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- EMDB-30555: Cryo-EM structure of human DUOX1-DUOXA1 in low-calcium state -

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Basic information

Entry
Database: EMDB / ID: EMD-30555
TitleCryo-EM structure of human DUOX1-DUOXA1 in low-calcium state
Map data
Sample
  • Complex: human DUOX1-DUOXA1 complex
    • Protein or peptide: Dual oxidase 1
    • Protein or peptide: Isoform 2 of Dual oxidase maturation factor 1
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsDUOX / DUOXA / NOX / NADPH / FAD / Haem / ELECTRON TRANSPORT
Function / homology
Function and homology information


NADH oxidase H202-forming activity / regulation of thyroid hormone generation / NADPH oxidase H202-forming activity / cuticle development / NAD(P)H oxidase (H2O2-forming) / Thyroxine biosynthesis / positive regulation of hydrogen peroxide biosynthetic process / superoxide-generating NAD(P)H oxidase activity / hormone biosynthetic process / NAD(P)H oxidase H2O2-forming activity ...NADH oxidase H202-forming activity / regulation of thyroid hormone generation / NADPH oxidase H202-forming activity / cuticle development / NAD(P)H oxidase (H2O2-forming) / Thyroxine biosynthesis / positive regulation of hydrogen peroxide biosynthetic process / superoxide-generating NAD(P)H oxidase activity / hormone biosynthetic 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 / hydrogen peroxide metabolic process / positive regulation of wound healing / cell leading edge / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to cAMP / positive regulation of neuron differentiation / hydrogen peroxide catabolic process / peroxidase activity / defense response / cytokine-mediated signaling pathway / protein localization / protein transport / NADP binding / regulation of inflammatory response / response to oxidative stress / apical plasma membrane / calcium ion binding / heme binding / endoplasmic reticulum membrane / enzyme binding / cell surface / endoplasmic reticulum / membrane / plasma membrane
Similarity search - Function
Dual oxidase maturation factor / Dual oxidase, peroxidase domain / Dual oxidase maturation factor / Ferric reductase, NAD binding domain / : / Ferric reductase NAD binding domain / FAD-binding 8 / FAD-binding domain / Ferric reductase transmembrane component-like domain / Ferric reductase like transmembrane component ...Dual oxidase maturation factor / Dual oxidase, peroxidase domain / Dual oxidase maturation factor / Ferric reductase, NAD binding domain / : / Ferric reductase NAD binding domain / FAD-binding 8 / FAD-binding domain / Ferric reductase transmembrane component-like domain / Ferric reductase like transmembrane component / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / EF hand / Haem peroxidase superfamily / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Dual oxidase maturation factor 1 / Dual oxidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsChen L / Wu JX
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91957201 China
National Natural Science Foundation of China (NSFC)31622021 China
CitationJournal: Nat Commun / Year: 2021
Title: Structures of human dual oxidase 1 complex in low-calcium and high-calcium states.
Authors: Jing-Xiang Wu / Rui Liu / Kangcheng Song / Lei Chen /
Abstract: Dual oxidases (DUOXs) produce hydrogen peroxide by transferring electrons from intracellular NADPH to extracellular oxygen. They are involved in many crucial biological processes and human diseases, ...Dual oxidases (DUOXs) produce hydrogen peroxide by transferring electrons from intracellular NADPH to extracellular oxygen. They are involved in many crucial biological processes and human diseases, especially in thyroid diseases. DUOXs are protein complexes co-assembled from the catalytic DUOX subunits and the auxiliary DUOXA subunits and their activities are regulated by intracellular calcium concentrations. Here, we report the cryo-EM structures of human DUOX1-DUOXA1 complex in both high-calcium and low-calcium states. These structures reveal the DUOX1 complex is a symmetric 2:2 hetero-tetramer stabilized by extensive inter-subunit interactions. Substrate NADPH and cofactor FAD are sandwiched between transmembrane domain and the cytosolic dehydrogenase domain of DUOX. In the presence of calcium ions, intracellular EF-hand modules might enhance the catalytic activity of DUOX by stabilizing the dehydrogenase domain in a conformation that allows electron transfer.
History
DepositionSep 19, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d3e
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30555.png

Downloads & links

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Map

FileDownload / File: emd_30555.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 180 pix.
= 188.1 Å		1.05 Å/pix.
x 180 pix.
= 188.1 Å		1.05 Å/pix.
x 180 pix.
= 188.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.08888595 - 0.18415707
Average (Standard dev.)0.0010360425 (±0.0075276108)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 188.09999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0451.0451.045
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z188.100188.100188.100
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0890.1840.001

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Supplemental data

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Additional map: consensus map by relion

Fileemd_30555_additional_1.map
Annotationconsensus map by relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human DUOX1-DUOXA1 complex

EntireName: human DUOX1-DUOXA1 complex
Components
  • Complex: human DUOX1-DUOXA1 complex
    • Protein or peptide: Dual oxidase 1
    • Protein or peptide: Isoform 2 of Dual oxidase maturation factor 1
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: human DUOX1-DUOXA1 complex

SupramoleculeName: human DUOX1-DUOXA1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Dual oxidase 1

MacromoleculeName: Dual oxidase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 177.483828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGFCLALAWT LLVGAWTPLG AQNPISWEVQ RFDGWYNNLM EHRWGSKGSR LQRLVPASYA DGVYQPLGEP HLPNPRDLSN TISRGPAGL ASLRNRTVLG VFFGYHVLSD LVSVETPGCP AEFLNIRIPP GDPMFDPDQR GDVVLPFQRS RWDPETGRSP S NPRDPANQ ...String:
MGFCLALAWT LLVGAWTPLG AQNPISWEVQ RFDGWYNNLM EHRWGSKGSR LQRLVPASYA DGVYQPLGEP HLPNPRDLSN TISRGPAGL ASLRNRTVLG VFFGYHVLSD LVSVETPGCP AEFLNIRIPP GDPMFDPDQR GDVVLPFQRS RWDPETGRSP S NPRDPANQ VTGWLDGSAI YGSSHSWSDA LRSFSRGQLA SGPDPAFPRD SQNPLLMWAA PDPATGQNGP RGLYAFGAER GN REPFLQA LGLLWFRYHN LWAQRLARQH PDWEDEELFQ HARKRVIATY QNIAVYEWLP SFLQKTLPEY TGYRPFLDPS ISS EFVAAS EQFLSTMVPP GVYMRNASCH FQGVINRNSS VSRALRVCNS YWSREHPSLQ SAEDVDALLL GMASQIAERE DHVL VEDVR DFWPGPLKFS RTDHLASCLQ RGRDLGLPSY TKARAALGLS PITRWQDINP ALSRSNDTVL EATAALYNQD LSWLE LLPG GLLESHRDPG PLFSTIVLEQ FVRLRDGDRY WFENTRNGLF SKKEIEEIRN TTLQDVLVAV INIDPSALQP NVFVWH KGD PCPQPRQLST EGLPACAPSV VRDYFEGSGF GFGVTIGTLC CFPLVSLLSA WIVARLRMRN FKRLQGQDRQ SIVSEKL VG GMEALEWQGH KEPCRPVLVY LQPGQIRVVD GRLTVLRTIQ LQPPQKVNFV LSSNRGRRTL LLKIPKEYDL VLLFNLEE E RQALVENLRG ALKESGLSIQ EWELREQELM RAAVTREQRR HLLETFFRHL FSQVLDINQA DAGTLPLDSS QKVREALTC ELSRAEFAES LGLKPQDMFV ESMFSLADKD GNGYLSFREF LDILVVFMKG SPEEKSRLMF RMYDFDGNGL ISKDEFIRML RSFIEISNN CLSKAQLAEV VESMFRESGF QDKEELTWED FHFMLRDHNS ELRFTQLCVK GVEVPEVIKD LCRRASYISQ D MICPSPRV SARCSRSDIE TELTPQRLQC PMDTDPPQEI RRRFGKKVTS FQPLLFTEAH REKFQRSCLH QTVQQFKRFI EN YRRHIGC VAVFYAIAGG LFLERAYYYA FAAHHTGITD TTRVGIILSR GTAASISFMF SYILLTMCRN LITFLRETFL NRY VPFDAA VDFHRLIAST AIVLTVLHSV GHVVNVYLFS ISPLSVLSCL FPGLFHDDGS EFPQKYYWWF FQTVPGLTGV VLLL ILAIM YVFASHHFRR RSFRGFWLTH HLYILLYVLL IIHGSFALIQ LPRFHIFFLV PAIIYGGDKL VSLSRKKVEI SVVKA ELLP SGVTHLRFQR PQGFEYKSGQ WVRIACLALG TTEYHPFTLT SAPHEDTLSL HIRAAGPWTT RLREIYSAPT GDRCAR YPK LYLDGPFGEG HQEWHKFEVS VLVGGGIGVT PFASILKDLV FKSSVSCQVF CKKIYFIWVT RTQRQFEWLA DIIREVE EN DHQDLVSVHI YITQLAEKFD LRTTMLYICE RHFQKVLNRS LFTGLRSITH FGRPPFEPFF NSLQEVHPQV RKIGVFSC G PPGMTKNVEK ACQLINRQDR THFSHHYENF

UniProtKB: Dual oxidase 1

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Macromolecule #2: Isoform 2 of Dual oxidase maturation factor 1

MacromoleculeName: Isoform 2 of Dual oxidase maturation factor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.579188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATLGHTFPF YAGPKPTFPM DTTLASIIMI FLTALATFIV ILPGIRGKTR LFWLLRVVTS LFIGAAILAV NFSSEWSVGQ VSTNTSYKA FSSEWISADI GLQVGLGGVN ITLTGTPVQQ LNETINYNEE FTWRLGENYA EEYAKALEKG LPDPVLYLAE K FTPRSPCG ...String:
MATLGHTFPF YAGPKPTFPM DTTLASIIMI FLTALATFIV ILPGIRGKTR LFWLLRVVTS LFIGAAILAV NFSSEWSVGQ VSTNTSYKA FSSEWISADI GLQVGLGGVN ITLTGTPVQQ LNETINYNEE FTWRLGENYA EEYAKALEKG LPDPVLYLAE K FTPRSPCG LYRQYRLAGH YTSAMLWVAF LCWLLANVML SMPVLVYGGY MLLATGIFQL LALLFFSMAT SLTSPCPLHL GA SVLHTHH GPAFWITLTT GLLCVLLGLA MAVAHRMQPH RLKAFFNQSV DEDPMLEWSP EEGGLLSPRY RSMADSPKSQ DIP LSEASS TKAYYRPRRL SLVPADVRGL APAALSALPG ALLAQAWRAL LPGLRCPKAG KESRLGPPHS PWRFGPEGCE ERWA EHTGD SPRPLRGRGT GRLWRWGSKE RRACGVRAML PRLVSNSGLK RPSCLDLPKC WDYRRDARAF FHLLEPTPCV TSRHT PLI

UniProtKB: Dual oxidase maturation factor 1

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Macromolecule #4: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 4 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #5: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 5 / Number of copies: 2 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Macromolecule #6: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 6 / Number of copies: 2 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #8: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 8 / Number of copies: 4
Molecular weightTheoretical: 22.99 Da

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 125984
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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