9GEQ | pdb_00009geq

Native dimeric Myeloperoxidase bound to nucleosome core particle; composite map

PDB DOI: https://doi.org/10.2210/pdb9GEQ/pdb
EM Map EMD-51301: EMDB EMDataResource
NAKB: 9GEQ

Classification: IMMUNE SYSTEM
Organism(s): Xenopus laevis, synthetic construct, Homo sapiens
Expression System: Escherichia coli
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

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.12 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 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., Raunser, S., Zychlinsky, A.

To be published.

Macromolecule Content

Total Structure Weight: 315.43 kDa
Atom Count: 20,888
Modeled Residue Count: 2,163
Deposited Residue Count: 2,228
Unique protein chains: 6
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84233
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62799
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06897
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02281
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloperoxidase light chain	K [auth M], M [auth K]	108	Homo sapiens	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05164
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloperoxidase light chain	L [auth N], N [auth L]	466	Homo sapiens	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05164
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain L [auth N] Focus chain N [auth L]	Go to GlyGen: P05164-1
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Widom-601 DNA (133-MER)	I	147	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Length	Organism	Image
Widom-601 DNA (133-MER)	J	147	synthetic construct
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	O, P	6		N-Glycosylation	Interactions Focus chain O Focus chain P Interactions & Density Focus chain O Focus chain P
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain R [auth M] SDF format, chain W [auth K] MOL2 format, chain R [auth M] MOL2 format, chain W [auth K] mmCIF format, chain R [auth M] mmCIF format, chain W [auth K]	R [auth M], W [auth K]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain R [auth M] Focus chain W [auth K] Interactions & Density Focus chain R [auth M] Focus chain W [auth K]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain S [auth N] SDF format, chain T [auth N] SDF format, chain X [auth L] SDF format, chain Y [auth L] MOL2 format, chain S [auth N] MOL2 format, chain T [auth N] MOL2 format, chain X [auth L] MOL2 format, chain Y [auth L] mmCIF format, chain S [auth N] mmCIF format, chain T [auth N] mmCIF format, chain X [auth L] mmCIF format, chain Y [auth L]	S [auth N], T [auth N], X [auth L], Y [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain S [auth N] Focus chain T [auth N] Focus chain X [auth L] Focus chain Y [auth L] Interactions & Density Focus chain S [auth N] Focus chain T [auth N] Focus chain X [auth L] Focus chain Y [auth L]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain U [auth N] SDF format, chain Z [auth L] MOL2 format, chain U [auth N] MOL2 format, chain Z [auth L] mmCIF format, chain U [auth N] mmCIF format, chain Z [auth L]	U [auth N], Z [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain U [auth N] Focus chain Z [auth L] Interactions & Density Focus chain U [auth N] Focus chain Z [auth L]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Q [auth M] SDF format, chain V [auth K] MOL2 format, chain Q [auth M] MOL2 format, chain V [auth K] mmCIF format, chain Q [auth M] mmCIF format, chain V [auth K]	Q [auth M], V [auth K]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Q [auth M] Focus chain V [auth K] Interactions & Density Focus chain Q [auth M] Focus chain V [auth K]