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Yorodumi- EMDB-21962: CryoEM structure of mouse DUOX1-DUOXA1 complex in the absence of NADPH -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21962 | |||||||||
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Title | CryoEM structure of mouse DUOX1-DUOXA1 complex in the absence of NADPH | |||||||||
Map data | cryoEM structure of the mouse DUOX1-DUOXA1 complex | |||||||||
Sample |
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Function / homology | Function and homology information regulation of thyroid hormone generation / Thyroxine biosynthesis / NAD(P)H oxidase (H2O2-forming) / cuticle development / positive regulation of hydrogen peroxide biosynthetic process / superoxide-generating NAD(P)H oxidase activity / hormone biosynthetic process / hydrogen peroxide metabolic process / NAD(P)H oxidase H2O2-forming activity / NADPH oxidase complex ...regulation of thyroid hormone generation / Thyroxine biosynthesis / NAD(P)H oxidase (H2O2-forming) / cuticle development / positive regulation of hydrogen peroxide biosynthetic process / superoxide-generating NAD(P)H oxidase activity / hormone biosynthetic process / hydrogen peroxide metabolic process / NAD(P)H oxidase H2O2-forming activity / NADPH oxidase complex / thyroid hormone generation / superoxide anion generation / hydrogen peroxide biosynthetic process / positive regulation of cell motility / positive regulation of wound healing / cell leading edge / response to cAMP / positive regulation of neuron differentiation / reactive oxygen species metabolic process / peroxidase activity / defense response / cytokine-mediated signaling pathway / positive regulation of reactive oxygen species metabolic process / protein transport / regulation of inflammatory response / response to oxidative stress / apical plasma membrane / calcium ion binding / endoplasmic reticulum membrane / heme binding / cell surface / endoplasmic reticulum / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Sun J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Structures of mouse DUOX1-DUOXA1 provide mechanistic insights into enzyme activation and regulation. Authors: Ji Sun / Abstract: DUOX1, an NADPH oxidase family member, catalyzes the production of hydrogen peroxide. DUOX1 is expressed in various tissues, including the thyroid and respiratory tract, and plays a crucial role in ...DUOX1, an NADPH oxidase family member, catalyzes the production of hydrogen peroxide. DUOX1 is expressed in various tissues, including the thyroid and respiratory tract, and plays a crucial role in processes such as thyroid hormone biosynthesis and innate host defense. DUOX1 co-assembles with its maturation factor DUOXA1 to form an active enzyme complex. However, the molecular mechanisms for activation and regulation of DUOX1 remain mostly unclear. Here, I present cryo-EM structures of the mammalian DUOX1-DUOXA1 complex, in the absence and presence of substrate NADPH, as well as DUOX1-DUOXA1 in an unexpected dimer-of-dimers configuration. These structures reveal atomic details of the DUOX1-DUOXA1 interaction, a lipid-mediated NADPH-binding pocket and the electron transfer path. Furthermore, biochemical and structural analyses indicate that the dimer-of-dimers configuration represents an inactive state of DUOX1-DUOXA1, suggesting an oligomerization-dependent regulatory mechanism. Together, my work provides structural bases for DUOX1-DUOXA1 activation and regulation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21962.map.gz | 43.8 MB | EMDB map data format | |
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Header (meta data) | emd-21962-v30.xml emd-21962.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
Images | emd_21962.png | 136.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21962 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21962 | HTTPS FTP |
-Validation report
Summary document | emd_21962_validation.pdf.gz | 407.3 KB | Display | EMDB validaton report |
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Full document | emd_21962_full_validation.pdf.gz | 406.9 KB | Display | |
Data in XML | emd_21962_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_21962_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21962 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21962 | HTTPS FTP |
-Related structure data
Related structure data | 6wxrMC 6wxuC 6wxvC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21962.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryoEM structure of the mouse DUOX1-DUOXA1 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : mouse DUOX1-DUOXA1 complex
Entire | Name: mouse DUOX1-DUOXA1 complex |
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Components |
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-Supramolecule #1: mouse DUOX1-DUOXA1 complex
Supramolecule | Name: mouse DUOX1-DUOXA1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 220 KDa |
-Macromolecule #1: Dual oxidase 1
Macromolecule | Name: Dual oxidase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 175.739812 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GPSRGAQNSI SWEVQRFDGW YNNLMEHRWG SKGSRLQRLV PASYADGVYQ PLKEPYLPNP RHLSNRVMRG SAGQPSLRNR TVLGVFFGY HVLSDLVSVE TPGCPAEFLN IYIPHGDPVF DPDKRGNVVL PFQRSRWDRN TGQSPSNPRD QSNQVTGWLD G SAIYGSSH ...String: GPSRGAQNSI SWEVQRFDGW YNNLMEHRWG SKGSRLQRLV PASYADGVYQ PLKEPYLPNP RHLSNRVMRG SAGQPSLRNR TVLGVFFGY HVLSDLVSVE TPGCPAEFLN IYIPHGDPVF DPDKRGNVVL PFQRSRWDRN TGQSPSNPRD QSNQVTGWLD G SAIYGSSH SWSDTLRSFS GGQLASGPDP AFPSDSQSSL LMWMAPDPST GQGGPRGVYA FGAQRGNREP FLQALGLLWF RY HNLCARK LAQEHPHWGD EELFQHARKR VIATYQNIAM YEWLPSFLKQ TPPEYPGYRP FLDPSISPEF VVASEQFLST MVP SGVYMR NASCHFQGIP SHNSSVSGAL RVCNSYWSRE HPKLQRAEDV DALLLGMASQ IAEREDHVVV EDMQDFWPGP LKFS RTDYL ASCLQRGRDL GLPSYTKARE ALGLSPISHW QDINPALSRS NGTVLEATAA LYNQDLSRLE LLPGGLLESH GDPGP LFST IVLDQFVRLR DGDRYWFENT RNGLFSKEEI AEIRNTSLRD ILVAVTNVDP SALQPNVFFW LAGDPCPQPS QLSAKG LPA CAPLFIRDYF EGSGFGFGLT IGTLCCFPLV SLLSAWIVAR LRKRNFKRLQ RQDRQSIMSE KLVGGVEALE WQGRNEP CR PVLVHLQPGQ IRVVDGRLTV LRTIQLRPPQ QVNLILSSNR GRRTLLLKIP KEYDLVLLFN MEEERQALVE NVRGALKE N GLSFQEWELR EQELMRAAVT RQQRGHLLET FFRHLFSQVL DINQADAGTL PLDSSTKVRE ALTCELSRAE FADSLGLKP QDMFVESMFS LADKDGNGYL SFREFLDILV VFMKGSPEEK SRLMFRMYDF DGNGLISKDE FIRMLRSFIE ISNNCLSKAQ LAEVVESMF RESGFQDKEE LTWEDFHFML RDHDSDLRFT QLCVKGVEVP EVIKNLCRRA SYISQEKICP SPRMSAHCAR N NMKTASSP QRLQCPMDTD PPQEIRRRFG KKVTSFQPLL FTEAHREKFQ RSRRHQTVQQ FKRFIENYRR HIGCVAVFYT IT GALFLER AYYYAFAAHH SGITDTTRVG IILSRGTAAS ISFMFSYILL TMCRNLITFL RETFLNRYIP FDAAVDFHRL IAS TAIILT VLHSAGHVVN VYLFSISPLS VLSCLFPGLF HDDGSEFPQK YYWWFFQTVP GLTGVLLLLA LAIMYVFASH HFRR RSFRG FWLTHHLYIF LYILLIIHGS FALIQMPRFH IFFLVPAIIY VGDKLVSLSR KKVEISVVKA ELLPSGVTHL RFQRP QGFE YKSGQWVRIA CLALGTTEYH PFTLTSAPHE DTLSLHIRAA GPWTTRLREI YSPPTGDTCA RYPKLYLDGP FGEGHQ EWH KFEVSVLVGG GIGVTPFASI LKDLVFKSSV SCQVFCKKIY FIWVTRTQRQ FEWLADIIRE VEENDRQDLV SVHIYIT QL AEKFDLRTTM LYICERHFQK VLNRSLFTGL RSITHFGRPP FEPFFNSLQE VHPQVRKIGV FSCGPPGMTK NVEKACQL I NRQDRTHFSH HYENF |
-Macromolecule #2: Dual oxidase maturation factor 1
Macromolecule | Name: Dual oxidase maturation factor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 37.619738 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAALGHTLPF YTGTKPTFPM DTTLAVIITI FLTALVTFII ILPGIRGKTR LFWLLRVVTS LFIGAVILAV NFSSEWSVGH VNANTTYKA FSPKWVSVDV GLQIGLGGVN ITLTGTPVQQ LNETINYNEA FAWRLGRSYA EEYAKALEKG LPDPVLYLAE K FTPRSPCG ...String: MAALGHTLPF YTGTKPTFPM DTTLAVIITI FLTALVTFII ILPGIRGKTR LFWLLRVVTS LFIGAVILAV NFSSEWSVGH VNANTTYKA FSPKWVSVDV GLQIGLGGVN ITLTGTPVQQ LNETINYNEA FAWRLGRSYA EEYAKALEKG LPDPVLYLAE K FTPRSPCG LYNQYRLAGH YASAMLWVAF LCWLLANVML SMPVLVYGGH MLLATGLFQL LALFFFSMTT SLISPCPLRL GT AVLHTHH GPAFWITLAT GLLCILLGLV MAVAHRMQPH RLKAFFNQSS EDPVLEWGSE EGGLLSPHYR SIAESPETQD IPM SVASSE TCFKEEHPKE SDCSL |
-Macromolecule #4: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 1 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ChemComp-FAD: |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #6: PROTOPORPHYRIN IX CONTAINING FE
Macromolecule | Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 6 / Number of copies: 2 / Formula: HEM |
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Molecular weight | Theoretical: 616.487 Da |
Chemical component information | ChemComp-HEM: |
-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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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.13) / Number images used: 534337 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-6wxr: |