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- EMDB-51295: Recombinant Myeloperoxidase bound to nucleosome core particle -

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Basic information

Entry
Database: EMDB / ID: EMD-51295
TitleRecombinant Myeloperoxidase bound to nucleosome core particle
Map dataMain map, sharpened using PHENIX
Sample
  • Complex: rMPO/nucleosome complex
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • DNA: Widom-601 DNA (145-MER)
    • DNA: Widom-601 DNA (145-MER)
    • Protein or peptide: Myeloperoxidase light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsPeroxidase / innate immunity / histone / acidic patch / IMMUNE SYSTEM
Function / homology
Function and homology information


myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / azurophil granule / response to food ...myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / azurophil granule / response to food / response to mechanical stimulus / defense response to fungus / removal of superoxide radicals / secretory granule / hydrogen peroxide catabolic process / peroxidase activity / defense response / structural constituent of chromatin / azurophil granule lumen / nucleosome / heterochromatin formation / nucleosome assembly / heparin binding / response to lipopolysaccharide / response to oxidative stress / lysosome / defense response to bacterium / protein heterodimerization activity / intracellular membrane-bounded organelle / heme binding / Neutrophil degranulation / chromatin binding / negative regulation of apoptotic process / extracellular space / DNA binding / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
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 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. ...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 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2B 1.1 / Myeloperoxidase / Histone H2A type 1 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsRaisch T / Burn GL / Tacke S / Winkler M / Prumbaum D / Thee S / Zychlinsky A / Raunser S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Myeloperoxidase transforms chromatin into Neutrophil Extracellular Traps
Authors: Burn GL / Raisch T / Tacke S / Winkler M / Prumbaum D / Thee S / Raunser S / Zychlinsky A
History
DepositionAug 7, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51295.png

Downloads & links

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Map

FileDownload / File: emd_51295.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map, sharpened using PHENIX
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 220 pix.
= 266.2 Å		1.21 Å/pix.
x 220 pix.
= 266.2 Å		1.21 Å/pix.
x 220 pix.
= 266.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-23.975118999999999 - 34.332787000000003
Average (Standard dev.)-0.000000000000036 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 266.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_51295_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_51295_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_51295_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : rMPO/nucleosome complex

EntireName: rMPO/nucleosome complex
Components
  • Complex: rMPO/nucleosome complex
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • DNA: Widom-601 DNA (145-MER)
    • DNA: Widom-601 DNA (145-MER)
    • Protein or peptide: Myeloperoxidase light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: rMPO/nucleosome complex

SupramoleculeName: rMPO/nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.631616 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQS SAVMALQEAS EAYLVALFED TNLCAIHAKR VTIMPKDIQ LARRIRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 9.99077 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KRHRKVLRDN IQGITKPAIR RLARRGGVKR ISGLIYEETR GVLKVFLENV IRDAVTYTEH AKRKTVTAMD VVYALKRQGR TLYGFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 12.183232 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVRN DEELNKLLG RVTIAQGGVL PNIQSVLLPK KT

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 10.792419 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RRKTRKESYA IYVYKVLKQV HPDTGISSKA MSIMNSFVND VFERIAGEAS RLAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKA VTKYTSA

UniProtKB: Histone H2B 1.1

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Macromolecule #7: Myeloperoxidase light chain

MacromoleculeName: Myeloperoxidase light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.823312 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: CPEQDKYRTI TGMCNNRRSP TLGASNRAFV RWLPAEYEDG FSLPYGWTPG VKRNGFPVAL ARAVSNEIVR FPTDQLTPDQ ERSLMFMQW GQLLDHDLDF TPEPAARASF VTGVNCETSC VQQPPCFPLK IPPNDPRIKN QADCIPFFRS CPACPGSNIT I RNQINALT ...String:
CPEQDKYRTI TGMCNNRRSP TLGASNRAFV RWLPAEYEDG FSLPYGWTPG VKRNGFPVAL ARAVSNEIVR FPTDQLTPDQ ERSLMFMQW GQLLDHDLDF TPEPAARASF VTGVNCETSC VQQPPCFPLK IPPNDPRIKN QADCIPFFRS CPACPGSNIT I RNQINALT SFVDASMVYG SEEPLARNLR NMSNQLGLLA VNQRFQDNGR ALLPFDNLHD DPCLLTNRSA RIPCFLAGDT RS SEMPELT SMHTLLLREH NRLATELKSL NPRWDGERLY QEARKIVGAM VQIITYRDYL PLVLGPTAMR KYLPTYRSYN DSV DPRIAN VFTNAFRYGH TLIQPFMFRL DNRYQPMEPN PRVPLSRVFF ASWRVVLEGG IDPILRGLMA TPAKLNRQNQ IAVD EIRER LFEQVMRIGL DLPALNMQRS RDHGLPGYNA WRRFCGLPQP ETVGQLGTVL RNLKLARKLM EQYGTPNNID IWMGG VSEP LKRKGRVGPL LACIIGTQFR KLRDGDRFWW ENEGVFSMQQ RQALAQISLP RIICDNTGIT TVSKNNIFMS NSYPRD FVN CSTLPALNLA SWRE

UniProtKB: Myeloperoxidase

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Macromolecule #5: Widom-601 DNA (145-MER)

MacromoleculeName: Widom-601 DNA (145-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.610043 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String:
(DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DG)(DA)(DT)

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Macromolecule #6: Widom-601 DNA (145-MER)

MacromoleculeName: Widom-601 DNA (145-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.13877 KDa
SequenceString: (DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String:
(DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DG)(DA)(DT)

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 663555
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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