6WI8: PDB entry 6WI8

Inhibitor compound-induced confrontational change in Ring1b-Bmi1 domain structure. Determined by X-ray diffraction at 3.09 Å resolution. Released 14 Apr 2021.

Method: X-ray diffraction
Resolution: 3.09 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,166
Mol. weight: 49.17 kDa
Ligands: ZN
Released: 14 Apr 2021

Explore 6WI8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WI8 contains 22 α-helices and 33 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: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
α-helix	26-28	3
β-strand	30	1	1
β-strand	37-39	3	2
α-helix	46-49	4
β-strand	50	1	3
β-strand	57	1	3
α-helix	58	1
β-strand	61-64	4	4
β-strand	70-72	3	4
α-helix	73-81	9
β-strand	86	1	5
β-strand	93	1	5
β-strand	100-102	3	4
α-helix	104-110	7
β-strand	1006-1008	3	2
α-helix	1009-1011	3
α-helix	1013-1015	3
β-strand	1017-1018	2	1
β-strand	1023-1024	2	1
β-strand	1028-1031	4	6
β-strand	1036-1039	4	6
α-helix	1040-1046	7
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	1086-1098	13

Chain B: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	21-25	5
α-helix	26-28	3
β-strand	37-40	4	8
β-strand	50	1	9
β-strand	57	1	9
β-strand	61-64	4	10
β-strand	70-72	3	10
α-helix	73-79	7
β-strand	86	1	11
β-strand	93	1	11
β-strand	100-102	3	10
α-helix	104-110	7
β-strand	1005-1008	4	8
α-helix	1009-1011	3
α-helix	1013-1016	4
β-strand	1017	1	12
β-strand	1024	1	12
β-strand	1028-1031	4	13
β-strand	1036-1039	4	13
α-helix	1040-1046	7
β-strand	1052	1	14
β-strand	1059	1	14
α-helix	1065-1068	4
β-strand	1069-1071	3	13
α-helix	1073-1082	10
α-helix	1086-1098	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RING2,Polycomb complex protein BMI-1 chimera	A, B	protein	211	Homo sapiens	P35226 (AlphaFold model), Q99496 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6WI8_1 E3 ubiquitin-protein ligase RING2,Polycomb complex protein BMI-1 chimera (chains A, B)
TQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLH
RFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPSMHRTTRIKITELN
PHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDK
TLQDIVYKLVPGLFKNEMKRRRDFYAAHPSA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

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 P35226 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WI7 1.7 Å, RING1B-BMI1 fusion in closed conformation
2H0D 2.5 Å, Structure of a Bmi-1-Ring1B Polycomb group ubiquitin ligase complex
5FR6 2.51 Å, The structure of polycomb ULD 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
9V6S 3.0 Å, Cryo-EM structure of a single cPRC1 complex engaged on one face of an endogenous 147-bp…
8GRM 3.05 Å, Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome
9DDE 3.2 Å, ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome

Browse structure collections

About this viewer

MolViewer shows 6WI8 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.