6NYA: Ubiquitin E1

Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin. Determined by X-ray diffraction at 2.06 Å resolution. Released 7 Aug 2019.

Method: X-ray diffraction
Resolution: 2.06 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Triticum aestivum
Chains: 6
Atoms: 20,705
Mol. weight: 295.71 kDa
Ligands: ATP, MG
Released: 7 Aug 2019

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

Secondary structure: helices and β-sheets

6NYA contains 155 α-helices and 132 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: 68 helices, 51 β-strands

Element	Residues	Length	Sheet
α-helix	16-26	11
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	91-100	10
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	158	1	3
β-strand	160-166	7	1
β-strand	171-173	3	4
β-strand	175	1	5
α-helix	179-182	4
β-strand	183-185	3	6
β-strand	186-189	4	7
β-strand	194-197	4	7
β-strand	210-214	5	6
β-strand	217	1	8
α-helix	220-223	4
β-strand	228-229	2	6
β-strand	231-234	4	7
β-strand	237-239	3	7
α-helix	244-246	3
β-strand	251	1	8
β-strand	254-258	5	6
α-helix	259-261	3
β-strand	262-264	3	4
α-helix	269-274	6
β-strand	278	1	1
α-helix	283-285	3
α-helix	286-305	20
α-helix	309-312	4
α-helix	316-332	17
α-helix	334-337	4
α-helix	341-343	3
α-helix	345-353	9
β-strand	358	1	3
α-helix	360-379	20
β-strand	381	1	5
α-helix	383-385	3
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	9
α-helix	444-456	13
β-strand	465-469	5	9
α-helix	472	1
β-strand	473	1	10
α-helix	474	1
α-helix	476-480	5
α-helix	487-489	3
β-strand	493	1	10
α-helix	494-505	12
α-helix	507-509	3
β-strand	513-516	4	9
α-helix	518-520	3
α-helix	522-524	3
α-helix	530-534	5
β-strand	538-541	4	9
α-helix	546-559	14
β-strand	563-569	7	9
β-strand	572-578	7	9
β-strand	583	1	11
α-helix	586-588	3
α-helix	592-595	4
α-helix	599-603	5
α-helix	609-621	13
α-helix	622-626	5
α-helix	627-636	10
α-helix	640-645	6
α-helix	651-663	13
α-helix	669-681	13
α-helix	682-686	5
α-helix	687-694	8
β-strand	700	1	12
β-strand	706	1	12
α-helix	717-720	4
α-helix	725-741	17
α-helix	755-763	9
α-helix	767-770	4
α-helix	799-804	6
α-helix	806-807	2
α-helix	830-844	15
α-helix	847-849	3
α-helix	852-859	8
α-helix	862-864	3
α-helix	867-885	19
α-helix	891-893	3
β-strand	896-900	5	9
β-strand	905-909	5	9
α-helix	910-912	3
β-strand	913	1	11
α-helix	914-915	2
β-strand	916-919	4	13
β-strand	922-925	4	13
β-strand	930-934	5	14
β-strand	938	1	15
α-helix	939-945	7
α-helix	946-950	5
β-strand	953-959	7	16
β-strand	962-966	5	16
α-helix	971-978	8
β-strand	981	1	15
α-helix	982-990	9
α-helix	993-995	3
β-strand	1000-1003	4	14
β-strand	1004-1008	5	16
β-strand	1014-1015	2	16
β-strand	1019-1023	5	14

Chain B: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	0-7	8	17
β-strand	12-18	7	17
β-strand	22	1	18
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	17
β-strand	47	1	9
β-strand	48-49	2	17
β-strand	55	1	18
α-helix	57-59	3
β-strand	66-70	5	17
β-strand	75	1	9

Chain C: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-18	11
β-strand	29-34	6	16
β-strand	38-47	10	16
β-strand	59-65	7	16
β-strand	76-79	4	16
β-strand	88	1	19
β-strand	94	1	19
α-helix	97-99	3
α-helix	121-133	13
α-helix	145-150	6
α-helix	153-167	15
α-helix	168-170	3
α-helix	171-172	2
α-helix	175-180	6

Chain D: 65 helices, 51 β-strands

Element	Residues	Length	Sheet
α-helix	16-26	11
α-helix	28-34	7
β-strand	38-42	5	20
α-helix	46-58	13
β-strand	62-66	5	20
β-strand	70	1	21
α-helix	71	1
α-helix	73-77	5
α-helix	84-86	3
β-strand	90	1	21
α-helix	91-100	10
β-strand	108-110	3	20
α-helix	117-122	6
β-strand	125-128	4	20
α-helix	134-147	14
β-strand	150-157	8	20
β-strand	158	1	22
β-strand	160-166	7	20
β-strand	171-173	3	23
β-strand	175	1	24
α-helix	179-182	4
β-strand	183-185	3	25
β-strand	186-189	4	26
β-strand	194-197	4	26
β-strand	210-214	5	25
β-strand	217	1	27
α-helix	220-223	4
β-strand	228-229	2	25
β-strand	231-234	4	26
β-strand	237-239	3	26
α-helix	244-246	3
β-strand	251	1	27
β-strand	254-258	5	25
α-helix	259-261	3
β-strand	262-264	3	23
α-helix	269-274	6
β-strand	278	1	20
α-helix	283-285	3
α-helix	286-305	20
α-helix	309-312	4
α-helix	316-332	17
α-helix	334-337	4
α-helix	345-353	9
β-strand	358	1	22
α-helix	360-379	20
β-strand	381	1	24
α-helix	383-385	3
β-strand	388-392	5	20
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	28
α-helix	444-456	13
β-strand	465-469	5	28
α-helix	472	1
β-strand	473	1	29
α-helix	474	1
α-helix	476-480	5
α-helix	487-489	3
β-strand	493	1	29
α-helix	494-505	12
α-helix	507-509	3
β-strand	513-516	4	28
α-helix	518-520	3
α-helix	522-524	3
α-helix	530-534	5
β-strand	538-541	4	28
α-helix	546-559	14
β-strand	563-569	7	28
β-strand	572-578	7	28
β-strand	583	1	30
α-helix	586-588	3
α-helix	599-603	5
α-helix	609-621	13
α-helix	622-626	5
α-helix	627-636	10
α-helix	640-644	5
α-helix	651-663	13
α-helix	669-681	13
α-helix	682-686	5
α-helix	687-694	8
β-strand	700	1	31
β-strand	706	1	31
α-helix	725-741	17
α-helix	752-754	3
α-helix	755-763	9
α-helix	767-770	4
α-helix	799-802	4
α-helix	806-807	2
α-helix	830-844	15
α-helix	847-849	3
α-helix	852-859	8
α-helix	862-864	3
α-helix	867-885	19
α-helix	891-893	3
β-strand	896-900	5	28
β-strand	905-909	5	28
α-helix	910-912	3
β-strand	913	1	30
α-helix	914-915	2
β-strand	916-919	4	32
β-strand	922-925	4	32
β-strand	930-934	5	33
β-strand	938	1	34
α-helix	939-948	10
β-strand	953-959	7	35
β-strand	962-966	5	35
α-helix	971-977	7
β-strand	981	1	34
α-helix	982-990	9
α-helix	993-995	3
β-strand	1000-1003	4	33
β-strand	1004-1008	5	35
β-strand	1014-1015	2	35
β-strand	1019-1023	5	33

Chain E: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	36
β-strand	12-17	6	36
β-strand	22	1	37
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	36
β-strand	48-49	2	36
β-strand	55	1	37
α-helix	57-59	3
β-strand	66-70	5	36
β-strand	75	1	28

Chain F: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-18	11
β-strand	29-34	6	35
β-strand	38-46	9	35
β-strand	60-65	6	35
β-strand	76-79	4	35
β-strand	88	1	38
β-strand	93	1	35
β-strand	94	1	38
α-helix	97-99	3
α-helix	121-133	13
α-helix	143-150	8
α-helix	153-167	15
α-helix	168-170	3
α-helix	171-172	2
α-helix	175-177	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-activating enzyme E1 1	A, D	protein	1017	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P22515 (AlphaFold model)
Ubiquitin	B, E	protein	85	Triticum aestivum	P69326 (AlphaFold model)
Ubiquitin-conjugating enzyme E2-34 kDa	C, F	protein	197	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P14682 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6NYA_1 Ubiquitin-activating enzyme E1 1 (chains A, D)
GAMAGEIDESLYSRQLYVLGKEAMLKMQTSNVLILGLKGLGVEIAKNVVLAGVKSMTVFD
PEPVQLADLSTQFFLTEKDIGQKRGDVTRAKLAELNAYVPVNVLDSLDDVTQLSQFQVVV
ATDTVSLEDKVKINEFCHSSGIRFISSETRGLFGNTFVDLGDEFTVLDPTGEEPRTGMVS
DIEPDGTVTMLDDNRHGLEDGNFVRFSEVEGLDKLNDGTLFKVEVLGPFAFRIGSVKEYG
EYKKGGIFTEVKVPRKISFKSLKQQLSNPEFVFSDFAKFDRAAQLHLGFQALHQFAVRHN
GELPRTMNDEDANELIKLVTDLSVQQPEVLGEGVDVNEDLIKELSYQARGDIPGVVAFFG
GLVAQEVLKACSGKFTPLKQFMYFDSLESLPDPKNFPRNEKTTQPVNSRYDNQIAVFGLD
FQKKIANSKVFLVGSGAIGCEMLKNWALLGLGSGSDGYIVVTDNDSIEKSNLNRQFLFRP
KDVGKNKSEVAAEAVCAMNPDLKGKINAKIDKVGPETEEIFNDSFWESLDFVTNALDNVD
ARTYVDRRCVFYRKPLLESGTLGTKGNTQVIIPRLTESYSSSRDPPEKSIPLCTLRSFPN
KIDHTIAWAKSLFQGYFTDSAENVNMYLTQPNFVEQTLKQSGDVKGVLESISDSLSSKPH
NFEDCIKWARLEFEKKFNHDIKQLLFNFPKDAKTSNGEPFWSGAKRAPTPLEFDIYNNDH
FHFVVAGASLRAYNYGIKSDDSNSKPNVDEYKSVIDHMIIPEFTPNANLKIQVNDDDPDP
NANAANGSDEIDQLVSSLPDPSTLAGFKLEPVDFEKDDDTNHHIEFITACSNCRAQNYFI
ETADRQKTKFIAGRIIPAIATTTSLVTGLVNLELYKLIDNKTDIEQYKNGFVNLALPFFG
FSEPIASPKGEYNNKKYDKIWDRFDIKGDIKLSDLIEHFEKDEGLEITMLSYGVSLLYAS
FFPPKKLKERLNLPITQLVKLVTKKDIPAHVSTMILEICADDKEGEDVEVPFITIHL

Sequence of entity 2 (B, E), FASTA

>6NYA_2 Ubiquitin (chains B, E)
MHHHHHHGAMQIFVRTLTGRTITLEVESSDTIDNVRARIQDREGIPPDQQRLIFAGRQLE
DGRTLADYNIQRESTLHLVLRLRGG

Sequence of entity 3 (C, F), FASTA

>6NYA_3 Ubiquitin-conjugating enzyme E2-34 kDa (chains C, F)
GAMASRKSTASSLLLRQYRELTDPKKAIPSFHIELEDDSNIFTWNIGVMVLNEDSIYHGG
FFKAQMRFPEDFPFSPPQFRFTPAIYHPNVYRDGRLCISILHQSGDPMTDEPDAETWSPV
QTVESVLISIVSLLEDPNINSPANVDAAVDYRKNPEQYKQRVKMEVERSKQDIPKGFIMP
TSESAYISQSKLDEPES

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
MG	Magnesium ion	Mg	2

Water and common crystallization additives (SO4, EDO) are not listed.

Primary citation

Structural insights into E1 recognition and the ubiquitin-conjugating activity of the E2 enzyme Cdc34. Williams, K.M., Qie, S., Atkison, J.H. et al. Nat Commun (2019) 10:3296-3296. DOI 10.1038/s41467-019-11061-8 · PubMed

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
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
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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