7K5J: E1-E2-ubiquitin thioester mimetic

Structure of an E1-E2-ubiquitin thioester mimetic. Determined by X-ray diffraction at 3.42 Å resolution. Released 28 Apr 2021.

Method: X-ray diffraction
Resolution: 3.42 Å
Organisms: Triticum aestivum, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 24
Atoms: 76,643
Mol. weight: 1169.49 kDa
Ligands: AMP
Released: 28 Apr 2021

Explore 7K5J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7K5J contains 534 α-helices and 495 β-strands across 24 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: 58 helices, 48 β-strands

Element	Residues	Length	Sheet
α-helix	20-34	15
β-strand	38-42	5	19
α-helix	46-58	13
β-strand	62-66	5	19
β-strand	70	1	20
α-helix	71	1
α-helix	73-77	5
α-helix	84-86	3
β-strand	90	1	20
α-helix	91-100	10
β-strand	108-110	3	19
α-helix	117-122	6
β-strand	125-128	4	19
α-helix	134-145	12
β-strand	150-155	6	19
β-strand	158	1	21
β-strand	160-166	7	19
β-strand	171-173	3	22
α-helix	179-182	4
β-strand	183-185	3	23
β-strand	186-189	4	24
β-strand	194-197	4	24
β-strand	210-217	8	23
α-helix	220-222	3
β-strand	228-229	2	23
β-strand	231-234	4	24
β-strand	237-239	3	24
β-strand	251-257	7	23
β-strand	262-264	3	22
α-helix	269-274	6
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
β-strand	358	1	21
α-helix	360-379	20
α-helix	383-385	3
β-strand	389-392	4	19
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	25
α-helix	444-456	13
β-strand	465-469	5	25
β-strand	473	1	26
α-helix	476-479	4
α-helix	487-489	3
β-strand	493	1	26
α-helix	494-505	12
α-helix	507-509	3
β-strand	513-516	4	25
α-helix	518-520	3
α-helix	522-524	3
α-helix	530-534	5
β-strand	538-541	4	25
α-helix	546-559	14
β-strand	563-569	7	25
β-strand	570	1	27
β-strand	572-578	7	25
β-strand	583	1	28
α-helix	600-604	5
α-helix	609-624	16
α-helix	626-636	11
α-helix	640-644	5
α-helix	653-661	9
α-helix	669-681	13
α-helix	682-686	5
α-helix	687-694	8
β-strand	700	1	29
β-strand	706	1	29
α-helix	717-720	4
α-helix	725-742	18
α-helix	755-763	9
α-helix	767-770	4
α-helix	799-804	6
α-helix	806-807	2
α-helix	818-821	4
α-helix	830-844	15
α-helix	847-849	3
α-helix	852-860	9
α-helix	862-864	3
β-strand	865	1	27
α-helix	867-885	19
β-strand	896-900	5	25
β-strand	905-909	5	25
α-helix	910-912	3
β-strand	913	1	28
α-helix	914-915	2
β-strand	916-919	4	30
β-strand	922-925	4	30
β-strand	930-934	5	31
β-strand	938	1	32
α-helix	939-948	10
β-strand	953-959	7	33
β-strand	962-966	5	33
α-helix	971-977	7
β-strand	981	1	32
α-helix	982-990	9
α-helix	993-995	3
β-strand	1000-1003	4	31
β-strand	1004-1008	5	33
β-strand	1014-1015	2	33
β-strand	1019-1023	5	31

Chain B: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
β-strand	29-34	6	33
β-strand	38-46	9	33
β-strand	48	1	34
β-strand	56	1	34
β-strand	60-65	6	33
α-helix	74-75	2
β-strand	76-79	4	33
β-strand	93-94	2	33
α-helix	121-133	13
α-helix	143-150	8
α-helix	153-168	16
α-helix	171-172	2

Chain C: 57 helices, 48 β-strands

Element	Residues	Length	Sheet
α-helix	20-34	15
β-strand	38-42	5	35
α-helix	46-58	13
β-strand	62-66	5	35
β-strand	70	1	36
α-helix	71	1
α-helix	73-77	5
α-helix	84-86	3
β-strand	90	1	36
α-helix	91-100	10
β-strand	108-110	3	35
α-helix	117-122	6
β-strand	125-128	4	35
α-helix	134-145	12
β-strand	150-155	6	35
β-strand	158	1	37
β-strand	160-166	7	35
β-strand	171-173	3	38
α-helix	179-182	4
β-strand	183-185	3	39
β-strand	186-189	4	40
β-strand	194-197	4	40
β-strand	210-216	7	39
α-helix	220-222	3
β-strand	228-229	2	39
β-strand	231-234	4	40
β-strand	237-239	3	40
β-strand	252-257	6	39
β-strand	262-264	3	38
α-helix	269-274	6
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
β-strand	358	1	37
α-helix	360-379	20
α-helix	383-385	3
β-strand	389-392	4	35
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	41
α-helix	444-456	13
β-strand	465-469	5	41
β-strand	473	1	42
α-helix	476-479	4
α-helix	487-489	3
β-strand	493	1	42
α-helix	494-505	12
α-helix	507-509	3
β-strand	513-516	4	41
α-helix	518-520	3
α-helix	522-524	3
α-helix	530-534	5
β-strand	538-541	4	41
α-helix	546-559	14
β-strand	563-569	7	41
β-strand	570	1	43
β-strand	572-578	7	41
β-strand	583	1	44
α-helix	601-604	4
α-helix	609-624	16
α-helix	626-636	11
α-helix	640-644	5
α-helix	652-663	12
α-helix	669-681	13
α-helix	682-686	5
α-helix	687-694	8
β-strand	700	1	45
β-strand	706	1	45
α-helix	717-720	4
α-helix	725-742	18
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	852-860	9
α-helix	862-864	3
β-strand	865	1	43
α-helix	867-885	19
β-strand	896-900	5	41
β-strand	905-909	5	41
α-helix	910-912	3
β-strand	913	1	44
α-helix	914-915	2
β-strand	916-919	4	46
β-strand	922-925	4	46
β-strand	930-934	5	47
β-strand	938	1	48
α-helix	939-948	10
β-strand	953-959	7	49
β-strand	962-966	5	49
α-helix	971-978	8
β-strand	981	1	48
α-helix	982-990	9
α-helix	993-995	3
β-strand	1000-1003	4	47
β-strand	1004-1008	5	49
β-strand	1014-1015	2	49
β-strand	1019-1023	5	47

Chain D: 59 helices, 49 β-strands

Element	Residues	Length	Sheet
α-helix	20-34	15
β-strand	38-42	5	3
α-helix	46-58	13
β-strand	62-66	5	3
α-helix	69	1
β-strand	70	1	4
α-helix	71	1
α-helix	73-77	5
α-helix	84-86	3
β-strand	90	1	4
α-helix	91-100	10
β-strand	108-110	3	3
α-helix	117-122	6
β-strand	125-128	4	3
α-helix	134-145	12
β-strand	150-157	8	3
β-strand	158	1	5
β-strand	160-166	7	3
β-strand	171-173	3	6
α-helix	179-182	4
β-strand	183-185	3	7
β-strand	186-189	4	8
β-strand	194-197	4	8
β-strand	210-214	5	7
α-helix	220-222	3
β-strand	228-229	2	7
β-strand	231-234	4	8
β-strand	237-239	3	8
β-strand	254-257	4	7
β-strand	262-264	3	6
α-helix	269-274	6
β-strand	279-280	2	3
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
β-strand	358	1	5
α-helix	360-379	20
α-helix	383-385	3
β-strand	389-392	4	3
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
β-strand	473	1	10
α-helix	476-479	4
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	570	1	11
β-strand	572-578	7	9
β-strand	583	1	12
α-helix	601-604	4
α-helix	609-624	16
α-helix	626-636	11
α-helix	640-644	5
α-helix	652-661	10
α-helix	669-681	13
α-helix	682-686	5
α-helix	687-694	8
β-strand	700	1	13
β-strand	706	1	13
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	818-821	4
α-helix	830-844	15
α-helix	847-849	3
α-helix	852-860	9
α-helix	862-864	3
β-strand	865	1	11
α-helix	867-885	19
β-strand	896-900	5	9
β-strand	905-909	5	9
α-helix	910-912	3
β-strand	913	1	12
α-helix	914-915	2
β-strand	916-919	4	14
β-strand	922-925	4	14
β-strand	930-934	5	15
β-strand	938	1	16
α-helix	939-948	10
β-strand	953-959	7	17
β-strand	962-966	5	17
α-helix	971-977	7
β-strand	981	1	16
α-helix	982-990	9
α-helix	993-995	3
β-strand	1000-1003	4	15
β-strand	1004-1008	5	17
β-strand	1014-1015	2	17
β-strand	1019-1023	5	15

Chain E: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
β-strand	29-34	6	49
β-strand	38-47	10	49
β-strand	59-65	7	49
α-helix	74-75	2
β-strand	76-79	4	49
β-strand	93	1	49
α-helix	121-133	13
α-helix	143-150	8
α-helix	153-167	15
α-helix	168-170	3

Chain F: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
β-strand	29-34	6	17
β-strand	38-46	9	17
β-strand	48	1	18
β-strand	56	1	18
β-strand	60-65	6	17
α-helix	74-75	2
β-strand	76-79	4	17
β-strand	93-94	2	17
α-helix	121-133	13
α-helix	143-150	8
α-helix	153-168	16

Chain G: 57 helices, 51 β-strands

Element	Residues	Length	Sheet
α-helix	20-34	15
β-strand	38-42	5	50
α-helix	46-58	13
β-strand	62-66	5	50
β-strand	70	1	51
α-helix	71	1
α-helix	73-77	5
α-helix	84-86	3
β-strand	90	1	51
α-helix	91-100	10
β-strand	108-110	3	50
α-helix	117-122	6
β-strand	125-128	4	50
α-helix	134-145	12
β-strand	150-155	6	50
β-strand	158	1	52
β-strand	160-166	7	50
β-strand	171-173	3	53
α-helix	179-182	4
β-strand	183-185	3	54
β-strand	186-189	4	55
β-strand	194-197	4	55
β-strand	210-214	5	54
β-strand	217	1	56
α-helix	220-222	3
β-strand	228-229	2	54
β-strand	231-234	4	55
β-strand	237-239	3	55
β-strand	251	1	56
β-strand	254-257	4	54
β-strand	262-264	3	53
α-helix	269-274	6
β-strand	279-280	2	50
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
β-strand	358	1	52
α-helix	360-379	20
α-helix	383-385	3
β-strand	389-392	4	50
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	57
α-helix	444-456	13
β-strand	465-469	5	57
β-strand	473	1	58
α-helix	476-479	4
α-helix	487-489	3
β-strand	493	1	58
α-helix	494-505	12
α-helix	507-509	3
β-strand	513-516	4	57
α-helix	518-520	3
α-helix	522-524	3
α-helix	530-534	5
β-strand	538-541	4	57
α-helix	546-559	14
β-strand	563-569	7	57
β-strand	570	1	59
β-strand	572-578	7	57
β-strand	583	1	60
α-helix	601-604	4
α-helix	609-624	16
α-helix	626-636	11
α-helix	640-644	5
α-helix	652-663	12
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	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	852-860	9
α-helix	862-864	3
β-strand	865	1	59
α-helix	867-885	19
β-strand	896-900	5	57
β-strand	905-909	5	57
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	63
β-strand	938	1	64
α-helix	939-948	10
β-strand	953-959	7	65
β-strand	962-966	5	65
α-helix	971-978	8
β-strand	981	1	64
α-helix	982-990	9
α-helix	993-995	3
β-strand	1000-1003	4	63
β-strand	1004-1008	5	65
β-strand	1014-1015	2	65
β-strand	1019-1023	5	63

Chain H: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
β-strand	29-34	6	65
β-strand	38-46	9	65
β-strand	60-65	6	65
α-helix	74-75	2
β-strand	76-79	4	65
β-strand	93-94	2	65
α-helix	121-133	13
α-helix	143-150	8
α-helix	153-167	15

16 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	M, N, O, P, Q, R, W, X	protein	83	Triticum aestivum	P69326 (AlphaFold model)
Ubiquitin-activating enzyme E1 1	A, C, D, G, I, K, S, U	protein	1017	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P22515 (AlphaFold model)
Ubiquitin-conjugating enzyme E2-34 kDa	B, E, F, H, J, L, T, V	protein	197	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P14682 (AlphaFold model)

Sequence of entity 1 (M, N, O, P, Q, R, W, X), FASTA

>7K5J_1 Ubiquitin (chains M, N, O, P, Q, R, W, X)
MHHHHHHMQIFVRTLTGRTITLEVESSDTIDNVRARIQDREGIPPDQQRLIFAGRQLEDG
RTLADYNIQRESTLHLVLRLRGG

Sequence of entity 2 (A, C, D, G, I, K, S, U), FASTA

>7K5J_2 Ubiquitin-activating enzyme E1 1 (chains A, C, D, G, I, K, S, U)
GAMAGEIDESLYSRQLYVLGKEAMLKMQTSNVLILGLKGLGVEIAKNVVLAGVKSMTVFD
PEPVQLADLSTQFFLTEKDIGQKRGDVTRAKLAELNAYVPVNVLDSLDDVTQLSQFQVVV
ATDTVSLEDKVKINEFCHSSGIRFISSETRGLFGNTFVDLGDEFTVLDPTGEEPRTGMVS
DIEPDGTVTMLDDNRHGLEDGNFVRFSEVEGLDKLNDGTLFKVEVLGPFAFRIGSVKEYG
EYKKGGIFTEVKVPRKISFKSLKQQLSNPEFVFSDFAKFDRAAQLHLGFQALHQFAVRHN
GELPRTMNDEDANELIKLVTDLSVQQPEVLGEGVDVNEDLIKELSYQARGDIPGVVAFFG
GLVAQEVLKACSGKFTPLKQFMYFDSLESLPDPKNFPRNEKTTQPVNSRYDNQIAVFGLD
FQKKIANSKVFLVGSGAIGCEMLKNWALLGLGSGSDGYIVVTDNDSIEKSNLNRQFLFRP
KDVGKNKSEVAAEAVCAMNPDLKGKINAKIDKVGPETEEIFNDSFWESLDFVTNALDNVD
ARTYVDRRCVFYRKPLLESGTLGTKGNTQVIIPRLTESYSSSRDPPEKSIPLCTLRSFPN
KIDHTIAWAKSLFQGYFTDSAENVNMYLTQPNFVEQTLKQSGDVKGVLESISDSLSSKPH
NFEDCIKWARLEFEKKFNHDIKQLLFNFPKDAKTSNGEPFWSGAKRAPTPLEFDIYNNDH
FHFVVAGASLRAYNYGIKSDDSNSKPNVDEYKSVIDHMIIPEFTPNANLKIQVNDDDPDP
NANAANGSDEIDQLVSSLPDPSTLAGFKLEPVDFEKDDDTNHHIEFITACSNCRAQNYFI
ETADRQKTKFIAGRIIPAIATTTSLVTGLVNLELYKLIDNKTDIEQYKNGFVNLALPFFG
FSEPIASPKGEYNNKKYDKIWDRFDIKGDIKLSDLIEHFEKDEGLEITMLSYGVSLLYAS
FFPPKKLKERLNLPITQLVKLVTKKDIPAHVSTMILEICADDKEGEDVEVPFITIHL

Sequence of entity 3 (B, E, F, H, J, L, T, V), FASTA

>7K5J_3 Ubiquitin-conjugating enzyme E2-34 kDa (chains B, E, F, H, J, L, T, V)
GAMASRKSTASSLLLRQYRELTDPKKAIPSFHIELEDDSNIFTWNIGVMVLNEDSIYHGG
FFKAQMRFPEDFPFSPPQFRFTPAIYHPNVYRDGRLCISILHQSGDPMTDEPDAETWSPV
QTVESVLISIVSLLEDPNINSPKNVDAAVDYRKNPEQYKQRVKMEVERSKQDIPKGFIMP
TSESAYISQSKLDEPES

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	7

Primary citation

Crystal structures of an E1-E2-ubiquitin thioester mimetic reveal molecular mechanisms of transthioesterification. Yuan, L., Lv, Z., Adams, M.J. et al. Nat Commun (2021) 12:2370-2370. DOI 10.1038/s41467-021-22598-y · PubMed

Other PDB entries of the same protein (UniProt P69326 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6NYA 2.06 Å, Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin
7SOL 2.25 Å, Crystal Structures of the bispecific ubiquitin/FAT10 activating enzyme, Uba6
5TTE 3.5 Å, Crystal Structure of an RBR E3 ubiquitin ligase in complex with an E2-Ub thioester…
8YSY Ubiquitin(native) from Oryza sativa subsp. japonica (Rice)
8YUM Ubiquitin(late folding intermediate, F') from Oryza sativa subsp. japonica (Rice)

Browse structure collections

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