4S3O: PCGF5-RING1B-UbcH5c complex

PCGF5-RING1B-UbcH5c complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 15 Jul 2015.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,635
Mol. weight: 88.36 kDa
Ligands: ZN
Released: 15 Jul 2015

Explore 4S3O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4S3O contains 47 α-helices and 45 β-strands across 6 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	1-15	15
α-helix	17-18	2
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	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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	13-16	4
α-helix	18-20	3
α-helix	21-24	4
α-helix	30-32	3
β-strand	37	1	5
α-helix	42-45	4
α-helix	46-49	4
β-strand	50	1	6
β-strand	57	1	6
β-strand	61-64	4	7
β-strand	70-72	3	7
α-helix	73-80	8
β-strand	86	1	8
β-strand	93	1	8
α-helix	97-99	3
β-strand	100-102	3	7
α-helix	104-113	10

Chain C: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	5
α-helix	9-12	4
α-helix	13-16	4
β-strand	17	1	12
β-strand	24	1	12
β-strand	28-31	4	13
β-strand	36-39	4	13
α-helix	40-46	7
β-strand	52	1	14
β-strand	59	1	14
α-helix	65-68	4
β-strand	69-71	3	13
α-helix	73-82	10
α-helix	86-98	13

Chain D: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1-15	15
α-helix	17-18	2
β-strand	21-26	6	3
β-strand	29-38	10	3
α-helix	39-40	2
β-strand	49-55	7	3
α-helix	64-65	2
β-strand	66-69	4	3
β-strand	75	1	4
β-strand	78	1	4
β-strand	83	1	3
β-strand	84	1	4
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain E: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	13-16	4
α-helix	18-20	3
α-helix	23-25	3
α-helix	42-45	4
α-helix	46-49	4
β-strand	50	1	9
β-strand	57	1	9
β-strand	61-64	4	10
β-strand	70-72	3	10
α-helix	73-80	8
β-strand	86	1	11
β-strand	93	1	11
α-helix	97-99	3
β-strand	100-102	3	10
α-helix	104-113	10

Chain F: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	13-16	4
β-strand	17	1	15
β-strand	24	1	15
β-strand	28-31	4	16
β-strand	36-39	4	16
α-helix	40-47	8
β-strand	52	1	17
α-helix	58	1
β-strand	59	1	17
α-helix	60	1
α-helix	65-68	4
β-strand	69-71	3	16
α-helix	73-82	10
α-helix	86-100	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D3	A, D	protein	148	Homo sapiens	P61077 (AlphaFold model)
E3 ubiquitin-protein ligase RING2	B, E	protein	118	Homo sapiens	Q99496 (AlphaFold model)
Polycomb group RING finger protein 5	C, F	protein	117	Homo sapiens	Q86SE9 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>4S3O_1 Ubiquitin-conjugating enzyme E2 D3 (chains A, D)
GSALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTD
YPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPL
VPEIARIYKTDRDKYNRISREWTQKYAM

Sequence of entity 2 (B, E), FASTA

>4S3O_2 E3 ubiquitin-protein ligase RING2 (chains B, E)
GSMSQAVQTNGTQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDML
KNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPS

Sequence of entity 3 (C, F), FASTA

>4S3O_3 Polycomb group RING finger protein 5 (chains C, F)
MATQRKHLVKDFNPYITCYICKGYLIKPTTVTECLHTFCKTCIVQHFEDSNDCPRCGNQV
HETNPLEMLRLDNTLEEIIFKLVPGLREQELERESEFWKKNKPQENGQDLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

BMI1-RING1B is an autoinhibited RING E3 ubiquitin ligase. Taherbhoy, A.M., Huang, O.W., Cochran, A.G. Nat Commun (2015) 6:7621-7621. DOI 10.1038/ncomms8621 · 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
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…
3RPG 2.65 Å, Bmi1/Ring1b-UbcH5c complex structure

Browse structure collections

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