6ZHS: Uba1

Uba1 bound to two E2 (Ubc13) molecules. Determined by X-ray diffraction at 2.35 Å resolution. Released 12 Jan 2022.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 3
Atoms: 10,686
Mol. weight: 150.23 kDa
Released: 12 Jan 2022

Explore 6ZHS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZHS contains 76 α-helices and 64 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: 61 helices, 49 β-strands

Element	Residues	Length	Sheet
α-helix	20-23	4
α-helix	28-34	7
β-strand	38-42	5	1
α-helix	46-58	13
β-strand	62-66	5	1
β-strand	70	1	2
α-helix	71	1
α-helix	73-77	5
α-helix	84-86	3
β-strand	90	1	2
α-helix	91-99	9
β-strand	108-110	3	1
α-helix	117-122	6
β-strand	125-128	4	1
α-helix	134-147	14
β-strand	150-157	8	1
β-strand	160-166	7	1
β-strand	171-173	3	3
β-strand	175	1	4
α-helix	179-182	4
β-strand	183-185	3	5
β-strand	186-189	4	6
β-strand	194-197	4	6
α-helix	198-200	3
β-strand	210-214	5	5
α-helix	220-223	4
β-strand	228-229	2	5
β-strand	231-232	2	6
β-strand	237-239	3	6
α-helix	244-246	3
β-strand	254-258	5	5
β-strand	262-264	3	3
α-helix	269-274	6
β-strand	278-279	2	1
α-helix	280	1
α-helix	283-285	3
α-helix	288-305	18
α-helix	309-312	4
α-helix	316-332	17
α-helix	334-337	4
α-helix	345-353	9
α-helix	360-379	20
β-strand	381	1	4
α-helix	383-385	3
β-strand	388-392	5	1
α-helix	394-396	3
α-helix	418-424	7
α-helix	426-433	8
β-strand	436-440	5	7
α-helix	444-456	13
β-strand	465-469	5	7
β-strand	473	1	8
α-helix	476-480	5
α-helix	487-489	3
β-strand	493	1	8
α-helix	494-505	12
α-helix	507-509	3
β-strand	513-516	4	7
α-helix	522-524	3
α-helix	530-535	6
β-strand	538-541	4	7
α-helix	546-559	14
β-strand	563-569	7	7
β-strand	570	1	9
β-strand	572-578	7	7
β-strand	583	1	10
α-helix	594-598	5
α-helix	599-603	5
α-helix	609-621	13
α-helix	622-626	5
α-helix	627-634	8
α-helix	640-647	8
α-helix	651-663	13
α-helix	669-680	12
α-helix	681-686	6
α-helix	687-694	8
β-strand	700	1	11
β-strand	706	1	11
α-helix	717-720	4
α-helix	725-742	18
α-helix	755-763	9
α-helix	768-770	3
α-helix	796-803	8
α-helix	808-810	3
α-helix	826-828	3
α-helix	830-844	15
α-helix	852-859	8
β-strand	865	1	9
α-helix	867-885	19
α-helix	891-893	3
β-strand	896-900	5	7
β-strand	905-909	5	7
α-helix	910-912	3
β-strand	913	1	10
α-helix	914-915	2
β-strand	916-919	4	12
β-strand	922-925	4	12
β-strand	931-934	4	13
β-strand	938	1	14
α-helix	939-950	12
β-strand	953-959	7	15
β-strand	962-966	5	15
α-helix	971-978	8
β-strand	981	1	14
α-helix	982-990	9
α-helix	993-995	3
β-strand	1000-1003	4	13
β-strand	1004-1008	5	15
β-strand	1014-1015	2	15
β-strand	1020-1023	4	13

Chain B: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-17	14
α-helix	19-20	2
β-strand	23-27	5	16
β-strand	34-40	7	16
α-helix	41-42	2
β-strand	51-57	7	16
α-helix	66-67	2
β-strand	68-71	4	16
β-strand	77	1	17
β-strand	80	1	17
β-strand	86	1	17
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15

Chain C: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-17	15
α-helix	19-20	2
β-strand	23-27	5	18
β-strand	34-40	7	18
α-helix	41-42	2
β-strand	51-57	7	18
α-helix	66-67	2
β-strand	68-71	4	18
β-strand	77	1	19
β-strand	80	1	19
β-strand	86	1	19
α-helix	101-113	13
α-helix	125-131	7
α-helix	133-147	15
β-strand	149	1	18
α-helix	150	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-activating enzyme E1 1	A	protein	1024	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P22515 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 13	B, C	protein	154	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P52490 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6ZHS_1 Ubiquitin-activating enzyme E1 1 (chains A)
MSSNNSGLSAAGEIDESLYSRQLYVLGKEAMLKMQTSNVLILGLKGLGVEIAKNVVLAGV
KSMTVFDPEPVQLADLSTQFFLTEKDIGQKRGDVTRAKLAELNAYVPVNVLDSLDDVTQL
SQFQVVVATDTVSLEDKVKINEFCHSSGIRFISSETRGLFGNTFVDLGDEFTVLDPTGEE
PRTGMVSDIEPDGTVTMLDDNRHGLEDGNFVRFSEVEGLDKLNDGTLFKVEVLGPFAFRI
GSVKEYGEYKKGGIFTEVKVPRKISFKSLKQQLSNPEFVFSDFAKFDRAAQLHLGFQALH
QFAVRHNGELPRTMNDEDANELIKLVTDLSVQQPEVLGEGVDVNEDLIKELSYQARGDIP
GVVAFFGGLVAQEVLKACSGKFTPLKQFMYFDSLESLPDPKNFPRNEKTTQPVNSRYDNQ
IAVFGLDFQKKIANSKVFLVGSGAIGCEMLKNWALLGLGSGSDGYIVVTDNDSIEKSNLN
RQFLFRPKDVGKNKSEVAAEAVCAMNPDLKGKINAKIDKVGPETEEIFNDSFWESLDFVT
NALDNVDARTYVDRRCVFYRKPLLESGTLGTKGNTQVIIPRLTESYSSSRDPPEKSIPLC
TLRSFPNKIDHTIAWAKSLFQGYFTDSAENVNMYLTQPNFVEQTLKQSGDVKGVLESISD
SLSSKPHNFEDCIKWARLEFEKKFNHDIKQLLFNFPKDAKTSNGEPFWSGAKRAPTPLEF
DIYNNDHFHFVVAGASLRAYNYGIKSDDSNSKPNVDEYKSVIDHMIIPEFTPNANLKIQV
NDDDPDPNANAANGSDEIDQLVSSLPDPSTLAGFKLEPVDFEKDDDTNHHIEFITACSNC
RAQNYFIETADRQKTKFIAGRIIPAIATTTSLVTGLVNLELYKLIDNKTDIEQYKNGFVN
LALPFFGFSEPIASPKGEYNNKKYDKIWDRFDIKGDIKLSDLIEHFEKDEGLEITMLSYG
VSLLYASFFPPKKLKERLNLPITQLVKLVTKKDIPAHVSTMILEICADDKEGEDVEVPFI
TIHL

Sequence of entity 2 (B, C), FASTA

>6ZHS_2 Ubiquitin-conjugating enzyme E2 13 (chains B, C)
GMASLPKRIIKETEKLVSDPVPGITAEPHDDNLRYFQVTIEGPEQSPYEDGIFELELYLP
DDYPMEAPKVRFLTKIYHPNIDRLGRICLDVLKTNWSPALQIRTVLLSIQALLASPNPND
PLANDVAEDWIKNEQGAKAKAREWTKLYAKKKPE

Primary citation

ATP induced conformational changes facilitate E1-E2 disulfide bridging in the ubiquitin system. Misra, M., Schaefer, A., Kuhn, M. et al. To be published.

Other PDB entries of the same protein (UniProt P22515 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ZH9 1.72 Å, Uba1 in complex with ATP
6ZQH 2.03 Å, Yeast Uba1 in complex with ubiquitin
6NYA 2.06 Å, Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin
5TR4 2.2 Å, Structure of Ubiquitin activating enzyme (Uba1) in complex with ubiquitin and TAK-243
5L6H 2.3 Å, Uba1 in complex with Ub-ABPA3 covalent adduct
6ZHT 2.3 Å, Uba1-Ubc13 disulfide mediated complex
4NNJ 2.4 Å, Crystal structure of Uba1 in complex with ubiquitin-AMP and thioesterified ubiquitin
5L6J 2.68 Å, Uba1 in complex with Ub-MLN7243 covalent adduct
3CMM 2.7 Å, Crystal Structure of the Uba1-Ubiquitin Complex
5L6I 2.76 Å, Uba1 in complex with Ub-MLN4924 covalent adduct
6ZHU 3.18 Å, Yeast Uba1 in complex with Ubc3 and ATP
7K5J 3.42 Å, Structure of an E1-E2-ubiquitin thioester mimetic

Browse structure collections

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