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- EMDB-67951: Cryo-EM structure of mouse myeloperoxidase in complex with Fab fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-67951
TitleCryo-EM structure of mouse myeloperoxidase in complex with Fab fragments of antibodies mAb-A46 and mAb-B88
Map data
Sample
  • Complex: Complex of mAb-A46 Fab, mAb-B88 Fab and Myeloperoxidase
    • Complex: mAb-A46 Fab
      • Protein or peptide: mAb-A46 Fab Heavy chain
      • Protein or peptide: mAb-A46 Fab Light chain
    • Complex: mAb-B88 Fab
      • Protein or peptide: mAb-B88 Fab Heavy chain
      • Protein or peptide: mAb-B88 Fab Light chain
    • Complex: rmMyeloperoxidase
      • Protein or peptide: Myeloperoxidase light chain
      • Protein or peptide: Myeloperoxidase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsMyeloperoxidase / IMMUNE SYSTEM
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
Myeloperoxidase / Myeloperoxidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsFujii T / Irie M / Torizawa T
Funding support1 items
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 / Kato Y / Tsujimoto K / ...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, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67951.png

Downloads & links

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Map

FileDownload / File: emd_67951.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 400 pix.
= 354.8 Å		0.89 Å/pix.
x 400 pix.
= 354.8 Å		0.89 Å/pix.
x 400 pix.
= 354.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.887 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.075635 - 3.4394643
Average (Standard dev.)0.0007682938 (±0.036627427)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 354.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67951_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67951_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_67951_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Sample components

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Entire : Complex of mAb-A46 Fab, mAb-B88 Fab and Myeloperoxidase

EntireName: Complex of mAb-A46 Fab, mAb-B88 Fab and Myeloperoxidase
Components
  • Complex: Complex of mAb-A46 Fab, mAb-B88 Fab and Myeloperoxidase
    • Complex: mAb-A46 Fab
      • Protein or peptide: mAb-A46 Fab Heavy chain
      • Protein or peptide: mAb-A46 Fab Light chain
    • Complex: mAb-B88 Fab
      • Protein or peptide: mAb-B88 Fab Heavy chain
      • Protein or peptide: mAb-B88 Fab Light chain
    • Complex: rmMyeloperoxidase
      • Protein or peptide: Myeloperoxidase light chain
      • Protein or peptide: Myeloperoxidase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Complex of mAb-A46 Fab, mAb-B88 Fab and Myeloperoxidase

SupramoleculeName: Complex of mAb-A46 Fab, mAb-B88 Fab and Myeloperoxidase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: mAb-A46 Fab

SupramoleculeName: mAb-A46 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: mAb-B88 Fab

SupramoleculeName: mAb-B88 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #4: rmMyeloperoxidase

SupramoleculeName: rmMyeloperoxidase / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: mAb-A46 Fab Heavy chain

MacromoleculeName: mAb-A46 Fab Heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.219986 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQSGPE LVKPGASVKL SCKASGYTFT NYDINWVKQR PGQGLEWIGW IYPRDGSTTY NEKFKDKATL TVDTSSSTAY MELHSLTSE DSAVYFCARY QYDAYFDVWG TGTTVTVSSA KTTAPSVYPL APVCGDTTGS SVTLGCLVKG YFPEPVTLTW N SGSLSSGV ...String:
QVQLQQSGPE LVKPGASVKL SCKASGYTFT NYDINWVKQR PGQGLEWIGW IYPRDGSTTY NEKFKDKATL TVDTSSSTAY MELHSLTSE DSAVYFCARY QYDAYFDVWG TGTTVTVSSA KTTAPSVYPL APVCGDTTGS SVTLGCLVKG YFPEPVTLTW N SGSLSSGV HTFPAVLQSD LYTLSSSVTV TSSTWPSQSI TCNVAHPASS TKVDKKIEPR GPTIKP

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Macromolecule #2: mAb-A46 Fab Light chain

MacromoleculeName: mAb-A46 Fab Light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.52107 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVLTQSPSS LSASLGGKVT ITCKASQDIN KYIAWYQHKP GKGPRLLIHY TSTLQPGIPS RFSGSGSGRD YSFSISNLEP EDIAAYYCL QYDSLWTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK ...String:
DIVLTQSPSS LSASLGGKVT ITCKASQDIN KYIAWYQHKP GKGPRLLIHY TSTLQPGIPS RFSGSGSGRD YSFSISNLEP EDIAAYYCL QYDSLWTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRNEC

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Macromolecule #3: mAb-B88 Fab Heavy chain

MacromoleculeName: mAb-B88 Fab Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.99499 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLQHSGPV LVKPGASVKM SCKASGYTFT HYYMSWVKQS HGKSLEWIGV INPYNGVISY NQRFKGKATL TVDKSSSTAY MELNSLTSE DSAVYYCARG PGERYFDVWG TGTSVTVSSA KTTAPSVYPL APVCGDTTGS SVTLGCLVKG YFPEPVTLTW N SGSLSSGV ...String:
EVQLQHSGPV LVKPGASVKM SCKASGYTFT HYYMSWVKQS HGKSLEWIGV INPYNGVISY NQRFKGKATL TVDKSSSTAY MELNSLTSE DSAVYYCARG PGERYFDVWG TGTSVTVSSA KTTAPSVYPL APVCGDTTGS SVTLGCLVKG YFPEPVTLTW N SGSLSSGV HTFPAVLQSD LYTLSSSVTV TSSTWPSQSI TCNVAHPASS TKVDKKIEPR GPTIKP

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Macromolecule #4: mAb-B88 Fab Light chain

MacromoleculeName: mAb-B88 Fab Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.874383 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSHKF MSTSVGDRVS ITCKASQDVR TAVAWYQQKP GQSPKLLIYW ASTRHTGVPD RFTGSGSGTD YTLTFNSVQA EDLALYYCQ QHYSTPWTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIVMTQSHKF MSTSVGDRVS ITCKASQDVR TAVAWYQQKP GQSPKLLIYW ASTRHTGVPD RFTGSGSGTD YTLTFNSVQA EDLALYYCQ QHYSTPWTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

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Macromolecule #5: Myeloperoxidase light chain

MacromoleculeName: Myeloperoxidase light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.020673 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
VTCPPNDKYR TITGHCNNRR SPTLGASNRA FVRWLPAEYE DGVSMPFGWT PGVNRNGFKV PLARQVSNAI VRFPNDQLTK DQERALMFM QWGQFLDHDI TLTPEPATRF SFFTG

UniProtKB: Myeloperoxidase

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Macromolecule #6: Myeloperoxidase

MacromoleculeName: Myeloperoxidase / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: myeloperoxidase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 54.517637 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: LNCETSCLQQ PPCFPLKIPP NDPRIKNQKD CIPFFRSCPA CTRNNITIRN QINALTSFVD ASGVYGSEDP LARKLRNLTN QLGLLAVNT RFQDNGRALM PFDSLHDDPC LLTNRSARIP CFLAGDMRSS EMPELTSMHT LFVREHNRLA TQLKRLNPRW N GEKLYQEA ...String:
LNCETSCLQQ PPCFPLKIPP NDPRIKNQKD CIPFFRSCPA CTRNNITIRN QINALTSFVD ASGVYGSEDP LARKLRNLTN QLGLLAVNT RFQDNGRALM PFDSLHDDPC LLTNRSARIP CFLAGDMRSS EMPELTSMHT LFVREHNRLA TQLKRLNPRW N GEKLYQEA RKIVGAMVQI ITYRDYLPLV LGPAAMKKYL PQYRSYNDSV DPRIANVFTN AFRYGHTLIQ PFMFRLNNQY RP TGPNPRV PLSKVFFASW RVVLEGGIDP ILRGLMATPA KLNRQNQIVV DEIRERLFEQ VMRIGLDLPA LNMQRSRDHG LPG YNAWRR FCGLPQPSTV GELGTVLKNL ELARKLMAQY GTPNNIDIWM GGVSEPLEPN GRVGQLLACL IGTQFRKLRD GDRF WWENP GVFSKQQRQA LASISLPRII CDNTGITTVS KNNIFMSNTY PRDFVSCNTL PKLNLTSWKE THHHHHHHHH H

UniProtKB: Myeloperoxidase

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Macromolecule #7: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 7 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #9: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 7.5 / Details: 20mM HEPES/pH7.5, 200mM NaCl, 0.03% DDM
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 529894
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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