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- PDB-8gz3: Structure of human phagocyte NADPH oxidase in the resting state -

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Basic information

Entry
Database: PDB / ID: 8gz3
TitleStructure of human phagocyte NADPH oxidase in the resting state
Components
  • (Cytochrome b-245 ...) x 2
  • 7D5 Fab heavy chain
  • 7D5 Fab light chain
  • Green Fluorescent Protein, Anti-Fab (kappa) nanobody[TP1170] chimera
KeywordsOXIDOREDUCTASE / NOX2 / p22 / CYBA / CYBB / TP1170 / NOX
Function / homology
Function and homology information


negative regulation of glomerular filtration by angiotensin / smooth muscle hypertrophy / superoxide-generating NADPH oxidase activity / Oxidoreductases; Acting on NADH or NADPH; With oxygen as acceptor / positive regulation of mucus secretion / hypoxia-inducible factor-1alpha signaling pathway / cellular response to L-glutamine / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of defense response to bacterium / mucus secretion ...negative regulation of glomerular filtration by angiotensin / smooth muscle hypertrophy / superoxide-generating NADPH oxidase activity / Oxidoreductases; Acting on NADH or NADPH; With oxygen as acceptor / positive regulation of mucus secretion / hypoxia-inducible factor-1alpha signaling pathway / cellular response to L-glutamine / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of defense response to bacterium / mucus secretion / NAD(P)H oxidase H2O2-forming activity / perinuclear endoplasmic reticulum / Cross-presentation of particulate exogenous antigens (phagosomes) / cytochrome complex assembly / NADPH oxidase complex / superoxide-generating NAD(P)H oxidase activity / respiratory burst / WNT5:FZD7-mediated leishmania damping / cellular response to phorbol 13-acetate 12-myristate / response to angiotensin / response to aldosterone / ROS and RNS production in phagocytes / regulation of release of sequestered calcium ion into cytosol / hydrogen peroxide biosynthetic process / superoxide anion generation / superoxide metabolic process / Detoxification of Reactive Oxygen Species / cellular response to cadmium ion / positive regulation of reactive oxygen species biosynthetic process / cellular response to angiotensin / monoatomic ion channel complex / tertiary granule membrane / cellular response to ethanol / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases Activate NADPH Oxidases / NADPH binding / specific granule membrane / positive regulation of superoxide anion generation / stress fiber / RAC1 GTPase cycle / positive regulation of endothelial cell proliferation / FAD binding / response to nutrient / positive regulation of smooth muscle cell proliferation / positive regulation of phagocytosis / secretory granule / response to interleukin-1 / establishment of localization in cell / response to activity / cellular response to glucose stimulus / cellular response to mechanical stimulus / defense response / cellular response to gamma radiation / response to nutrient levels / SH3 domain binding / positive regulation of interleukin-6 production / VEGFA-VEGFR2 Pathway / cellular response to tumor necrosis factor / phagocytic vesicle membrane / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / flavin adenine dinucleotide binding / nuclear envelope / positive regulation of cell growth / monoatomic ion transmembrane transport / response to hypoxia / electron transfer activity / endosome / apical plasma membrane / response to xenobiotic stimulus / protein heterodimerization activity / inflammatory response / innate immune response / focal adhesion / neuronal cell body / heme binding / Neutrophil degranulation / dendrite / endoplasmic reticulum membrane / membrane / metal ion binding / plasma membrane
Similarity search - Function
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 ...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 / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / 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 / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / NADPH oxidase 2 / Cytochrome b-245 light chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen, L. / Liu, R.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91957201 China
National Natural Science Foundation of China (NSFC)31821091 China
National Natural Science Foundation of China (NSFC)31870833 China
CitationJournal: Elife / Year: 2022
Title: Structure of human phagocyte NADPH oxidase in the resting state.
Authors: Rui Liu / Kangcheng Song / Jing-Xiang Wu / Xiao-Peng Geng / Liming Zheng / Xiaoyin Gao / Hailin Peng / Lei Chen /
Abstract: Phagocyte oxidase plays an essential role in the first line of host defense against pathogens. It oxidizes intracellular NADPH to reduce extracellular oxygen to produce superoxide anions that ...Phagocyte oxidase plays an essential role in the first line of host defense against pathogens. It oxidizes intracellular NADPH to reduce extracellular oxygen to produce superoxide anions that participate in pathogen killing. The resting phagocyte oxidase is a heterodimeric complex formed by two transmembrane proteins NOX2 and p22. Despite the physiological importance of this complex, its structure remains elusive. Here, we reported the cryo-EM structure of the functional human NOX2-p22 complex in nanodisc in the resting state. NOX2 shows a canonical 6-TM architecture of NOX and p22 has four transmembrane helices. M3, M4, and M5 of NOX2, and M1 and M4 helices of p22 are involved in the heterodimer formation. Dehydrogenase (DH) domain of NOX2 in the resting state is not optimally docked onto the transmembrane domain, leading to inefficient electron transfer and NADPH binding. Structural analysis suggests that the cytosolic factors might activate the NOX2-p22 complex by stabilizing the DH in a productive docked conformation.
History
DepositionSep 24, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome b-245 light chain
B: Cytochrome b-245 heavy chain
L: 7D5 Fab light chain
H: 7D5 Fab heavy chain
N: Green Fluorescent Protein, Anti-Fab (kappa) nanobody[TP1170] chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,73412
Polymers168,9265
Non-polymers3,8087
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Cytochrome b-245 ... , 2 types, 2 molecules AB

#1: Protein Cytochrome b-245 light chain / Cytochrome b(558) alpha chain / Cytochrome b558 subunit alpha / Neutrophil cytochrome b 22 kDa ...Cytochrome b(558) alpha chain / Cytochrome b558 subunit alpha / Neutrophil cytochrome b 22 kDa polypeptide / Superoxide-generating NADPH oxidase light chain subunit / p22 phagocyte B-cytochrome / p22-phox / p22phox


Mass: 21005.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYBA / Production host: Homo sapiens (human) / References: UniProt: P13498
#2: Protein Cytochrome b-245 heavy chain / CGD91-phox / Cytochrome b(558) subunit beta / Cytochrome b558 subunit beta / Heme-binding membrane ...CGD91-phox / Cytochrome b(558) subunit beta / Cytochrome b558 subunit beta / Heme-binding membrane glycoprotein gp91phox / NADPH oxidase 2 / Neutrophil cytochrome b 91 kDa polypeptide / Superoxide-generating NADPH oxidase heavy chain subunit / gp91-1 / gp91-phox / p22 phagocyte B-cytochrome


Mass: 65412.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYBB, NOX2 / Production host: Homo sapiens (human) / References: UniProt: P04839, Oxidoreductases

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Antibody , 3 types, 3 molecules LHN

#3: Antibody 7D5 Fab light chain


Mass: 17975.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fab cleaved from monoclonal antibody purchased from commercial supplier. The expression system is not known.
Source: (natural) Mus musculus (house mouse)
#4: Antibody 7D5 Fab heavy chain


Mass: 18315.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fab cleaved from monoclonal antibody purchased from commercial supplier. The expression system is not known.
Source: (natural) Mus musculus (house mouse)
#5: Antibody Green Fluorescent Protein, Anti-Fab (kappa) nanobody[TP1170] chimera


Mass: 46217.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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Sugars , 2 types, 3 molecules

#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 5 molecules

#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#10: Chemical ChemComp-LBN / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / (2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl 2-(trimethylammonio)ethyl phosphate


Mass: 760.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NADPH oxidase2 / Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 37.6 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84035 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å

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