9DBY

ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome

• PDB DOI: https://doi.org/10.2210/pdb9DBY/pdb
• EM Map EMD-46728: EMDB EMDataResource

• Classification: GENE REGULATION/DNA
• Organism(s): Xenopus laevis, synthetic construct, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-08-24 Released: 2024-11-20 
• Deposition Author(s): Godinez-Lopez, V., Valencia-Sanchez, M.I., Armache, J.P., Armache, K.-J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), The Mark Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental

Literature

Structural visualization of read-write mechanisms of histone H2A lysine 119 mono-ubiquitination by Polycomb Repressive Complex 1

Godinez-Lopez, V., Valencia-Sanchez, M.I., Armache, J.P., Armache, K.-J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A2B2C2D2E1F1G1H1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A6B2C2D1E1 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: 333.78 kDa 
• Atom Count: 14,368 
• Modelled Residue Count: 1,377 
• Deposited Residue Count: 2,330 
• Unique protein chains: 9
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	136	Xenopus laevis	Mutation(s): 1
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	103	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	130	Xenopus laevis	Mutation(s): 1
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	126	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	G	130	Xenopus laevis	Mutation(s): 2
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897  Go to UniProtKB:  P06897

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycomb complex protein BMI-1	K	326	Homo sapiens	Mutation(s): 0  Gene Names: BMI1, PCGF4, RNF51
UniProt & NIH Common Fund Data Resources
Find proteins for P35226 (Homo sapiens) Explore P35226  Go to UniProtKB:  P35226
PHAROS:  P35226 GTEx:  ENSG00000168283

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RING2	L	336	Homo sapiens	Mutation(s): 0  Gene Names: RNF2, BAP1, DING, HIPI3, RING1B EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q99496 (Homo sapiens) Explore Q99496  Go to UniProtKB:  Q99496
PHAROS:  Q99496 GTEx:  ENSG00000121481

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
RING1 and YY1-binding protein	M	228	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: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	N	76	Homo sapiens	Mutation(s): 1  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (187-MER)	I	187	synthetic construct

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (187-MER)	J	187	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	O [auth K], P [auth K], Q [auth L], R [auth L], S [auth M]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1
RECONSTRUCTION	cryoSPARC	4.4

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Godinez-Lopez, V., Valencia-Sanchez, M.I., Armache, J.P., Armache, K.-J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM115882
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA266978
The Mark Foundation	United States	--

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release