4DDG: Human OTUB1/UbcH5b~Ub/Ub

Crystal structure of human OTUB1/UbcH5b~Ub/Ub. Determined by X-ray diffraction at 3.3 Å resolution. Released 22 Feb 2012.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 18
Atoms: 26,568
Mol. weight: 377.62 kDa
Released: 22 Feb 2012

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

Secondary structure: helices and β-sheets

4DDG contains 174 α-helices and 192 β-strands across 18 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.

Chains A, B, C, J and K: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	0-15	16
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	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	131-141	11
α-helix	142-146	5
α-helix	1025-1044	20
β-strand	1048	1	3
α-helix	1049-1051	3
β-strand	1052-1053	2	4
α-helix	1054-1056	3
α-helix	1057-1060	4
α-helix	1066-1078	13
β-strand	1081-1083	3	4
β-strand	1085	1	3
α-helix	1091-1103	13
α-helix	1108-1127	20
α-helix	1132-1150	19
α-helix	1155-1162	8
α-helix	1165-1185	21
α-helix	1187-1190	4
α-helix	1191-1193	3
α-helix	1200-1207	8
β-strand	1215	1	5
α-helix	1217-1227	11
β-strand	1232-1235	4	4
β-strand	1246-1248	3	4
β-strand	1258-1262	5	4
β-strand	1264	1	5
β-strand	1265-1270	6	4

Chains D, E, F, M, N and O: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	16
β-strand	12-16	5	16
β-strand	22	1	17
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	16
β-strand	48-49	2	16
α-helix	50-51	2
β-strand	55	1	17
β-strand	66-71	6	16
β-strand	75	1	5

Chains G, H, I, P, Q and R: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	22
β-strand	12-16	5	22
β-strand	22	1	23
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	22
β-strand	48-49	2	22
β-strand	55	1	23
α-helix	56-59	4
β-strand	66-71	6	22
α-helix	72-74	3

Chain L: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	0-15	16
β-strand	21-26	6	38
β-strand	29-38	10	38
α-helix	39-40	2
β-strand	49-55	7	38
α-helix	64-65	2
β-strand	66-69	4	38
β-strand	78	1	39
β-strand	83	1	38
β-strand	84	1	39
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-141	11
α-helix	142-146	5
α-helix	1026-1044	19
β-strand	1048	1	40
α-helix	1049-1051	3
β-strand	1052-1053	2	41
α-helix	1054-1056	3
α-helix	1057-1060	4
α-helix	1066-1078	13
β-strand	1081-1083	3	41
β-strand	1085	1	40
α-helix	1091-1103	13
α-helix	1108-1127	20
α-helix	1132-1150	19
α-helix	1155-1162	8
α-helix	1165-1185	21
α-helix	1187-1190	4
α-helix	1191-1193	3
α-helix	1200-1207	8
β-strand	1215	1	42
α-helix	1217-1227	11
β-strand	1232-1235	4	41
β-strand	1246-1248	3	41
β-strand	1258-1262	5	41
β-strand	1264	1	42
β-strand	1265-1270	6	41

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1	A, B, C, J, K, L	protein	399	Homo sapiens	P62837 (AlphaFold model), Q96FW1 (AlphaFold model)
Polyubiquitin-C	D, E, F, G, H, I, M, N, O, P, Q, R	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, B, C, J, K, L), FASTA

>4DDG_1 Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1 (chains A, B, C, J, K, L)
GAMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPT
DYPFKPPKVAFTTRIYHPNINSNGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDP
LVPEIARIYKTDREKYNRIAREWTQKYAMGGSAYDEAIMAQQDRIQQEIAVQNPLVSERL
ELSVLYKEYAEDDNIYQQKIKDLHKKYSYIRKTRPDGNSFYRAFGFSHLEALLDDSKELQ
RFKAVSAKSKEDLVSQGFTEFTIEDFHNTFMDLIEQVEKQTSVADLLASFNDQSTSDYLV
VYLRLLTSGYLQRESKFFEHFIEGGRTVKEFCQQEVEPMCKESDHIHIIALAQALSVSIQ
VEYMDRGEGGTTNPHIFPEGSEPKVYLLYRPGHYDILYK

Sequence of entity 2 (D, E, F, G, H, I, M, N, O, P, Q, R), FASTA

>4DDG_2 Polyubiquitin-C (chains D, E, F, G, H, I, M, N, O, P, Q, R)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

OTUB1 Co-opts Lys48-Linked Ubiquitin Recognition to Suppress E2 Enzyme Function. Juang, Y.C., Landry, M.C., Sanches, M. et al. Mol Cell (2012) 45:384-397. DOI 10.1016/j.molcel.2012.01.011 · PubMed

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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