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- EMDB-58198: Structure of native human leukocyte myeloperoxidase -

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Basic information

Entry
Database: EMDB / ID: EMD-58198
TitleStructure of native human leukocyte myeloperoxidase
Map dataNone
Sample
  • Complex: Myeloperoxidase
    • Protein or peptide: Myeloperoxidase light chain
    • Protein or peptide: Myeloperoxidase
  • Ligand: CHLORIDE ION
  • Ligand: CALCIUM ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsInnate immunity / neutrophils / phagocytosis / NETosis / OXIDOREDUCTASE
Function / homology
Function and homology information


Events associated with phagocytolytic activity of PMN cells / neutrophil-mediated killing of symbiont cell / myeloperoxidase / positive regulation of cholesterol import / neutrophil extracellular trap / phagocytic vesicle lumen / neutrophil-mediated killing of bacterium / cytolytic granule / response to gold nanoparticle / thiocyanate peroxidase activity ...Events associated with phagocytolytic activity of PMN cells / neutrophil-mediated killing of symbiont cell / myeloperoxidase / positive regulation of cholesterol import / neutrophil extracellular trap / phagocytic vesicle lumen / neutrophil-mediated killing of bacterium / cytolytic granule / response to gold nanoparticle / thiocyanate peroxidase activity / 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 / response to mechanical stimulus / phagocytic vesicle / nucleosome binding / secretory granule / hydrogen peroxide catabolic process / peroxidase activity / defense response / azurophil granule lumen / heparin binding / response to lipopolysaccharide / response to oxidative stress / defense response to bacterium / lysosome / chromosome / chromatin binding / heme binding / negative regulation of apoptotic process / Neutrophil degranulation / extracellular exosome / 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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.18 Å
AuthorsLeitgeb U / Pfanzagl V / Guo Y / Emde T / Borek D
Funding support Austria, 3 items
OrganizationGrant numberCountry
Austrian Science FundV1039 Austria
Austrian Science FundPAT1634524 Austria
Austrian Science FundDOC9173924 Austria
CitationJournal: Int J Biol Macromol / Year: 2026
Title: Interface N-glycans drive myeloperoxidase dimerization in vitro.
Authors: Urban Leitgeb / Yirui Guo / Tabitha Emde / Valentina Ruocco / Theodor Simak / Ela Zdenkovic / Paul G Furtmüller / Dominika Borek / William M Nauseef / Chris Oostenbrink / Vera Pfanzagl /
Abstract: Myeloperoxidase (MPO) is a highly glycosylated heme oxidoreductase that, together with lactoperoxidase (LPO) and eosinophil peroxidase (EPO), contributes to host defence through the generation of ...Myeloperoxidase (MPO) is a highly glycosylated heme oxidoreductase that, together with lactoperoxidase (LPO) and eosinophil peroxidase (EPO), contributes to host defence through the generation of (pseudo)hypohalous acids. Among the human heme peroxidases, mature MPO forms a unique covalently linked homodimer. Dimerization enhances stability and is essential for some biological functions, including chromatin disruption during neutrophil extracellular trap formation. Thus, we hypothesized that MPO dimerization must reflect a tightly regulated step in MPO biosynthesis and is driven by specific structural elements. Cross-species sequence alignment indicated that N-glycosylation motifs were evolutionarily more conserved in MPO than in monomeric EPO and LPO. We investigated the role of N-glycans in MPO dimerization using in vitro monomerized glycosylated (mMPO) and deglycosylated (mMPOdg) monomeric variants of native human MPO. Small-angle X-ray scattering, isothermal titration calorimetry and crystal structures showed that glycosylated MPO monomers had a weak but biologically relevant affinity in the millimolar range, which was lost upon deglycosylation. Furthermore, we present the first cryogenic transmission electron microscopy structure of human MPO with at least one core N-acetylglucosamine residue resolved at each N-glycosylation site. Structural analysis suggests that an extensive hydrogen bonding network of interface N-glycans at position 483 and residues of the other monomer drives MPO homodimerization. Dimerization enhances stability without affecting enzymatic activity. Together, we show that N-glycans are essential to MPO dimerization, provide important insights into the impact of interface N-glycans on biophysical and biochemical properties of MPO and discuss the implications for the biological roles of MPO in health and disease.
History
DepositionMay 20, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58198.png

Downloads & links

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Map

FileDownload / File: emd_58198.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 256 pix.
= 240.64 Å		0.94 Å/pix.
x 256 pix.
= 240.64 Å		0.94 Å/pix.
x 256 pix.
= 240.64 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0839
Minimum - Maximum-0.30558512 - 0.6782149
Average (Standard dev.)-0.0002007852 (±0.019255523)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 240.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: None

Fileemd_58198_half_map_1.map
AnnotationNone
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Half map: #1

Fileemd_58198_half_map_2.map
Projections & Slices
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Sample components

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Entire : Myeloperoxidase

EntireName: Myeloperoxidase
Components
  • Complex: Myeloperoxidase
    • Protein or peptide: Myeloperoxidase light chain
    • Protein or peptide: Myeloperoxidase
  • Ligand: CHLORIDE ION
  • Ligand: CALCIUM ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Myeloperoxidase

SupramoleculeName: Myeloperoxidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 145 KDa

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Macromolecule #1: Myeloperoxidase light chain

MacromoleculeName: Myeloperoxidase light chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.894465 KDa
SequenceString:
VTCPEQDKYR TITGMCNNRR SPTLGASNRA FVRWLPAEYE DGFSLPYGWT PGVKRNGFPV ALARAVSNEI VRFPTDQLTP DQERSLMFM QWGQLLDHDL DFTPEPAARA SFVTG

UniProtKB: Myeloperoxidase

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Macromolecule #2: Myeloperoxidase

MacromoleculeName: Myeloperoxidase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: myeloperoxidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.305266 KDa
SequenceString: VNCETSCVQQ PPCFPLKIPP NDPRIKNQAD CIPFFRSCPA CPGSNITIRN QINALTSFVD ASMVYGSEEP LARNLRNMSN QLGLLAVNQ RFQDNGRALL PFDNLHDDPC LLTNRSARIP CFLAGDTRSS EMPELTSMHT LLLREHNRLA TELKSLNPRW D GERLYQEA ...String:
VNCETSCVQQ PPCFPLKIPP NDPRIKNQAD CIPFFRSCPA CPGSNITIRN QINALTSFVD ASMVYGSEEP LARNLRNMSN QLGLLAVNQ RFQDNGRALL PFDNLHDDPC LLTNRSARIP CFLAGDTRSS EMPELTSMHT LLLREHNRLA TELKSLNPRW D GERLYQEA RKIVGAMVQI ITYRDYLPLV LGPTAMRKYL PTYRSYNDSV DPRIANVFTN AFRYGHTLIQ PFMFRLDNRY QP MEPNPRV PLSRVFFASW RVVLEGGIDP ILRGLMATPA KLNRQNQIAV DEIRERLFEQ VMRIGLDLPA LNMQRSRDHG LPG YNAWRR FCGLPQPETV GQLGTVLRNL KLARKLMEQY GTPNNIDIWM GGVSEPLKRK GRVGPLLACI IGTQFRKLRD GDRF WWENE GVFSMQQRQA LAQISLPRII CDNTGITTVS KNNIFMSNSY PRDFVNCSTL PALNLASWRE AS

UniProtKB: Myeloperoxidase

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Macromolecule #7: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #9: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 9 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

Concentration5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1002582
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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