9DDE: NcPRC1RYBP

ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome. Determined by electron microscopy at 3.2 Å resolution. Released 20 Nov 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Xenopus laevis, synthetic construct, Homo sapiens
Chains: 15
Atoms: 15,394
Mol. weight: 355.68 kDa
Ligands: ZN
Released: 20 Nov 2024

Explore 9DDE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DDE contains 57 α-helices and 50 β-strands across 13 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chains B and F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-93	11
β-strand	97-98	2	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	47-72	26
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6
β-strand	101-102	2	6
α-helix	113-115	3

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	102-119	18

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-55	11
α-helix	64-76	13
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	46-72	27
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	3
α-helix	113-115	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	10
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	102-120	19

Chain K: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	11
α-helix	9-12	4
α-helix	13-15	3
β-strand	17	1	12
β-strand	24	1	12
β-strand	28-31	4	13
β-strand	36-39	4	13
α-helix	40-47	8
β-strand	52	1	14
β-strand	59	1	14
α-helix	65-68	4
β-strand	69-71	3	13
α-helix	73-82	10
α-helix	86-98	13

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.2	A, E	protein	136	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A type 1	C, G	protein	130	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B 1.1	D, H	protein	126	Xenopus laevis	P02281 (AlphaFold model)
DNA (187-mer)	I	DNA	187	synthetic construct
DNA (187-mer)	J	DNA	187	synthetic construct
Polycomb complex protein BMI-1	K	protein	326	Homo sapiens	P35226
E3 ubiquitin-protein ligase RING2	L	protein	336	Homo sapiens	Q99496
RING1 and YY1-binding protein	M	protein	228	Homo sapiens	Q8N488
Ubiquitin	N	protein	76	Homo sapiens	P0CG48
Histone H1.4	O	protein	219	Homo sapiens	P10412

Sequence of entity 1 (A, E), FASTA

>9DDE_1 Histone H3.2 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9DDE_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9DDE_3 Histone H2A type 1 (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPCK
TESAKSAKSK

Sequence of entity 4 (D, H), FASTA

>9DDE_4 Histone H2B 1.1 (chains D, H)
MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 5 (I), FASTA

>9DDE_5 DNA (187-MER) (chains I)
ATCGCGACACCGGCACTGGAACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGGATCGGGCATC
ACCCGAT

Sequence of entity 6 (J), FASTA

>9DDE_6 DNA (187-MER) (chains J)
ATCGGGTGATGCCCGATCCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAG
ACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGG
GGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTTCCAGTGCCGGTG
TCGCGAT

Sequence of entity 7 (K), FASTA

>9DDE_7 Polycomb complex protein BMI-1 (chains K)
MHRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQV
HKTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADE
DKRIITDDEIISLSIEFFDQNRLDRKVNKDKEKSKEEVNDKRYLRCPAAMTVMHLRKFLR
SKMDIPNTFQIDVMYEEEPLKDYYTLMDIAYIYTWRRNGPLPLKYRVRPTCKRMKISHQR
DGLTNAGELESDSGSDKANSPAGGIPSTSSCLPSPSTPVQSPHPQFPHISSTMNGTSNSP
SGNHQSSFANRPRKSSVNGSSATSSG

Sequence of entity 8 (L), FASTA

>9DDE_8 E3 ubiquitin-protein ligase RING2 (chains L)
MSQAVQTNGTQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKN
TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPSRDEY
EAHQERVLARINKHNNQQALSHSIEEGLKIQAMNRLQRGKKQQIENGSGAEDNGDSSHCS
NASTHSNQEAGPSNKRTKTSDDSGLELDNNNAAMAIDPVMDGASEIELVFRPHPTLMEKD
DSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIATASG
QFTVLNGSFSLELVSEKYWKVNKPMELYYAPTKEHK

Sequence of entity 9 (M), FASTA

>9DDE_9 RING1 and YY1-binding protein (chains M)
MTMGDKKSPTRPKRQAKPAADEGFWDCSVCTFRNSAEAFKCSICDVRKGTSTRKPRINSQ
LVAQQVAQQYATPPPPKKEKKEKVEKQDKEKPEKDKEISPSVTKKNTNKKTKPKSDILKD
PPSEANSIQSANATTKTSETNHTSRPRLKNVDRSTAQQLAVTVGNVTVIITDFKEKTRSS
STSSSTVTSSAGSEQQNQSSSGSESTDKGSSRSSTPKGDMSAVNDESF

Sequence of entity 10 (N), FASTA

>9DDE_10 Ubiquitin (chains N)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC

Sequence of entity 11 (O), FASTA

>9DDE_11 Histone H1.4 (chains O)
MSETAPAAPAAPAPAEKTPVKKKARKSAGAAKRKASGPPVSELITKAVAASKERSGVSLA
ALKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEAKPKA
KKAGAAKAKKPAGAAKKPKKATGAATPKKSAKKTPKKAKKPAAAAGAKKAKSPKKAKAAK
PKKAPKSPAKAKAVKPKAAKPKTAKPKAAKPKKAAAKKK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	5

Primary citation

Read-write mechanisms of H2A ubiquitination by Polycomb repressive complex 1. Lopez, V.G., Valencia-Sanchez, M.I., Abini-Agbomson, S. et al. Nature (2024) 636:755-761. DOI 10.1038/s41586-024-08183-5 · PubMed

Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome

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