8PP7 | pdb_00008pp7

human RYBP-PRC1 bound to mononucleosome

PDB DOI: https://doi.org/10.2210/pdb8PP7/pdb
NAKB: 8PP7
EM Map EMD-17797: EMDB EMDataResource

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

Deposited: 2023-07-06 Released: 2024-03-27
Deposition Author(s): Ciapponi, M., Benda, C., Mueller, J.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.91 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

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 31: 1023-1027

PubMed: 38528151 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-024-01258-x
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 413.74 kDa
Atom Count: 15,562
Modeled Residue Count: 1,471
Deposited Residue Count: 2,816
Unique protein chains: 6
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycomb complex protein BMI-1	A [auth K], C [auth M]	335	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35226
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RING2	B [auth L], D [auth N]	340	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99496
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3 (Fragment)	E [auth A], I [auth E]	135	Drosophila melanogaster	Mutation(s): 0 Gene Names: H3_1
UniProt
Find proteins for P02299 (Drosophila melanogaster) Explore P02299 Go to UniProtKB: P02299
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02299
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	F [auth B], J [auth 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 P84040 (Drosophila melanogaster) Explore P84040 Go to UniProtKB: P84040
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84040
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	G [auth C], K [auth G]	123	Drosophila melanogaster	Mutation(s): 0 Gene Names: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817... 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84051
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	H [auth D], L [auth H]	123	Drosophila melanogaster	Mutation(s): 0 Gene Names: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874... 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02283
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 7
DNA (215-mer)	M [auth J]	248	Homo sapiens
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 8
DNA (215-mer)	N [auth I]	248	Homo sapiens
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth K] SDF format, chain P [auth K] SDF format, chain Q [auth L] SDF format, chain R [auth L] SDF format, chain S [auth M] SDF format, chain T [auth M] SDF format, chain U [auth N] SDF format, chain V [auth N] MOL2 format, chain O [auth K] MOL2 format, chain P [auth K] MOL2 format, chain Q [auth L] MOL2 format, chain R [auth L] MOL2 format, chain S [auth M] MOL2 format, chain T [auth M] MOL2 format, chain U [auth N] MOL2 format, chain V [auth N] mmCIF format, chain O [auth K] mmCIF format, chain P [auth K] mmCIF format, chain Q [auth L] mmCIF format, chain R [auth L] mmCIF format, chain S [auth M] mmCIF format, chain T [auth M] mmCIF format, chain U [auth N] mmCIF format, chain V [auth N]	O [auth K] P [auth K] Q [auth L] R [auth L] S [auth M] O [auth K], P [auth K], Q [auth L], R [auth L], S [auth M], T [auth M], U [auth N], V [auth N]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain O [auth K] Focus chain P [auth K] Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth M] Focus chain T [auth M] Focus chain U [auth N] Focus chain V [auth N] Interactions & Density Focus chain O [auth K] Focus chain P [auth K] Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth M] Focus chain T [auth M] Focus chain U [auth N] Focus chain V [auth N]