5JH5: The Hierarchical Assembly of the Core of PRC1.1

Structural Basis for the Hierarchical Assembly of the Core of PRC1.1. Determined by X-ray diffraction at 2.55 Å resolution. Released 14 Sept 2016.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,015
Mol. weight: 78.55 kDa
Released: 14 Sept 2016

Explore 5JH5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5JH5 contains 34 α-helices and 30 β-strands across 4 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: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	1067-1074	8
α-helix	1079-1086	8
α-helix	1092-1095	4
α-helix	1099-1102	4
β-strand	1104-1106	3	1
α-helix	1115-1124	10
β-strand	1128-1130	3	1
α-helix	1138-1147	10
β-strand	1153-1155	3	1
β-strand	1160	1	2
α-helix	1161-1164	4
α-helix	1165-1168	4
β-strand	1177-1179	3	1
β-strand	1184	1	2
β-strand	1187	1	3
α-helix	1188-1195	8
β-strand	1217-1219	3	1
β-strand	1224	1	3
α-helix	1227-1236	10
β-strand	1242-1244	3	1
α-helix	1253-1259	7
α-helix	1265-1269	5
β-strand	1272-1274	3	1
α-helix	1284-1289	6
β-strand	1297-1299	3	1
α-helix	1308-1318	11
β-strand	1324-1325	2	1
β-strand	1331-1334	4	1

Chain B: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	13-17	5	4
α-helix	18-21	4
α-helix	25-33	9
β-strand	45-46	2	4
α-helix	52-64	13
α-helix	68-72	5
α-helix	87-92	6
α-helix	97-110	14
α-helix	113-125	13
α-helix	132-139	8
α-helix	147-156	10

Chain C: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	163-165	3
β-strand	168-175	8	5
β-strand	190-195	6	5
β-strand	199	1	6
α-helix	200-211	12
α-helix	215-217	3
β-strand	218-222	5	5
β-strand	225-226	2	5
α-helix	227-228	2
β-strand	232	1	6
α-helix	233-240	8
α-helix	244-245	2
α-helix	247	1
β-strand	248-254	7	5

Chain D: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	1596-1601	6	5
β-strand	1608-1611	4	7
β-strand	1620-1624	5	7
α-helix	1625-1632	8
α-helix	1636-1642	7
β-strand	1648-1652	5	7
α-helix	1653-1661	9
β-strand	1686-1691	6	7
α-helix	1694-1699	6
β-strand	1703-1707	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 2B	A	protein	281	Homo sapiens	Q8NHM5 (AlphaFold model)
S-phase kinase-associated protein 1	B	protein	162	Homo sapiens	P63208 (AlphaFold model)
Polycomb group RING finger protein 1	C	protein	109	Homo sapiens	Q9BSM1 (AlphaFold model)
BCL-6 corepressor-like protein 1	D	protein	122	Homo sapiens	Q5H9F3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5JH5_1 Lysine-specific demethylase 2B (chains A)
GTRDGAAHVMHREVWMAVFSYLSHQDLCVCMRVCRTWNRWCCDKRLWTRIDLNHCKSITP
LMLSGIIRRQPVSLDLSWTNISKKQLSWLINRLPGLRDLVLSGCSWIAVSALCSSSCPLL
RTLDVQWVEGLKDAQMRDLLSPPTDNRPGQMDNRSKLRNIVELRLAGLDITDASLRLIIR
HMPLLSKLHLSYCNHVTDQSINLLTAVGTTTRDSLTEINLSDCNKVTDQCLSFFKRCGNI
CHIDLRYCKQVTKEGCEQFIAEMSVSVQFGQVEEKLLQKLS

Sequence of entity 2 (B), FASTA

>5JH5_2 S-phase kinase-associated protein 1 (chains B)
PSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQW
CTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCK
TVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

Sequence of entity 3 (C), FASTA

>5JH5_3 Polycomb group RING finger protein 1 (chains C)
GTRLPFSSFDHSKAHYYRYDEQLNLCLERLSSGKDKNKSVLQNKYVRCSVRAEVRHLRRV
LCHRLMLNPQHVQLLFDNEVLPDHMTMKQIWLSRWFGKPSPLLLQYSVK

Sequence of entity 4 (D), FASTA

>5JH5_4 BCL-6 corepressor-like protein 1 (chains D)
METRDDFMFELSDKPLLPCYNLQVSVSRGPCNWFLFSDVLKRLKLSSRIFQARFPHFEIT
TMPKAEFYRQVASSQLLTPAERPGGLDDRSPPGSSETVELVRYEPDLLRLLGSEVEFQSC
NS

Primary citation

KDM2B Recruitment of the Polycomb Group Complex, PRC1.1, Requires Cooperation between PCGF1 and BCORL1. Wong, S.J., Gearhart, M.D., Taylor, A.B. et al. Structure (2016) 24:1795-1801. DOI 10.1016/j.str.2016.07.011 · 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
8HCU 2.2 Å, Crystal structure of BCOR/PCGF1/KDM2B complex
6BVA 2.66 Å, Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex.

Browse structure collections

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