8PP6

human RYBP-PRC1 bound to H2AK118ub1 nucleosome

• PDB DOI: https://doi.org/10.2210/pdb8PP6/pdb
• EM Map EMD-17796: EMDB EMDataResource
• NAKB: 8PP6

• Classification: GENE REGULATION
• Organism(s): Drosophila melanogaster, Homo sapiens
• Expression System: Escherichia coli, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2023-07-06 Released: 2024-04-03 
• Deposition Author(s): Ciapponi, M., Benda, C., Mueller, J.
• Funding Organization(s): German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.18 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of the histone ubiquitination read-write mechanism of RYBP-PRC1.

Ciapponi, M., Karlukova, E., Schkolziger, S., Benda, C., Muller, J.

(2024) Nat Struct Mol Biol 

• PubMed: 38528151 
• DOI: https://doi.org/10.1038/s41594-024-01258-x
• Primary Citation of Related Structures:  
  8PP6, 8PP7


• PubMed Abstract: 
  

  Histone H2A monoubiquitination (H2Aub1) by the PRC1 subunit RING1B entails a positive feedback loop, mediated by the RING1B-interacting protein RYBP. We uncover that human RYBP-PRC1 binds unmodified nucleosomes via RING1B but H2Aub1-modified nucleosomes via RYBP. RYBP interactions with both ubiquitin and the nucleosome acidic patch create the high binding affinity that favors RYBP- over RING1B-directed PRC1 binding to H2Aub1-modified nucleosomes; this enables RING1B to monoubiquitinate H2A in neighboring unmodified nucleosomes.

---

Organizational Affiliation: 

Laboratory of Chromatin Biology, Max-Planck Institute of Biochemistry, Martinsried, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A6B2C1D1 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: 294.32 kDa 
• Atom Count: 13,318 
• Modelled Residue Count: 1,184 
• Deposited Residue Count: 1,771 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3 (Fragment)	A, E	135	Drosophila melanogaster	Mutation(s): 0  Gene Names: H3_1
UniProt
Find proteins for A0A7L0PXJ3 (Mesembrinibis cayennensis) Explore A0A7L0PXJ3  Go to UniProtKB:  A0A7L0PXJ3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	104	Drosophila melanogaster	Mutation(s): 0  Gene Names: His4r, BcDNA:RH52884, Dmel\CG3379, FBtr0082962, H4r, His4-88CD, His4R, CG3379, Dmel_CG3379
UniProt
Find proteins for A0A0B4KFZ9 (Drosophila melanogaster) Explore A0A0B4KFZ9  Go to UniProtKB:  A0A0B4KFZ9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	123	Drosophila melanogaster	Mutation(s): 0  Gene Names:  His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A:CG33829, CG33829, His2A:CG33832, CG33832, His2A:CG33835, CG33835, His2A:CG33838, CG33838, His2A:CG33841, CG33841, His2A:CG33844, CG33844, His2A:CG33847, CG33847, His2A:CG33850, CG33850, His2A:CG33862, CG33862, His2A:CG33865, CG33865
UniProt
Find proteins for P84051 (Drosophila melanogaster) Explore P84051  Go to UniProtKB:  P84051

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	D, H	123	Drosophila melanogaster	Mutation(s): 0  Gene Names:  His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, CG33880, His2B:CG33882, CG33882, His2B:CG33884, CG33884, His2B:CG33886, CG33886, His2B:CG33888, CG33888, His2B:CG33890, CG33890, His2B:CG33892, CG33892, His2B:CG33894, CG33894, His2B:CG33896, CG33896, His2B:CG33898, CG33898, His2B:CG33900, CG33900, His2B:CG33902, CG33902, His2B:CG33904, CG33904, His2B:CG33906, CG33906, His2B:CG33908, CG33908, His2B:CG33910, CG33910
UniProt
Find proteins for P02283 (Drosophila melanogaster) Explore P02283  Go to UniProtKB:  P02283

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
RING1 and YY1-binding protein	K	232	Homo sapiens	Mutation(s): 0  Gene Names: RYBP, DEDAF, YEAF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N488 (Homo sapiens) Explore Q8N488  Go to UniProtKB:  Q8N488
PHAROS:  Q8N488 GTEx:  ENSG00000163602

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-40S ribosomal protein S27a (Fragment)	L [auth M]	73	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A
UniProt & NIH Common Fund Data Resources
Find proteins for J3QTR3 (Homo sapiens) Explore J3QTR3  Go to UniProtKB:  J3QTR3
GTEx:  ENSG00000143947

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (215-MER)	I	248	Homo sapiens

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (215-MER)	J	248	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	M [auth K]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.18 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Ciapponi, M., Benda, C., Mueller, J.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release