6ZHU: Yeast Uba1

Yeast Uba1 in complex with Ubc3 and ATP. Determined by X-ray diffraction at 3.18 Å resolution. Released 12 Jan 2022.

Method: X-ray diffraction
Resolution: 3.18 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae
Chains: 8
Atoms: 37,219
Mol. weight: 596.1 kDa
Ligands: MG, ATP
Released: 12 Jan 2022

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

Secondary structure: helices and β-sheets

6ZHU contains 271 α-helices and 221 β-strands across 8 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: 63 helices, 48 β-strands

Element	Residues	Length	Sheet
α-helix	16-26	11
α-helix	28-34	7
β-strand	38-42	5	10
α-helix	46-58	13
β-strand	62-66	5	10
β-strand	70	1	11
α-helix	71	1
α-helix	74-77	4
α-helix	84-86	3
β-strand	90	1	11
α-helix	91-100	10
β-strand	108-110	3	10
α-helix	117-122	6
β-strand	125-128	4	10
α-helix	134-147	14
β-strand	150-157	8	10
β-strand	158	1	12
β-strand	160-166	7	10
β-strand	171-173	3	13
β-strand	175	1	14
α-helix	180-182	3
β-strand	183-185	3	15
β-strand	186-189	4	16
β-strand	194-197	4	16
α-helix	205-206	2
β-strand	210-214	5	15
β-strand	217	1	17
α-helix	220-223	4
β-strand	228-229	2	15
β-strand	231-232	2	16
β-strand	237-239	3	16
β-strand	251	1	17
β-strand	254-258	5	15
α-helix	259-261	3
β-strand	262-264	3	13
α-helix	269-274	6
β-strand	278	1	10
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	345-354	10
β-strand	358	1	12
α-helix	360-379	20
β-strand	381	1	14
α-helix	383-385	3
β-strand	388-392	5	10
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	18
α-helix	444-456	13
β-strand	465-469	5	18
β-strand	473	1	19
α-helix	476-480	5
α-helix	487-489	3
β-strand	493	1	19
α-helix	494-505	12
α-helix	507-509	3
β-strand	513-516	4	18
α-helix	522-524	3
α-helix	530-534	5
β-strand	538-541	4	18
α-helix	546-558	13
β-strand	563-569	7	18
β-strand	572-578	7	18
β-strand	583	1	20
α-helix	590-598	9
α-helix	599-603	5
α-helix	609-620	12
α-helix	621-626	6
α-helix	627-636	10
α-helix	640-646	7
α-helix	651-663	13
α-helix	669-681	13
α-helix	682-686	5
α-helix	687-694	8
α-helix	725-741	17
α-helix	744-746	3
α-helix	752-754	3
α-helix	755-763	9
α-helix	795-804	10
α-helix	806-807	2
α-helix	808-810	3
α-helix	830-844	15
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	18
β-strand	905-909	5	18
α-helix	910-912	3
β-strand	913	1	20
α-helix	914-915	2
β-strand	916-919	4	21
β-strand	922-925	4	21
β-strand	930-934	5	22
β-strand	938	1	23
α-helix	939-945	7
α-helix	946-950	5
β-strand	953-959	7	22
β-strand	962-966	5	22
α-helix	971-978	8
β-strand	981	1	23
α-helix	982-990	9
α-helix	993-995	3
β-strand	1000-1008	9	22
β-strand	1014-1015	2	22
β-strand	1019-1023	5	22

Chain B: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
β-strand	30-33	4	1
α-helix	34-36	3
β-strand	41-47	7	1
β-strand	59-65	7	1
α-helix	74-75	2
β-strand	76-78	3	1
β-strand	88	1	2
β-strand	93	1	1
β-strand	94	1	2
α-helix	97-99	3
α-helix	121-133	13
α-helix	144-151	8
α-helix	154-168	15

Chain C: 62 helices, 50 β-strands

Element	Residues	Length	Sheet
α-helix	16-26	11
α-helix	28-34	7
β-strand	38-42	5	37
α-helix	46-58	13
β-strand	62-66	5	37
β-strand	70	1	38
α-helix	71	1
α-helix	74-77	4
α-helix	84-86	3
β-strand	90	1	38
α-helix	91-100	10
β-strand	108-110	3	37
α-helix	117-122	6
β-strand	125-128	4	37
α-helix	134-147	14
β-strand	150-157	8	37
β-strand	158	1	39
β-strand	160-166	7	37
β-strand	171-173	3	40
β-strand	175	1	41
α-helix	179-182	4
β-strand	183-185	3	42
β-strand	186-189	4	43
β-strand	194-197	4	43
β-strand	210-214	5	42
β-strand	217	1	44
β-strand	228-229	2	42
β-strand	231-232	2	43
β-strand	237-239	3	43
β-strand	251	1	44
β-strand	254-258	5	42
α-helix	259-261	3
β-strand	262-264	3	40
α-helix	269-274	6
α-helix	276-277	2
β-strand	278-280	3	37
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	345-354	10
β-strand	358	1	39
α-helix	360-379	20
β-strand	381	1	41
α-helix	383-385	3
β-strand	388-392	5	37
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	45
α-helix	444-456	13
β-strand	465-469	5	45
β-strand	473	1	46
α-helix	476-478	3
α-helix	487-489	3
β-strand	493	1	46
α-helix	494-505	12
α-helix	507-509	3
β-strand	513-516	4	45
α-helix	522-524	3
α-helix	530-534	5
β-strand	538-541	4	45
α-helix	546-558	13
β-strand	563-569	7	45
β-strand	572-578	7	45
β-strand	583	1	47
α-helix	595-598	4
α-helix	599-603	5
α-helix	609-621	13
α-helix	622-626	5
α-helix	627-636	10
α-helix	640-646	7
α-helix	651-663	13
α-helix	669-681	13
α-helix	682-686	5
α-helix	687-694	8
β-strand	700	1	48
β-strand	706	1	48
α-helix	725-741	17
α-helix	744-746	3
α-helix	752-754	3
α-helix	755-762	8
α-helix	768-770	3
α-helix	797-804	8
α-helix	806-807	2
α-helix	808-810	3
α-helix	830-844	15
α-helix	852-860	9
α-helix	862-864	3
α-helix	867-885	19
α-helix	891-893	3
β-strand	896-900	5	45
β-strand	905-909	5	45
α-helix	910-912	3
β-strand	913	1	47
α-helix	914-915	2
β-strand	916-919	4	49
β-strand	922-925	4	49
β-strand	930-934	5	5
β-strand	938	1	50
α-helix	939-949	11
β-strand	953-959	7	5
β-strand	962-966	5	5
α-helix	971-978	8
β-strand	981	1	50
α-helix	982-990	9
α-helix	993-995	3
β-strand	1000-1008	9	5
β-strand	1014-1015	2	5
β-strand	1019-1023	5	5

Chain D: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	29-34	6	5
β-strand	38-46	9	5
β-strand	60-65	6	5
α-helix	74-75	2
β-strand	76-78	3	5
β-strand	88	1	6
β-strand	93	1	5
β-strand	94	1	6
α-helix	97-99	3
α-helix	121-133	13
α-helix	144-151	8
α-helix	154-168	15
α-helix	171-172	2
α-helix	175-177	3

Chain E: 62 helices, 47 β-strands

Element	Residues	Length	Sheet
α-helix	16-26	11
α-helix	28-34	7
β-strand	38-42	5	24
α-helix	46-58	13
β-strand	62-66	5	24
β-strand	70	1	25
α-helix	71	1
α-helix	73-77	5
α-helix	84-86	3
β-strand	90	1	25
α-helix	91-101	11
β-strand	108-110	3	24
α-helix	117-122	6
β-strand	125-128	4	24
α-helix	134-147	14
β-strand	150-157	8	24
β-strand	160-166	7	24
β-strand	171-173	3	26
β-strand	175	1	27
α-helix	179-182	4
β-strand	183-185	3	28
β-strand	186-189	4	29
β-strand	194-197	4	29
α-helix	205-206	2
β-strand	210-214	5	28
β-strand	228-229	2	28
β-strand	231-232	2	29
β-strand	237-239	3	29
β-strand	254-258	5	28
α-helix	259-261	3
β-strand	262-264	3	26
α-helix	269-274	6
β-strand	278-280	3	24
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
α-helix	360-379	20
β-strand	381	1	27
α-helix	383-385	3
β-strand	388-392	5	24
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	30
α-helix	444-456	13
β-strand	465-469	5	30
β-strand	473	1	31
α-helix	476-480	5
α-helix	487-489	3
β-strand	493	1	31
α-helix	494-505	12
α-helix	507-509	3
β-strand	513-516	4	30
α-helix	522-524	3
α-helix	530-534	5
β-strand	538-541	4	30
α-helix	546-558	13
β-strand	563-569	7	30
β-strand	572-578	7	30
β-strand	583	1	32
α-helix	591-598	8
α-helix	599-603	5
α-helix	609-621	13
α-helix	622-626	5
α-helix	627-636	10
α-helix	640-646	7
α-helix	651-663	13
α-helix	669-681	13
α-helix	682-686	5
α-helix	687-694	8
β-strand	700	1	33
β-strand	706	1	33
α-helix	725-741	17
α-helix	744-746	3
α-helix	752-754	3
α-helix	755-763	9
α-helix	796-804	9
α-helix	806-807	2
α-helix	808-810	3
α-helix	830-844	15
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	30
β-strand	905-909	5	30
α-helix	910-912	3
β-strand	913	1	32
α-helix	914-915	2
β-strand	916-919	4	34
β-strand	922-925	4	34
β-strand	930-934	5	35
β-strand	938	1	36
α-helix	939-948	10
β-strand	953-959	7	3
β-strand	962-966	5	3
α-helix	971-978	8
β-strand	981	1	36
α-helix	982-990	9
α-helix	993-995	3
β-strand	1000-1003	4	35
β-strand	1004-1008	5	3
β-strand	1014-1015	2	3
β-strand	1019-1023	5	35

Chain F: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-19	12
β-strand	29-34	6	3
β-strand	38-46	9	3
β-strand	60-65	6	3
β-strand	76-79	4	3
β-strand	88	1	4
β-strand	94	1	4
α-helix	121-133	13
α-helix	143-151	9
α-helix	154-168	15

Chain G: 59 helices, 48 β-strands

Element	Residues	Length	Sheet
α-helix	16-26	11
α-helix	28-34	7
β-strand	38-42	5	51
α-helix	46-58	13
β-strand	62-66	5	51
β-strand	70	1	52
α-helix	71	1
α-helix	74-77	4
α-helix	84-86	3
β-strand	90	1	52
α-helix	91-100	10
β-strand	108-110	3	51
α-helix	117-122	6
β-strand	125-128	4	51
α-helix	134-147	14
β-strand	150-157	8	51
β-strand	158	1	53
β-strand	160-166	7	51
β-strand	171-173	3	54
β-strand	175	1	55
α-helix	179-182	4
β-strand	183-185	3	56
β-strand	186-189	4	57
β-strand	194-197	4	57
α-helix	205-206	2
β-strand	210-214	5	56
β-strand	228-229	2	56
β-strand	231-232	2	57
β-strand	237-239	3	57
β-strand	254-258	5	56
α-helix	259-261	3
β-strand	262-264	3	54
α-helix	269-274	6
β-strand	278	1	51
α-helix	288-305	18
α-helix	309-312	4
α-helix	316-332	17
α-helix	334-336	3
α-helix	345-354	10
β-strand	358	1	53
α-helix	360-379	20
β-strand	381	1	55
α-helix	383-385	3
β-strand	388-392	5	51
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	58
α-helix	444-456	13
β-strand	465-469	5	58
β-strand	473	1	59
α-helix	476-478	3
α-helix	487-489	3
β-strand	493	1	59
α-helix	494-505	12
α-helix	507-509	3
β-strand	513-516	4	58
α-helix	522-524	3
α-helix	530-534	5
β-strand	538-541	4	58
α-helix	546-559	14
β-strand	563-569	7	58
β-strand	572-578	7	58
β-strand	583	1	60
α-helix	593-598	6
α-helix	599-603	5
α-helix	609-621	13
α-helix	622-626	5
α-helix	627-636	10
α-helix	640-646	7
α-helix	651-663	13
α-helix	669-681	13
α-helix	682-686	5
α-helix	687-694	8
β-strand	700	1	61
β-strand	706	1	61
α-helix	725-741	17
α-helix	752-754	3
α-helix	755-763	9
α-helix	798-804	7
α-helix	806-807	2
α-helix	808-810	3
α-helix	830-845	16
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	58
β-strand	905-909	5	58
α-helix	910-912	3
β-strand	913	1	60
α-helix	914-915	2
β-strand	916-919	4	62
β-strand	922-925	4	62
β-strand	930-934	5	8
β-strand	938	1	63
α-helix	939-949	11
β-strand	953-959	7	8
β-strand	962-966	5	8
α-helix	971-978	8
β-strand	981	1	63
α-helix	982-990	9
α-helix	993-995	3
β-strand	1000-1008	9	8
β-strand	1014-1015	2	8
β-strand	1019-1023	5	8

Chain H: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
β-strand	29-33	5	7
β-strand	38	1	8
β-strand	41-47	7	7
β-strand	59-65	7	7
α-helix	74-75	2
β-strand	76-78	3	7
β-strand	88	1	9
β-strand	93	1	7
β-strand	94	1	9
α-helix	97-99	3
α-helix	121-133	13
α-helix	144-151	8
α-helix	154-168	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2-34 kDa	B, D, F, H	protein	295	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P14682 (AlphaFold model)
Ubiquitin-activating enzyme E1 1	A, C, E, G	protein	1024	Saccharomyces cerevisiae	P22515 (AlphaFold model)

Sequence of entity 1 (B, D, F, H), FASTA

>6ZHU_1 Ubiquitin-conjugating enzyme E2-34 kDa (chains B, D, F, H)
MSSRKSTASSLLLRQYRELTDPKKAIPSFHIELEDDSNIFTWNIGVMVLNEDSIYHGGFF
KAQMRFPEDFPFSPPQFRFTPAIYHPNVYRDGRLCISILHQSGDPMTDEPDAETWSPVQT
VESVLISIVSLLEDPNINSPANVDAAVDYRKNPEQYKQRVKMEVERSKQDIPKGFIMPTS
ESAYISQSKLDEPESNKDMADNFWYDSDLDDDENGSVILQDDDYDDGNNHIPFEDDDVYN
YNDNDDDDERIEFEDDDDDDDDSIDNDSVMDRKQPHKAEDESEDVEDVERVSKKI

Sequence of entity 2 (A, C, E, G), FASTA

>6ZHU_2 Ubiquitin-activating enzyme E1 1 (chains A, C, E, G)
MSSNNSGLSAAGEIDESLYSRQLYVLGKEAMLKMQTSNVLILGLKGLGVEIAKNVVLAGV
KSMTVFDPEPVQLADLSTQFFLTEKDIGQKRGDVTRAKLAELNAYVPVNVLDSLDDVTQL
SQFQVVVATDTVSLEDKVKINEFCHSSGIRFISSETRGLFGNTFVDLGDEFTVLDPTGEE
PRTGMVSDIEPDGTVTMLDDNRHGLEDGNFVRFSEVEGLDKLNDGTLFKVEVLGPFAFRI
GSVKEYGEYKKGGIFTEVKVPRKISFKSLKQQLSNPEFVFSDFAKFDRAAQLHLGFQALH
QFAVRHNGELPRTMNDEDANELIKLVTDLSVQQPEVLGEGVDVNEDLIKELSYQARGDIP
GVVAFFGGLVAQEVLKACSGKFTPLKQFMYFDSLESLPDPKNFPRNEKTTQPVNSRYDNQ
IAVFGLDFQKKIANSKVFLVGSGAIGCEMLKNWALLGLGSGSDGYIVVTDNDSIEKSNLN
RQFLFRPKDVGKNKSEVAAEAVCAMNPDLKGKINAKIDKVGPETEEIFNDSFWESLDFVT
NALDNVDARTYVDRRCVFYRKPLLESGTLGTKGNTQVIIPRLTESYSSSRDPPEKSIPLC
TLRSFPNKIDHTIAWAKSLFQGYFTDSAENVNMYLTQPNFVEQTLKQSGDVKGVLESISD
SLSSKPHNFEDCIKWARLEFEKKFNHDIKQLLFNFPKDAKTSNGEPFWSGAKRAPTPLEF
DIYNNDHFHFVVAGASLRAYNYGIKSDDSNSKPNVDEYKSVIDHMIIPEFTPNANLKIQV
NDDDPDPNANAANGSDEIDQLVSSLPDPSTLAGFKLEPVDFEKDDDTNHHIEFITACSNC
RAQNYFIETADRQKTKFIAGRIIPAIATTTSLVTGLVNLELYKLIDNKTDIEQYKNGFVN
LALPFFGFSEPIASPKGEYNNKKYDKIWDRFDIKGDIKLSDLIEHFEKDEGLEITMLSYG
VSLLYASFFPPKKLKERLNLPITQLVKLVTKKDIPAHVSTMILEICADDKEGEDVEVPFI
TIHL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4

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 P14682 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6NYD 1.65 Å, Crystal Structure of S. cerevisiae Ubc3 (Cdc34)
6NYA 2.06 Å, Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin
7K5J 3.42 Å, Structure of an E1-E2-ubiquitin thioester mimetic

Browse structure collections

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