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- EMDB-37159: Cryo-EM structure of NADPH oxidase 2 in complex with p22phox and EROS -

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Basic information

Entry
Database: EMDB / ID: EMD-37159
TitleCryo-EM structure of NADPH oxidase 2 in complex with p22phox and EROS
Map data
Sample
  • Complex: NADPH oxidase 2 in complex with Cytochrome b-245 light chain, Cytochrome b-245 chaperone 1 and a monoclonal antibody
    • Protein or peptide: Cytochrome b-245 light chain
    • Protein or peptide: Cytochrome b-245 heavy chain
    • Protein or peptide: monoclonal antibody 7G5 heavy chain
    • Protein or peptide: Cytochrome b-245 chaperone 1
    • Protein or peptide: monoclonal antibody 7G5 light chain
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
KeywordsNADPH oxidase / IMMUNE SYSTEM
Function / homology
Function and homology information


smooth muscle hypertrophy / cellular response to L-glutamine / positive regulation of toll-like receptor 2 signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / superoxide-generating NAD(P)H oxidase activity / respiratory burst after phagocytosis / positive regulation of defense response to bacterium / mucus secretion / Cross-presentation of particulate exogenous antigens (phagosomes) / perinuclear endoplasmic reticulum ...smooth muscle hypertrophy / cellular response to L-glutamine / positive regulation of toll-like receptor 2 signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / superoxide-generating NAD(P)H oxidase activity / respiratory burst after phagocytosis / positive regulation of defense response to bacterium / mucus secretion / Cross-presentation of particulate exogenous antigens (phagosomes) / perinuclear endoplasmic reticulum / cytochrome complex assembly / NADPH oxidase complex / WNT5:FZD7-mediated leishmania damping / respiratory burst / regulation of release of sequestered calcium ion into cytosol / ROS and RNS production in phagocytes / cellular response to ethanol / superoxide anion generation / Oxidoreductases / response to angiotensin / hydrogen peroxide biosynthetic process / positive regulation of mucus secretion / positive regulation of reactive oxygen species biosynthetic process / monoatomic ion channel complex / response to aldosterone / superoxide metabolic process / Detoxification of Reactive Oxygen Species / tertiary granule membrane / RHO GTPases Activate NADPH Oxidases / RAC2 GTPase cycle / RAC3 GTPase cycle / specific granule membrane / positive regulation of phagocytosis / monoatomic ion transmembrane transport / RAC1 GTPase cycle / cellular response to cadmium ion / response to nutrient / secretory granule / establishment of localization in cell / defense response / VEGFA-VEGFR2 Pathway / SH3 domain binding / phagocytic vesicle membrane / positive regulation of angiogenesis / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / nuclear envelope / flavin adenine dinucleotide binding / electron transfer activity / oxidoreductase activity / endosome / response to xenobiotic stimulus / inflammatory response / protein heterodimerization activity / innate immune response / neuronal cell body / dendrite / heme binding / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome b-245 chaperone 1 / Cytochrome b-245 chaperone 1 / Eros / Cytochrome b245, heavy chain / Cytochrome b558 alpha-subunit / Cytochrome Cytochrome b558 alpha-subunit / Ferric reductase, NAD binding domain / Ferric reductase NAD binding domain / FAD-binding 8 / FAD-binding domain / Ferric reductase transmembrane component-like domain ...Cytochrome b-245 chaperone 1 / Cytochrome b-245 chaperone 1 / Eros / Cytochrome b245, heavy chain / Cytochrome b558 alpha-subunit / Cytochrome Cytochrome b558 alpha-subunit / 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 / 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
Similarity search - Domain/homology
Cytochrome b-245 heavy chain / Cytochrome b-245 light chain / Cytochrome b-245 chaperone 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsLiang SY / Liu AJ / Liu YZ / Ye RD
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of NADPH oxidase 2 in complex with p22phox and EROS
Authors: Liang SY / Liu AJ / Liu YZ / Ye RD
History
DepositionAug 11, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37159.png

Downloads & links

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Map

FileDownload / File: emd_37159.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.7554282 - 2.9300365
Average (Standard dev.)-0.0008505151 (±0.047837034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37159_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_37159_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NADPH oxidase 2 in complex with Cytochrome b-245 light chain, Cyt...

EntireName: NADPH oxidase 2 in complex with Cytochrome b-245 light chain, Cytochrome b-245 chaperone 1 and a monoclonal antibody
Components
  • Complex: NADPH oxidase 2 in complex with Cytochrome b-245 light chain, Cytochrome b-245 chaperone 1 and a monoclonal antibody
    • Protein or peptide: Cytochrome b-245 light chain
    • Protein or peptide: Cytochrome b-245 heavy chain
    • Protein or peptide: monoclonal antibody 7G5 heavy chain
    • Protein or peptide: Cytochrome b-245 chaperone 1
    • Protein or peptide: monoclonal antibody 7G5 light chain
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

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Supramolecule #1: NADPH oxidase 2 in complex with Cytochrome b-245 light chain, Cyt...

SupramoleculeName: NADPH oxidase 2 in complex with Cytochrome b-245 light chain, Cytochrome b-245 chaperone 1 and a monoclonal antibody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cytochrome b-245 light chain

MacromoleculeName: Cytochrome b-245 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.663218 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QIEWAMWANE QALASGLILI TGGIVATAGR FTQWYFGAYS IVAGVFVCLL EYPRGKRKKG STMERWGQKY MTAVVKLFGP FTRNYYVRA VLHLLLSVPA GFLLATILGT ACLAIASGIY LLAAVRGEQW TPIE

UniProtKB: Cytochrome b-245 light chain

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Macromolecule #2: Cytochrome b-245 heavy chain

MacromoleculeName: Cytochrome b-245 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Oxidoreductases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.853066 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VNEGLSIFVI LVWLGLNVFL FVWYYRVYDI PPKFFYTRKL LGSALALARA PAACLNFNCM LILLPVCRNL LSFLRGSSAC CSTRVRRQL DRNLTFHKMV AWMIALHSAI HTIAHLFNVE WCVNARVNNS DPYSVALSEL GDRQNESYLN FARKRIKNPE G GLYLAVTL ...String:
VNEGLSIFVI LVWLGLNVFL FVWYYRVYDI PPKFFYTRKL LGSALALARA PAACLNFNCM LILLPVCRNL LSFLRGSSAC CSTRVRRQL DRNLTFHKMV AWMIALHSAI HTIAHLFNVE WCVNARVNNS DPYSVALSEL GDRQNESYLN FARKRIKNPE G GLYLAVTL LAGITGVVIT LCLILIITSS TKTIRRSYFE VFWYTHHLFV IFFIGLAIHG AERIVRGQTA ESLAVHNITV CE QKISEWG KIKECPIPQF AGNPPMTWKW IVGPMFLYLC ERLVRFWRSQ QKVVITKVVT HPFKTIELQM KKKGFKMEVG QYI FVKCPK VSKLEWHPFT LTSAPEEDFF SIHIRIVGDW TEGLFNACGC DKQEFQDAWK LPKIAVDGPF GTASEDVFSY EVVM LVGAG IGVTPFASIL KSVWYKYCNN ATNLKLKKIY FYWLCRDTHA FEWFADLLQL LESQMQERNN AGFLSYNIYL TGWDE SQAN HFAVHHDEEK DVITGLKQKT LYGRPNWDNE FKTIASQHPN TRIGVFLCGP EALAETLSKQ SISNSESGPR GVHFIF NKE NF

UniProtKB: Cytochrome b-245 heavy chain

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Macromolecule #3: monoclonal antibody 7G5 heavy chain

MacromoleculeName: monoclonal antibody 7G5 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 23.484305 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSLEESGGDL VKPGASLTLT CTASGIDFSG YHYMCWVRQA PGKGLEWIGC THSGDGTTYY ARWAKGRFTI SKTSSTTVTL QMTSLTAAD TATYFCARRY VFSGGYSGLD SWGPGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
QSLEESGGDL VKPGASLTLT CTASGIDFSG YHYMCWVRQA PGKGLEWIGC THSGDGTTYY ARWAKGRFTI SKTSSTTVTL QMTSLTAAD TATYFCARRY VFSGGYSGLD SWGPGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSC

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Macromolecule #4: Cytochrome b-245 chaperone 1

MacromoleculeName: Cytochrome b-245 chaperone 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.4915 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MYLQVETRTS SRLHLKRAPG IRSWSLLVGI LSIGLAAAYY SGDSLGWKLF YVTGCLFVAV QNLEDWEEAI FDKSTGKVVL KTFSLYKKL LTLFRAGHDQ VVVLLHDVRD VSVEEEKVRY FGKGYMVVLR LATGFSHPLT QSAVMGHRSD VEAIAKLITS F LELH

UniProtKB: Cytochrome b-245 chaperone 1

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Macromolecule #5: monoclonal antibody 7G5 light chain

MacromoleculeName: monoclonal antibody 7G5 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 23.521154 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ALVMTQTPSS VSAAVRGTVT IKCQASENIY SNLAWYQQKP GQPPKLLIYG ASKLASGVPS RFKGSGSGTD YTLTIRDLEA ADAATYYCQ QFYDSLNTDN AFGGGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE ...String:
ALVMTQTPSS VSAAVRGTVT IKCQASENIY SNLAWYQQKP GQPPKLLIYG ASKLASGVPS RFKGSGSGTD YTLTIRDLEA ADAATYYCQ QFYDSLNTDN AFGGGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC

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Macromolecule #7: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 7 / Number of copies: 1 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM / POPC

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Macromolecule #8: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 8 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #10: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 10 / Number of copies: 1 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM / POPC

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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: 7.4
GridMaterial: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8gz3

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131926

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