7ND1: E3 ubiquitin-protein ligase RING2

First-in-class small molecule inhibitors of Polycomb Repressive Complex 1 (PRC1) RING domain. Determined by solution NMR. Released 16 Jun 2021.

Method: Solution NMR
Organism: Homo sapiens
Chains: 2
Atoms: 1,629
Mol. weight: 25.12 kDa
Ligands: U9E, ZN
Released: 16 Jun 2021

Explore 7ND1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ND1 contains 11 α-helices and 16 β-strands across 2 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
α-helix	21-25	5
β-strand	37-40	4	1
α-helix	46-49	4
β-strand	50	1	2
β-strand	57	1	2
β-strand	61-64	4	3
β-strand	70-72	3	3
α-helix	73-80	8
β-strand	86	1	4
β-strand	93	1	4
β-strand	100-102	3	3
α-helix	104-110	7

Chain H: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1005-1008	4	1
α-helix	1009-1011	3
α-helix	1013-1016	4
β-strand	1017	1	5
β-strand	1024	1	5
β-strand	1028-1031	4	6
β-strand	1036-1039	4	6
α-helix	1040-1047	8
β-strand	1052	1	7
β-strand	1059	1	7
α-helix	1065-1068	4
β-strand	1069-1071	3	6
α-helix	1073-1082	10
α-helix	1086-1100	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RING2	A	protein	112	Homo sapiens	Q99496 (AlphaFold model)
Polycomb complex protein BMI-1	H	protein	101	Homo sapiens	P35226 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7ND1_1 E3 ubiquitin-protein ligase RING2 (chains A)
GPTQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKEC
LHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPSMHR

Sequence of entity 2 (H), FASTA

>7ND1_2 Polycomb complex protein BMI-1 (chains H)
TTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT
RPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSA

Ligands and cofactors

ID	Name	Formula	Copies
U9E	3-(2-chlorophenyl)-4-ethyl-5-(1~{H}-indol-4-yl)-1~{H}-pyrrole-2-carboxylic acid	C21 H17 Cl N2 O2	1
ZN	Zinc ion	Zn	4

Primary citation

Small-molecule inhibitors targeting Polycomb repressive complex 1 RING domain. Shukla, S., Ying, W., Gray, F. et al. Nat Chem Biol (2021) 17:784-793. DOI 10.1038/s41589-021-00815-5 · PubMed

Other PDB entries of the same protein (UniProt Q99496 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3GS2 1.7 Å, Ring1B C-terminal domain/Cbx7 Cbox Complex
3IXS 1.7 Å, Ring1B C-terminal domain/RYBP C-terminal domain Complex
6WI7 1.7 Å, RING1B-BMI1 fusion in closed conformation
3H8H 2.0 Å, Structure of the C-terminal domain of human RNF2/RING1B;
4S3O 2.0 Å, PCGF5-RING1B-UbcH5c complex
2H0D 2.5 Å, Structure of a Bmi-1-Ring1B Polycomb group ubiquitin ligase complex
3RPG 2.65 Å, Bmi1/Ring1b-UbcH5c complex structure
28OE 2.74 Å, Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
9DBY 2.8 Å, ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
9V9Q 2.8 Å, Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified…
8PP7 2.91 Å, human RYBP-PRC1 bound to mononucleosome
9DGG 2.98 Å, ncPRC1RYBP bound to unmodified nucleosome

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