8SE9: Ubiquitin-like modifier-activating enzyme 7

Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex (Form 2). Determined by electron microscopy at 3.2 Å resolution. Released 11 Oct 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,195
Mol. weight: 164.14 kDa
Ligands: AMP
Released: 11 Oct 2023

Explore 8SE9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SE9 contains 75 α-helices and 77 β-strands across 4 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, 54 β-strands

Element	Residues	Length	Sheet
α-helix	25-30	6
β-strand	34	1	1
β-strand	35-38	4	2
α-helix	42-54	13
β-strand	58	1	1
β-strand	61-62	2	2
β-strand	66	1	3
α-helix	67	1
α-helix	69-71	3
α-helix	80-82	3
β-strand	86	1	3
α-helix	87-98	12
β-strand	106	1	2
α-helix	113-118	6
β-strand	121-124	4	2
α-helix	129-141	13
β-strand	145-147	3	2
β-strand	150-152	3	4
β-strand	153	1	5
β-strand	155-157	3	4
β-strand	158	1	6
β-strand	160-161	2	2
β-strand	166-168	3	7
β-strand	170	1	8
α-helix	175-177	3
β-strand	178-180	3	9
β-strand	181-183	3	10
β-strand	191-192	2	11
β-strand	193-194	2	10
α-helix	198-202	5
β-strand	208-210	3	9
β-strand	226-227	2	9
β-strand	229-230	2	11
β-strand	236-237	2	11
β-strand	252-256	5	9
α-helix	257-259	3
β-strand	260-262	3	7
α-helix	267-270	4
β-strand	276	1	12
α-helix	281-304	24
α-helix	307-309	3
α-helix	313-325	13
α-helix	328-330	3
α-helix	343-351	9
β-strand	356	1	5
α-helix	358-377	20
β-strand	379	1	8
α-helix	381-383	3
β-strand	386	1	12
β-strand	387	1	6
β-strand	390	1	4
α-helix	392-394	3
α-helix	396-397	2
α-helix	402-404	3
α-helix	416-419	4
α-helix	424-431	8
β-strand	434	1	13
β-strand	437-438	2	14
α-helix	442-454	13
β-strand	463	1	13
β-strand	464-467	4	14
β-strand	471	1	15
α-helix	477-479	3
α-helix	485-487	3
β-strand	491	1	15
α-helix	492-503	12
β-strand	509-512	4	14
α-helix	518-520	3
α-helix	526-529	4
β-strand	535-537	3	14
α-helix	542-555	14
β-strand	559-565	7	14
β-strand	568-574	7	14
α-helix	580-582	3
α-helix	586-592	7
α-helix	598-600	3
α-helix	608-623	16
α-helix	625-628	4
α-helix	629-633	5
α-helix	634-636	3
α-helix	645-652	8
α-helix	671-678	8
α-helix	679-683	5
α-helix	684-691	8
α-helix	714-716	3
α-helix	723-739	17
α-helix	751-755	5
α-helix	761-764	4
α-helix	765-769	5
α-helix	783-797	15
α-helix	806-808	3
α-helix	817-831	15
α-helix	835-837	3
α-helix	839-843	5
α-helix	849-852	4
α-helix	854-873	20
α-helix	878-880	3
β-strand	883-887	5	14
α-helix	888-890	3
β-strand	892-896	5	14
α-helix	897-901	5
β-strand	904-906	3	16
β-strand	909-911	3	16
β-strand	917-920	4	17
α-helix	926	1
β-strand	927	1	18
α-helix	928-938	11
β-strand	943-948	6	19
β-strand	951-955	5	19
α-helix	960-966	7
β-strand	970	1	18
α-helix	971-979	9
α-helix	982-984	3
β-strand	989-992	4	17
β-strand	993-996	4	19
α-helix	1005-1007	3
β-strand	1008-1011	4	17

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	82	1	20
β-strand	85-87	3	21
β-strand	93-95	3	21
β-strand	98	1	20
β-strand	103	1	22
α-helix	104-115	12
β-strand	122-126	5	21
β-strand	129-130	2	21
β-strand	136	1	22
α-helix	137-140	4
α-helix	142-143	2
β-strand	147-152	6	21
α-helix	153-154	2

Chain C: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-16	14
β-strand	22-26	5	23
β-strand	34-39	6	23
α-helix	46-48	3
β-strand	50	1	24
β-strand	51-56	6	23
α-helix	65-66	2
β-strand	67-70	4	23
β-strand	79	1	25
β-strand	84	1	23
β-strand	85	1	25
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15
β-strand	149	1	24

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	85-86	2	26
α-helix	104-115	12
β-strand	122-125	4	27
β-strand	130	1	27
α-helix	137-140	4
β-strand	147-148	2	26
β-strand	149-152	4	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme 7	A	protein	1012	Homo sapiens	P41226 (AlphaFold model)
Ubiquitin-like protein ISG15	B, D	protein	157	Homo sapiens	P05161 (AlphaFold model)
Ubiquitin/ISG15-conjugating enzyme E2 L6	C	protein	152	Homo sapiens	O14933 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8SE9_1 Ubiquitin-like modifier-activating enzyme 7 (chains A)
MDALDASKLLDEELYSRQLYVLGSPAMQRIQGARVLVSGLQGLGAEVAKNLVLMGVGSLT
LHDPHPTCWSDLAAQFLLSEQDLERSRAEASQELLAQLNRAVQVVVHTGDITEDLLLDFQ
VVVLTAAKLEEQLKVGTLCHKHGVCFLAADTRGLVGQLFCDFGEDFTVQDPTEAEPLTAA
IQHISQGSPGILTLRKGANTHYFRDGDLVTFSGIEGMVELNDCDPRSIHVREDGSLEIGD
TTTFSRYLRGGAITEVKRPKTVRHKSLDTALLQPHVVAQSSQEVHHAHCLHQAFCALHKF
QHLHGRPPQPWDPVDAETVVGLARDLEPLKRTEEEPLEEPLDEALVRTVALSSAGVLSPM
VAMLGAVAAQEVLKAISRKFMPLDQWLYFDALDCLPEDGELLPSPEDCALRGSRYDGQIA
VFGAGFQEKLRRQHYLLVGAGAIGCELLKVFALVGLGAGNSGGLTVVDMDHIERSNLSRQ
FLFRSQDVGRPKAEVAAAAARGLNPDLQVIPLTYPLDPTTEHIYGDNFFSRVDGVAAALD
SFQARRYVAARCTHYLKPLLEAGTSGTWGSATVFMPHVTEAYRAPASAAASEDAPYPVCT
VRYFPSTAEHTLQWARHEFEELFRLSAETINHHQQAHTSLADMDEPQTLTLLKPVLGVLR
VRPQNWQDCVAWALGHWKLCFHYGIKQLLRHFPPNKVLEDGTPFWSGPKQCPQPLEFDTN
QDTHLLYVLAAANLYAQMHGLPGSQDWTALRELLKLLPQPDPQQMAPIFASNLELASASA
EFGPEQQKELNKALEVWSVGPPLKPLMFEKDDDSNFHVDFVVAAASLRCQNYGIPPVNRA
QSKRIVGQIIPAIATTTAAVAGLLGLELYKVVSGPRPRSAFRHSYLHLAENYLIRYMPFA
PAIQTFHHLKWTSWDRLKVPAGQPERTLESLLAHLQEQHGLRVRILLHGSALLYAAGWSP
EKQAQHLPLRVTELVQQLTGQAPAPGQRVLVLELSCEGDDEDTAFPPLHYEL

Sequence of entity 2 (B, D), FASTA

>8SE9_2 Ubiquitin-like protein ISG15 (chains B, D)
MGWDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPL
ASQGLGPGSTVLLVVDKCDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDD
LFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGG

Sequence of entity 3 (C), FASTA

>8SE9_3 Ubiquitin/ISG15-conjugating enzyme E2 L6 (chains C)
MASMRVVKELEDLQKKPPPYLRNLSSDDANVLVWHALLLPDQPPYHLKAFNLRISFPPEY
PFKPPMIKFTTKIYHPNVDENGQICLPIISSENWKPSTKTSQVLEALNVLVNRPNIREPK
RMDLADLLTQNPELFRKNAEEFTLRFGVDRPS

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	1

Primary citation

Cryo-EM structures of Uba7 reveal the molecular basis for ISG15 activation and E1-E2 thioester transfer. Afsar, M., Liu, G., Jia, L. et al. Nat Commun (2023) 14:4786-4786. DOI 10.1038/s41467-023-39780-z · PubMed

Other PDB entries of the same protein (UniProt P41226 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SEB 3.24 Å, Cryo-EM structure of a single loaded human UBA7-UBE2L6-ISG15 adenylate complex
8SV8 3.38 Å, Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex…
8SEA 3.4 Å, Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex…
8OIF 3.5 Å, Structure of the UBE1L activating enzyme bound to ISG15 and UBE2L6
8WWX Ube1L acts akin to a mitt, that mediates UbcH8 binding and orchestrates "E1-E2"…

Browse structure collections

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