2H0D: B lymphoma Mo-MLV insertion region

Structure of a Bmi-1-Ring1B Polycomb group ubiquitin ligase complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 23 May 2006.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,624
Mol. weight: 23.11 kDa
Ligands: ZN
Released: 23 May 2006

Explore 2H0D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2H0D contains 12 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	1
α-helix	9-12	4
α-helix	13-15	3
β-strand	17	1	2
β-strand	24	1	2
β-strand	29-31	3	3
β-strand	37-38	2	3
α-helix	40-46	7
β-strand	52	1	4
β-strand	59	1	4
α-helix	65-68	4
β-strand	69-71	3	3
α-helix	73-82	10
α-helix	86-100	15

Chain B: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
α-helix	21-25	5
β-strand	37-39	3	1
α-helix	47-49	3
β-strand	50	1	5
β-strand	57	1	5
β-strand	61-64	4	6
β-strand	70-72	3	6
α-helix	73-81	9
β-strand	86	1	7
β-strand	93	1	7
α-helix	97-99	3
β-strand	100-102	3	6
α-helix	104-113	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
B lymphoma Mo-MLV insertion region	A	protein	97	Homo sapiens	P35226 (AlphaFold model)
Ubiquitin ligase protein RING2	B	protein	100	Homo sapiens	Q99496 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2H0D_1 B lymphoma Mo-MLV insertion region (chains A)
TRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTR
PLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAH

Sequence of entity 2 (B), FASTA

>2H0D_2 Ubiquitin ligase protein RING2 (chains B)
KTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCAD
CIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIY

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Structure of a Bmi-1-Ring1B Polycomb Group Ubiquitin Ligase Complex. Li, Z., Cao, R., Wang, M. et al. J Biol Chem (2006) 281:20643-20649. DOI 10.1074/jbc.M602461200 · 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
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
6WI8 3.09 Å, Inhibitor compound-induced confrontational change in Ring1b-Bmi1 domain structure
9DDE 3.2 Å, ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome

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