3RPG: Bmi1/Ring1b-UbcH5c complex structure

Name: PDB 3RPG: Bmi1/Ring1b-UbcH5c complex structure
Published: 2011-08-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Bmi1/Ring1b-UbcH5c complex structure. Determined by X-ray diffraction at 2.65 Å resolution. Released 17 Aug 2011.

Method: X-ray diffraction
Resolution: 2.65 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,912
Mol. weight: 44.26 kDa
Ligands: ZN
Released: 17 Aug 2011

Explore 3RPG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3RPG contains 18 α-helices and 24 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1-15	15
β-strand	21-25	5	1
β-strand	32-38	7	1
α-helix	39-40	2
β-strand	49-55	7	1
α-helix	64-65	2
β-strand	66-69	4	1
β-strand	75	1	2
β-strand	78	1	2
β-strand	83	1	1
β-strand	84	1	2
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain B: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	3
α-helix	9-16	8
β-strand	17	1	4
β-strand	24	1	4
β-strand	29-31	3	5
β-strand	37-38	2	5
α-helix	40-46	7
β-strand	52	1	6
β-strand	59	1	6
α-helix	65-68	4
β-strand	69-71	3	5
α-helix	73-82	10
α-helix	86-99	14

Chain C: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
α-helix	30-32	3
β-strand	37-40	4	3
α-helix	46-49	4
β-strand	50	1	7
β-strand	57	1	7
β-strand	61-64	4	8
β-strand	70-72	3	8
α-helix	73-81	9
β-strand	86	1	9
β-strand	93	1	9
α-helix	97-99	3
β-strand	100-102	3	8
α-helix	104-113	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D3	A	protein	149	Homo sapiens	P61077 (AlphaFold model)
Polycomb complex protein BMI-1	B	protein	117	Homo sapiens	P35226 (AlphaFold model)
E3 ubiquitin-protein ligase RING2	C	protein	121	Homo sapiens	Q99496 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3RPG_1 Ubiquitin-conjugating enzyme E2 D3 (chains A)
LGSALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPT
DYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDP
LVPEIARIYKTDRDKYNRISREWTQKYAM

Sequence of entity 2 (B), FASTA

>3RPG_2 Polycomb complex protein BMI-1 (chains B)
MHRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQV
HKTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGLEHHHHHH

Sequence of entity 3 (C), FASTA

>3RPG_3 E3 ubiquitin-protein ligase RING2 (chains C)
GPLGSMSQAVQTNGTQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICL
DMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYP
S

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Recognition of UbcH5c and the nucleosome by the Bmi1/Ring1b ubiquitin ligase complex. Bentley, M.L., Corn, J.E., Dong, K.C. et al. EMBO J (2011) 30:3285-3297. DOI 10.1038/emboj.2011.243 · PubMed

Other PDB entries of the same protein (UniProt P61077 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EGG 1.76 Å, Crystal structure of human ubiquitin-conjugating enzyme UBCH5C
1X23 1.85 Å, Crystal structure of ubch5c
4S3O 2.0 Å, PCGF5-RING1B-UbcH5c complex
8UQA 2.05 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker
5IFR 2.2 Å, Structure of the stable UBE2D3-UbDha conjugate
8UQ9 2.3 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker
8UQ8 2.34 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker
3UGB 2.35 Å, UbcH5c~Ubiquitin Conjugate
8AMS 2.4 Å, Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin
8UQB 2.48 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker…
6T7F 2.58 Å, RCR E3 ligase E2-Ubiquitin transthiolation intermediate
8UQC 2.61 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker…

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