8PP6 | pdb_00008pp6

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

(2024) Nat Struct Mol Biol 31: 1023-1027

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

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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 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: 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 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: 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, 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: 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... 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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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
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UniProt Group	Q8N488
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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 P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47
PHAROS: P0CG47 GTEx: ENSG00000170315
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG47
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Reference Sequence

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

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

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 M [auth K] MOL2 format, chain M [auth K] mmCIF format, chain M [auth K]	M [auth K]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth K] Interactions & Density Focus chain M [auth K]