9IHD | pdb_00009ihd

Nucleosome core particle bound by one molecule of DTT-reduced native monomeric myeloperoxidase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Myeloperoxidase transforms chromatin into neutrophil extracellular traps.

Burn, G.L.Raisch, T.Tacke, S.Winkler, M.Prumbaum, D.Thee, S.Gimber, N.Raunser, S.Zychlinsky, A.

(2025) Nature 647: 747-756

  • DOI: https://doi.org/10.1038/s41586-025-09523-9
  • Primary Citation of Related Structures:  
    9GEN, 9GEO, 9GEP, 9GEQ, 9GER, 9IHD, 9IHE, 9IHF

  • PubMed Abstract: 

    Neutrophils, the most abundant and biotoxic immune cells, extrude nuclear DNA into the extracellular space to maintain homeostasis. Termed neutrophil extracellular traps (NETs), these protein-modified and decondensed extracellular DNA scaffolds control infection and are involved in coagulation, autoimmunity and cancer 1,2 . Here we show how myeloperoxidase (MPO), a highly expressed neutrophil protein, disassembles nucleosomes, thereby facilitating NET formation, yet also binds stably to NETs extracellularly. We describe how the oligomeric status of MPO governs both outcomes. MPO dimers interact with nucleosomal DNA using one protomer and concurrently dock into the nucleosome acidic patch with the other protomer. As a consequence, dimeric MPO displaces DNA from the core complex, culminating in nucleosome disassembly. On the other hand, MPO monomers stably interact with the nucleosome acidic patch without making concomitant DNA contacts, explaining how monomeric MPO binds to and licences NETs to confer hypohalous acid production in the extracellular space 3 . Our data demonstrate that the binding of MPO to chromatin is governed by specific molecular interactions that transform chromatin into a non-replicative, non-encoding state that offers new biological functions in a cell-free manner. We propose that MPO is, to our knowledge, the first member of a class of proteins that convert chromatin into an immune effector.


  • Organizational Affiliation
    • Department of Cellular Microbiology, Max Planck Institute for Infection Biology, Berlin, Germany.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
99Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
87Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1
C, G
111Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H
96Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Myeloperoxidase light chainK [auth M]108Homo sapiensMutation(s): 0 
EC: 1.11.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for P05164 (Homo sapiens)
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PHAROS:  P05164
GTEx:  ENSG00000005381 
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UniProt GroupP05164
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Myeloperoxidase light chainL [auth N]466Homo sapiensMutation(s): 0 
EC: 1.11.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for P05164 (Homo sapiens)
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PHAROS:  P05164
GTEx:  ENSG00000005381 
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UniProt GroupP05164
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P05164-1
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Entity ID: 5
MoleculeChains LengthOrganismImage
Widom-601 DNA (145-MER)147synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
Widom-601 DNA (145-MER)147synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Data collection, Database references
  • Version 1.2: 2025-10-01
    Changes: Data collection, Database references
  • Version 1.3: 2025-12-03
    Changes: Data collection, Database references