5ULH: RNF165

Structure of RNF165 in complex with a UbcH5b~Ub conjugate. Determined by X-ray diffraction at 1.95 Å resolution. Released 7 Jun 2017.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,289
Mol. weight: 36.45 kDa
Ligands: SCN, ZN
Released: 7 Jun 2017

Explore 5ULH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ULH contains 14 α-helices and 21 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	21-26	6	1
β-strand	29-38	10	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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	3
β-strand	48-49	2	3
α-helix	50-51	2
β-strand	55	1	4
α-helix	57-59	3
β-strand	66-71	6	3

Chain C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	292	1
β-strand	293	1	5
α-helix	294	1
β-strand	300	1	5
β-strand	307-309	3	6
β-strand	315-317	3	6
α-helix	318-325	8
β-strand	330	1	7
β-strand	337	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D2	A	protein	152	Homo sapiens	P62837 (AlphaFold model)
Ubiquitin	B	protein	76	Homo sapiens	P0CG47 (AlphaFold model)
E3 ubiquitin-protein ligase RNF165	C	protein	92	Homo sapiens	Q6ZSG1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5ULH_1 Ubiquitin-conjugating enzyme E2 D2 (chains A)
GPLGSMALKRIHKELNDLARDPPAQSSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIH
FPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSISSLLSDPNP
DDPLVPEIARIYKTDREKYNRIAREWTQKYAM

Sequence of entity 2 (B), FASTA

>5ULH_2 Ubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (C), FASTA

>5ULH_3 E3 ubiquitin-protein ligase RNF165 (chains C)
GPLGSGAVQNTIERFTFPHKYKKGKGKKDEGEESDTDEKCTICLSMLEDGEDVRRLPCAH
LFHQLCVDQWLAMSKKCPICRVDIETQLGADS

Ligands and cofactors

ID	Name	Formula	Copies
SCN	Thiocyanate ion	C N S	2
ZN	Zinc ion	Zn	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Discovery of new non-covalent ubiquitin binding sites on UbcH5. Middleton, A.J., Wright, J.D., Day, C.L. To be published.

Other PDB entries of the same protein (UniProt P62837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GLS 1.25 Å, Crystal Structure of Human UBCH5B C85E
2ESK 1.36 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type
6SQO 1.41 Å, Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub
2ESQ 1.44 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly
2ESO 1.5 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala
2ESP 1.52 Å, Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala
4V3L 1.53 Å, RNF38-UB-UbcH5B-Ub complex
7AI0 1.56 Å, Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal…
5D1M 1.58 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)
3L1Y 1.6 Å, Crystal structure of human UBC4 E2 conjugating enzyme
5D1L 1.62 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A)
6HPR 1.7 Å, Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub

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