal cells / Notch binding / negative regulation of cold-induced thermogenesis / positive regulation of leukocyte chemotaxis / CD163 mediating an anti-inflammatory response / positive regulation of vascular endothelial cell proliferation / positive regulation of epidermal growth factor receptor signaling pathway / cell adhesion mediated by integrin / Signaling by EGFR / regulation of protein secretion / growth factor binding / amyloid precursor protein catabolic process / membrane protein ectodomain proteolysis / Collagen degradation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of protein secretion / positive regulation of blood vessel endothelial cell migration / positive regulation of G1/S transition of mitotic cell cycle / Growth hormone receptor signaling / positive regulation of chemokine production / Nuclear signaling by ERBB4 / Notch signaling pathway / negative regulation of inflammatory response to antigenic stimulus / spleen development / Constitutive Signaling by NOTCH1 HD Domain Mutants / Activated NOTCH1 Transmits Signal to the Nucleus / B cell differentiation / protein localization to plasma membrane / PDZ domain binding / cell motility / negative regulation of transforming growth factor beta receptor signaling pathway / protein processing / metalloendopeptidase activity / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SH3 domain binding / Golgi lumen / metallopeptidase activity / actin cytoskeleton / protein transport / integrin binding / peptidase activity / T cell differentiation in thymus / positive regulation of cell growth / endopeptidase activity / response to lipopolysaccharide / response to hypoxia / cell adhesion / positive regulation of cell migration / defense response to Gram-positive bacterium / response to xenobiotic stimulus / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / Golgi membrane / positive regulation of cell population proliferation / endoplasmic reticulum membrane / cell surface / proteolysis / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.84 Å | |||||||||
![]() | Zhao H / Dai Y / Wang Y / Lee CH | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of mature human ADAM17/iRhom2 sheddase complex in complex with ADAM17 prodomain Authors: Zhao H / Dai Y / Wang Y / Lee CH | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 157 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.8 KB 16.8 KB | Display Display | ![]() |
Images | ![]() | 69.5 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() | 154.5 MB 154.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 769.9 KB | Display | ![]() |
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Full document | ![]() | 769.5 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8snmMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.986 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_40629_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40629_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : mature human ADAM17/iRhom2 sheddase complex in complex with ADAM1...
Entire | Name: mature human ADAM17/iRhom2 sheddase complex in complex with ADAM17 prodomain |
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Components |
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-Supramolecule #1: mature human ADAM17/iRhom2 sheddase complex in complex with ADAM1...
Supramolecule | Name: mature human ADAM17/iRhom2 sheddase complex in complex with ADAM17 prodomain type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Inactive rhomboid protein 2
Macromolecule | Name: Inactive rhomboid protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 93.503258 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MASADKNGGS VSSVSSSRLQ SRKPPNLSIT IPPPEKETQA PGEQDSMLPE RKNPAYLKSV SLQEPRSRWQ ESSEKRPGFR RQASLSQSI RKGAAQWFGV SGDWEGQRQQ WQRRSLHHCS MRYGRLKASC QRDLELPSQE APSFQGTESP KPCKMPKIVD P LARGRAFR ...String: MASADKNGGS VSSVSSSRLQ SRKPPNLSIT IPPPEKETQA PGEQDSMLPE RKNPAYLKSV SLQEPRSRWQ ESSEKRPGFR RQASLSQSI RKGAAQWFGV SGDWEGQRQQ WQRRSLHHCS MRYGRLKASC QRDLELPSQE APSFQGTESP KPCKMPKIVD P LARGRAFR HPEEMDRPHA PHPPLTPGVL SLTSFTSVRS GYSHLPRRKR MSVAHMSLQA AAALLKGRSV LDATGQRCRV VK RSFAFPS FLEEDVVDGA DTFDSSFFSK EEMSSMPDDV FESPPLSASY FRGIPHSASP VSPDGVQIPL KEYGRAPVPG PRR GKRIAS KVKHFAFDRK KRHYGLGVVG NWLNRSYRRS ISSTVQRQLE SFDSHRPYFT YWLTFVHVII TLLVICTYGI APVG FAQHV TTQLVLRNKG VYESVKYIQQ ENFWVGPSSI DLIHLGAKFS PCIRKDGQIE QLVLRERDLE RDSGCCVQND HSGCI QTQR KDCSETLATF VKWQDDTGPP MDKSDLGQKR TSGAVCHQDP RTCEEPASSG AHIWPDDITK WPICTEQARS NHTGFL HMD CEIKGRPCCI GTKGSCEITT REYCEFMHGY FHEEATLCSQ VHCLDKVCGL LPFLNPEVPD QFYRLWLSLF LHAGVVH CL VSVVFQMTIL RDLEKLAGWH RIAIIFILSG ITGNLASAIF LPYRAEVGPA GSQFGLLACL FVELFQSWPL LERPWKAF L NLSAIVLFLF ICGLLPWIDN IAHIFGFLSG LLLAFAFLPY ITFGTSDKYR KRALILVSLL AFAGLFAALV LWLYIYPIN WPWIEHLTCF PFTSRFCEKY ELDQVLH UniProtKB: Inactive rhomboid protein 2 |
-Macromolecule #2: Disintegrin and metalloproteinase domain-containing protein 17 pr...
Macromolecule | Name: Disintegrin and metalloproteinase domain-containing protein 17 propeptide type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: ADAM 17 endopeptidase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.857287 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MRQSLLFLTS VVPFVLAPRP PDDPGFGPHQ RLEKLDSLLS DYDILSLSNI QQHSVRKRDL QTSTHVETLL TFSALKRHFK LYLTSSTER FSQNFKVVVV DGKNESEYTV KWQDFFTGHV VGEPDSRVLA HIRDDDVIIR INTDGAEYNI EPLWRFVNDT K DKRMLVYK ...String: MRQSLLFLTS VVPFVLAPRP PDDPGFGPHQ RLEKLDSLLS DYDILSLSNI QQHSVRKRDL QTSTHVETLL TFSALKRHFK LYLTSSTER FSQNFKVVVV DGKNESEYTV KWQDFFTGHV VGEPDSRVLA HIRDDDVIIR INTDGAEYNI EPLWRFVNDT K DKRMLVYK SEDIKNVSRL QSPKVCGYLK VDNEELLPKG LVDREPPEEL VHRVKR UniProtKB: Disintegrin and metalloproteinase domain-containing protein 17 |
-Macromolecule #3: Disintegrin and metalloproteinase domain-containing protein 17
Macromolecule | Name: Disintegrin and metalloproteinase domain-containing protein 17 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: ADAM 17 endopeptidase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 68.302641 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: RADPDPMKNT CKLLVVADHR FYRYMGRGEE STTTNYLIEL IDRVDDIYRN TSWDNAGFKG YGIQIEQIRI LKSPQEVKPG EKHYNMAKS YPNEEKDAWD VKMLLEQFSF DIAEEASKVC LAHLFTYQDF DMGTLGLAYV GSPRANSHGG VCPKAYYSPV G KKNIYLNS ...String: RADPDPMKNT CKLLVVADHR FYRYMGRGEE STTTNYLIEL IDRVDDIYRN TSWDNAGFKG YGIQIEQIRI LKSPQEVKPG EKHYNMAKS YPNEEKDAWD VKMLLEQFSF DIAEEASKVC LAHLFTYQDF DMGTLGLAYV GSPRANSHGG VCPKAYYSPV G KKNIYLNS GLTSTKNYGK TILTKEADLV TTHELGHNFG AEHDPDGLAE CAPNEDQGGK YVMYPIAVSG DHENNKMFSN CS KQSIYKT IESKAQECFQ ERSNKVCGNS RVDEGEECDP GIMYLNNDTC CNSDCTLKEG VQCSDRNSPC CKNCQFETAQ KKC QEAINA TCKGVSYCTG NSSECPPPGN AEDDTVCLDL GKCKDGKCIP FCEREQQLES CACNETDNSC KVCCRDLSGR CVPY VDAEQ KNLFLRKGKP CTVGFCDMNG KCEKRVQDVI ERFWDFIDQL SINTFGKFLA DNIVGSVLVF SLIFWIPFSI LVHCV DKKL DKQYESLSLF HPSNVEMLSS MDSASVRIIK PFPAPQTPGR LQPAPVIPSA PAAPKLDHQR MDTIQEDPST DSHMDE DGF EKDPFPNSST AAKSFEDLTD HPVTRSEKAA SFKLQRQNRV DSKETEC UniProtKB: Disintegrin and metalloproteinase domain-containing protein 17 |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #5: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.4 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152751 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |