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Yorodumi- EMDB-40631: Structure of mature human ADAM17/iRhom2 sheddase complex, conform... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40631 | |||||||||
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Title | Structure of mature human ADAM17/iRhom2 sheddase complex, conformation 2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Membrane protein complex / MEMBRANE PROTEIN / MEMBRANE PROTEIN-HYDROLASE complex | |||||||||
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 / 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 / interleukin-6 receptor binding / Notch receptor processing ...ADAM 17 endopeptidase / regulation of mast cell apoptotic process / signal release / 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 / interleukin-6 receptor binding / Notch receptor processing / tumor necrosis factor binding / protein transporter activity / positive regulation of T cell chemotaxis / TNF signaling / Signaling by EGFR / positive regulation of leukocyte chemotaxis / germinal center formation / Release of Hh-Np from the secreting cell / Regulated proteolysis of p75NTR / commissural neuron axon guidance / positive regulation of tumor necrosis factor-mediated signaling pathway / neutrophil mediated immunity / positive regulation of cyclin-dependent protein serine/threonine kinase activity / wound healing, spreading of epidermal cells / negative regulation of cold-induced thermogenesis / Notch binding / CD163 mediating an anti-inflammatory response / positive regulation of vascular endothelial cell proliferation / cell adhesion mediated by integrin / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of G1/S transition of mitotic cell cycle / regulation of protein secretion / growth factor binding / amyloid precursor protein catabolic process / cytokine binding / Collagen degradation / membrane protein ectodomain proteolysis / positive regulation of blood vessel endothelial cell migration / negative regulation of protein secretion / Growth hormone receptor signaling / positive regulation of chemokine production / Nuclear signaling by ERBB4 / spleen development / negative regulation of inflammatory response to antigenic stimulus / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / Activated NOTCH1 Transmits Signal to the Nucleus / B cell differentiation / negative regulation of transforming growth factor beta receptor signaling pathway / protein localization to plasma membrane / PDZ domain binding / cell motility / protein processing / metalloendopeptidase activity / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SH3 domain binding / Golgi lumen / integrin binding / metallopeptidase activity / positive regulation of tumor necrosis factor production / actin cytoskeleton / protein transport / peptidase activity / positive regulation of cell growth / endopeptidase activity / T cell differentiation in thymus / response to lipopolysaccharide / response to hypoxia / cell adhesion / positive regulation of cell migration / defense response to Gram-positive bacterium / apical plasma membrane / response to xenobiotic stimulus / membrane raft / Golgi membrane / endoplasmic reticulum lumen / positive regulation of cell population proliferation / endoplasmic reticulum membrane / cell surface / proteolysis / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.78 Å | |||||||||
Authors | Zhao H / Dai Y / Wang Y / Lee CH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Structure of mature human ADAM17/iRhom2 sheddase complex, conformation 2 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 | emd_40631.map.gz | 259.6 MB | EMDB map data format | |
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Header (meta data) | emd-40631-v30.xml emd-40631.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
Images | emd_40631.png | 60.3 KB | ||
Filedesc metadata | emd-40631.cif.gz | 6 KB | ||
Others | emd_40631_half_map_1.map.gz emd_40631_half_map_2.map.gz | 254.6 MB 254.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40631 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40631 | HTTPS FTP |
-Validation report
Summary document | emd_40631_validation.pdf.gz | 812.3 KB | Display | EMDB validaton report |
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Full document | emd_40631_full_validation.pdf.gz | 811.8 KB | Display | |
Data in XML | emd_40631_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_40631_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40631 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40631 | HTTPS FTP |
-Related structure data
Related structure data | 8snoMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40631.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8253 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_40631_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40631_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : mature human ADAM17/iRhom2 sheddase complex, conformation 2
Entire | Name: mature human ADAM17/iRhom2 sheddase complex, conformation 2 |
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Components |
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-Supramolecule #1: mature human ADAM17/iRhom2 sheddase complex, conformation 2
Supramolecule | Name: mature human ADAM17/iRhom2 sheddase complex, conformation 2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Disintegrin and metalloproteinase domain-containing protein 17
Macromolecule | Name: Disintegrin and metalloproteinase domain-containing protein 17 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ADAM 17 endopeptidase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 68.302641 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 #2: Inactive rhomboid protein 2
Macromolecule | Name: Inactive rhomboid protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 93.503258 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / 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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 66.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 325764 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |