6ZHT: Uba1-Ubc13 disulfide mediated complex

Uba1-Ubc13 disulfide mediated complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 12 Jan 2022.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 2
Atoms: 9,430
Mol. weight: 130.51 kDa
Released: 12 Jan 2022

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

Secondary structure: helices and β-sheets

6ZHT contains 68 α-helices and 57 β-strands across 2 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 B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-17	14
α-helix	19-20	2
β-strand	23-28	6	16
β-strand	31-40	10	16
α-helix	41-42	2
β-strand	50-57	8	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
β-strand	149-150	2	16
α-helix	151	1

Chain C: 60 helices, 49 β-strands

Element	Residues	Length	Sheet
α-helix	29-31	3
α-helix	33-35	3
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	91-102	12
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	180-182	3
β-strand	183-185	3	5
β-strand	186-189	4	6
β-strand	192	1	7
β-strand	195-197	3	6
β-strand	210-214	5	5
α-helix	220-223	4
β-strand	228-229	2	5
β-strand	231-234	4	6
β-strand	237-239	3	6
β-strand	242	1	7
β-strand	254-257	4	5
α-helix	259-261	3
β-strand	262-264	3	3
α-helix	269-274	6
β-strand	278	1	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	341-343	3
α-helix	345-354	10
α-helix	360-379	20
β-strand	381	1	4
β-strand	388-392	5	1
α-helix	394-396	3
α-helix	398-399	2
α-helix	418-424	7
α-helix	426-433	8
β-strand	436-440	5	8
α-helix	444-456	13
β-strand	465-469	5	8
β-strand	473	1	9
α-helix	487-489	3
β-strand	493	1	9
α-helix	494-505	12
α-helix	507-509	3
β-strand	513-516	4	8
α-helix	522-524	3
α-helix	530-535	6
β-strand	538-541	4	8
α-helix	546-558	13
β-strand	563-569	7	8
β-strand	572-578	7	8
β-strand	583	1	10
α-helix	587-589	3
α-helix	590-598	9
α-helix	599-604	6
α-helix	609-620	12
α-helix	621-626	6
α-helix	627-636	10
α-helix	640-646	7
α-helix	651-664	14
α-helix	669-681	13
α-helix	682-686	5
α-helix	687-694	8
β-strand	700	1	11
β-strand	706	1	11
α-helix	713-715	3
α-helix	725-741	17
α-helix	755-763	9
α-helix	796-804	9
α-helix	806-807	2
α-helix	808-811	4
α-helix	830-844	15
α-helix	847-849	3
α-helix	852-860	9
α-helix	867-885	19
α-helix	891-893	3
β-strand	896-900	5	8
β-strand	905-909	5	8
α-helix	910-912	3
β-strand	913	1	10
α-helix	914-915	2
β-strand	916-918	3	12
β-strand	923-925	3	12
β-strand	930-934	5	13
β-strand	938	1	14
α-helix	939-945	7
α-helix	946-950	5
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
β-strand	1000-1003	4	13
β-strand	1004-1008	5	15
β-strand	1014-1015	2	15
β-strand	1019-1023	5	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-activating enzyme E1 1	C	protein	1001	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P22515 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 13	B	protein	153	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P52490 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>6ZHT_1 Ubiquitin-activating enzyme E1 1 (chains C)
AVLGKEAMLKMQTSNVLILGLKGLGVEIAKNVVLAGVKSMTVFDPEPVQLADLSTQFFLT
EKDIGQKRGDVTRAKLAELNAYVPVNVLDSLDDVTQLSQFQVVVATDTVSLEDKVKINEF
CHSSGIRFISSETRGLFGNTFVDLGDEFTVLDPTGEEPRTGMVSDIEPDGTVTMLDDNRH
GLEDGNFVRFSEVEGLDKLNDGTLFKVEVLGPFAFRIGSVKEYGEYKKGGIFTEVKVPRK
ISFKSLKQQLSNPEFVFSDFAKFDRAAQLHLGFQALHQFAVRHNGELPRTMNDEDANELI
KLVTDLSVQQPEVLGEGVDVNEDLIKELSYQARGDIPGVVAFFGGLVAQEVLKACSGKFT
PLKQFMYFDSLESLPDPKNFPRNEKTTQPVNSRYDNQIAVFGLDFQKKIANSKVFLVGSG
AIGCEMLKNWALLGLGSGSDGYIVVTDNDSIEKSNANRQFLFRPKDVGKNKSEVAAEAVC
AMNPDLKGKINAKIDKVGPETEEIFNDSFWESLDFVTNALDNVDARTYVDRRCVFYRKPL
LESGTLGTKGNTQVIIPRLTESYSSSRDPPEKSIPLCTLRSFPNKIDHTIAWAKSLFQGY
FTDSAENVNMYLTQPNFVEQTLKQSGDVKGVLESISDSLSSKPHNFEDCIKWARLEFEKK
FNHDIKQLLFNFPKDAKTSNGEPFWSGAKRAPTPLEFDIYNNDHFHFVVAGASLRAYNYG
IKSDDSNSKPNVDEYKSVIDHMIIPEFTPNANLKIQVNDDDPDPNANAANGSDEIDQLVS
SLPDPSTLAGFKLEPVDFEKDDDTNHHIEFITACSNCRAQNYFIETADRQKTKFIAGRII
PAIATTTSLVTGLVNLELYKLIDNKTDIEQYKNGFVNLALPFFGFSEPIASPKGEYNNKK
YDKIWDRFDIKGDIKLSDLIEHFEKDEGLEITMLSYGVSLLYASFFPPKKLKERLNLPIT
QLVKLVTKKDIPAHVSTMILEICADDKEGEDVEVPFITIHL

Sequence of entity 2 (B), FASTA

>6ZHT_2 Ubiquitin-conjugating enzyme E2 13 (chains B)
GMASLPKRIIKETEKLVSDPVPGITAEPHDDNLRYFQVTIEGPEQSPYEDGIFELELYLP
DDYPMEAPKVRFLTKIYHPNIDRLGRICLDVLKTNWSPALQIRTVLLSIQALLASPNPND
PLANDVAEDWIKNEQGAKAKAREWTKLYAKKKP

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
6ZHS 2.35 Å, Uba1 bound to two E2 (Ubc13) molecules
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

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