9GEN | pdb_00009gen

Recombinant Myeloperoxidase bound to nucleosome core particle

• PDB DOI: https://doi.org/10.2210/pdb9GEN/pdb
• EM Map EMD-51295: EMDB EMDataResource
• NAKB: 9GEN

• Classification: IMMUNE SYSTEM
• Organism(s): Xenopus laevis, synthetic construct, Homo sapiens
• Expression System: Escherichia coli, Mus musculus
• Mutation(s): No 


• Deposited: 2024-08-07 Released: 2025-08-06 
• Deposition Author(s): Raisch, T., Burn, G.L., Tacke, S., Winkler, M., Prumbaum, D., Thee, S., Zychlinsky, A., Raunser, S.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.76 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Myeloperoxidase transforms chromatin into Neutrophil Extracellular Traps

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A6B2C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 246.21 kDa 
• Atom Count: 16,590 
• Modeled Residue Count: 1,623 
• Deposited Residue Count: 1,657 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	99	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233  Go to UniProtKB:  P84233

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	87	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	C, G	111	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897  Go to UniProtKB:  P06897

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	D, H	96	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloperoxidase light chain	K [auth L]	577	Homo sapiens	Mutation(s): 0  Gene Names: MPO EC: 1.11.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for P05164 (Homo sapiens) Explore P05164  Go to UniProtKB:  P05164
PHAROS:  P05164 GTEx:  ENSG00000005381
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P05164-1

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Widom-601 DNA (145-MER)	I	147	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
Widom-601 DNA (145-MER)	J	147	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	L, M [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.76 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Raisch, T., Burn, G.L., Tacke, S., Winkler, M., Prumbaum, D., Thee, S., Zychlinsky, A., Raunser, S.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release