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- PDB-21rt: Cryo-EM structure of mouse myeloperoxidase in complex with Fab fr... -

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Basic information

Entry
Database: PDB / ID: 21rt
TitleCryo-EM structure of mouse myeloperoxidase in complex with Fab fragments of antibodies mAb-A46 and mAb-B88
Components
  • Myeloperoxidase
  • Myeloperoxidase light chain
  • mAb-A46 Fab Heavy chain
  • mAb-A46 Fab Light chain
  • mAb-B88 Fab Heavy chain
  • mAb-B88 Fab Light chain
KeywordsIMMUNE SYSTEM / Myeloperoxidase
Function / homology
Function and homology information


hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / positive regulation of cholesterol import / cytolytic granule / neutrophil-mediated killing of symbiont cell / myeloperoxidase / response to yeast / thiocyanate peroxidase activity / neutrophil extracellular trap / neutrophil-mediated killing of bacterium ...hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / positive regulation of cholesterol import / cytolytic granule / neutrophil-mediated killing of symbiont cell / myeloperoxidase / response to yeast / thiocyanate peroxidase activity / neutrophil extracellular trap / neutrophil-mediated killing of bacterium / response to gold nanoparticle / respiratory burst involved in defense response / neutrophil extracellular trap formation / neutrophil-mediated killing of fungus / protein-containing complex destabilizing activity / low-density lipoprotein particle remodeling / nucleosome disassembly / azurophil granule / response to food / defense response to fungus / response to mechanical stimulus / nucleosome binding / Neutrophil degranulation / phagocytic vesicle / removal of superoxide radicals / secretory granule / hydrogen peroxide catabolic process / peroxidase activity / defense response / heparin binding / response to lipopolysaccharide / response to oxidative stress / chromosome / defense response to bacterium / lysosome / heme binding / mitochondrion / nucleoplasm / extracellular region / nucleus
Similarity search - Function
: / Lactoperoxidase-like, N-terminal domain / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myeloperoxidase / Myeloperoxidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsFujii, T. / Irie, M. / Torizawa, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Exp.Med. / Year: 2026
Title: Epitope-diverse autoantibodies induce neutrophil-epithelial niches driving kidney injury in ANCA-associated glomerulonephritis
Authors: Nishide, M. / Matsushita, H. / Mizuno, Y. / Nishimura, K. / Lelliott, P. / Kawada, S. / Fujii, T. / Kamikawaji, S. / Nonaka, T. / Motooka, D. / Metsugi, S. / Shimagami, H. / Miyamoto, A. / ...Authors: Nishide, M. / Matsushita, H. / Mizuno, Y. / Nishimura, K. / Lelliott, P. / Kawada, S. / Fujii, T. / Kamikawaji, S. / Nonaka, T. / Motooka, D. / Metsugi, S. / Shimagami, H. / Miyamoto, A. / Kato, Y. / Tsujimoto, K. / Edahiro, R. / Shirai, Y. / Yamamoto, Y. / Naito, Y. / Konaka, H. / Izumi, M. / Naito, M. / Nakanishi, Y. / Namba, T. / Inoue, K. / Takahashi, A. / Mizui, M. / Nakazawa, S. / Kakuta, Y. / Funakoshi, K. / Terada, M. / Irie, M. / Torizawa, T. / Omiya, R. / Smith, N. / Isaka, Y. / Nonomura, N. / Okada, Y. / Hattori, K. / Narazaki, M. / Kumanogoh, A.
History
DepositionDec 23, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mAb-A46 Fab Heavy chain
B: mAb-A46 Fab Light chain
C: mAb-B88 Fab Heavy chain
D: mAb-B88 Fab Light chain
E: Myeloperoxidase light chain
F: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,24810
Polymers163,1496
Non-polymers1,0994
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules EF

#5: Protein Myeloperoxidase light chain


Mass: 13020.673 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mpo / Cell line (production host): NS0 / Production host: Mus musculus (house mouse) / References: UniProt: P11247
#6: Protein Myeloperoxidase


Mass: 54517.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mpo / Cell line (production host): NS0 / Production host: Mus musculus (house mouse) / References: UniProt: Q6RFG4, myeloperoxidase

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Antibody , 4 types, 4 molecules ABCD

#1: Antibody mAb-A46 Fab Heavy chain


Mass: 24219.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody mAb-A46 Fab Light chain


Mass: 23521.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Antibody mAb-B88 Fab Heavy chain


Mass: 23994.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#4: Antibody mAb-B88 Fab Light chain


Mass: 23874.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)

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Sugars , 1 types, 2 molecules

#8: 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 , 2 types, 2 molecules

#7: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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

Component
IDNameTypeEntity IDParent-IDSource
1Complex of mAb-A46 Fab, mAb-B88 Fab and MyeloperoxidaseCOMPLEX#1-#60MULTIPLE SOURCES
2mAb-A46 FabCOMPLEX#1-#21RECOMBINANT
3mAb-B88 FabCOMPLEX#3-#41RECOMBINANT
4rmMyeloperoxidaseCOMPLEX#5-#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Mus musculus (house mouse)10090
43Mus musculus (house mouse)10090
54Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Homo sapiens (human)9606
43Homo sapiens (human)9606
54Mus musculus (house mouse)10090
Buffer solutionpH: 7.5 / Details: 20mM HEPES/pH7.5, 200mM NaCl, 0.03% DDM
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 529894 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 28.88 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00368126
ELECTRON MICROSCOPYf_angle_d0.574611043
ELECTRON MICROSCOPYf_chiral_restr0.04361186
ELECTRON MICROSCOPYf_plane_restr0.00421435
ELECTRON MICROSCOPYf_dihedral_angle_d16.73723053

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