8HCU: BCOR/PCGF1/KDM2B complex

Crystal structure of BCOR/PCGF1/KDM2B complex. Determined by X-ray diffraction at 2.2 Å resolution. Released 15 Nov 2023.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,592
Mol. weight: 55.32 kDa
Released: 15 Nov 2023

Explore 8HCU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8HCU contains 24 α-helices and 25 β-strands across 3 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: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	1104-1106	3	1
α-helix	1115-1124	10
β-strand	1128-1130	3	1
α-helix	1138-1145	8
β-strand	1153-1155	3	1
α-helix	1161-1164	4
α-helix	1165-1167	3
β-strand	1177-1179	3	1
α-helix	1188-1195	8
α-helix	1197-1198	2
β-strand	1217-1219	3	1
α-helix	1227-1236	10
β-strand	1242-1244	3	1
β-strand	1252	1	2
α-helix	1253-1259	7
α-helix	1266-1269	4
β-strand	1272-1274	3	1
β-strand	1280	1	2
α-helix	1285-1289	5
β-strand	1297-1299	3	1
α-helix	1308-1318	11
β-strand	1324-1328	5	1
β-strand	1331-1334	4	1

Chain B: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	163-165	3
β-strand	168-175	8	3
β-strand	191-195	5	3
β-strand	199	1	4
α-helix	200-211	12
β-strand	219-222	4	3
β-strand	225-226	2	3
α-helix	227-228	2
β-strand	232	1	4
α-helix	233-240	8
α-helix	244-245	2
α-helix	247	1
β-strand	248-253	6	3

Chain C: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	1637-1642	6	3
α-helix	1645-1648	4
β-strand	1650-1653	4	5
β-strand	1660-1665	6	5
α-helix	1666-1673	8
α-helix	1677-1683	7
β-strand	1689-1693	5	5
α-helix	1694-1702	9
α-helix	1705-1707	3
α-helix	1713-1715	3
β-strand	1723-1728	6	5
α-helix	1731-1736	6
β-strand	1740-1744	5	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cDNA FLJ55590, highly similar to JmjC domain-containing histone demethylation protein 1B	A	protein	235	Homo sapiens	Q8NHM5 (AlphaFold model)
Polycomb group RING finger protein 1	B	protein	105	Homo sapiens	Q9BSM1 (AlphaFold model)
BCL-6 corepressor	C	protein	142	Homo sapiens	Q6W2J9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8HCU_1 cDNA FLJ55590, highly similar to JmjC domain-containing histone demethylation protein 1B (chains A)
GTRIDLNHCKSITPLMLSGIIRRQPVSLDLSWTNISKKQLSWLINRLPGLRDLVLSGCSW
IAVSALCSSSCPLLRTLDVQWVEGLKDAQMRDLLSPPTDNRPGQMDNRSKLRNIVELRLA
GLDITDASLRLIIRHMPLLSKLHLSYCNHVTDQSINLLTAVGTTTRDSLTEINLSDCNKV
TDQCLSFFKRCGNICHIDLRYCKQVTKEGCEQFIAEMSVSVQFGQVEEKLLQKLS

Sequence of entity 2 (B), FASTA

>8HCU_2 Polycomb group RING finger protein 1 (chains B)
PFSSFDHSKAHYYRYDEQLNLCLERLSSGKDKNKSVLQNKYVRCSVRAEVRHLRRVLCHR
LMLNPQHVQLLFDNEVLPDHMTMKQIWLSRWFGKPSPLLLQYSVK

Sequence of entity 3 (C), FASTA

>8HCU_3 BCL-6 corepressor (chains C)
EPDDESGYDVLANPPGPEDQDDDDDAYSDVFEFEFSETPLLPCYNIQVSVAQGPRNWLLL
SDVLKKLKMSSRIFRCNFPNVEIVTIAEAEFYRQVSASLLFSCSKDLEAFNPESKELLDL
VEFTNEIQTLLGSSVEWLHPSD

Primary citation

Calcium modulates the tethering of BCOR-PRC1.1 enzymatic core to KDM2B via liquid-liquid phase separation. Chen, R., Shen, F., Zhang, Y. et al. Commun Biol (2024) 7:1112-1112. DOI 10.1038/s42003-024-06820-3 · PubMed

Other PDB entries of the same protein (UniProt Q8NHM5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4O64 2.13 Å, Zinc fingers of KDM2B
5JH5 2.55 Å, Structural Basis for the Hierarchical Assembly of the Core of PRC1.1
6BVA 2.66 Å, Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex.

Browse structure collections

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