8OIF: UBE1L activating enzyme

Structure of the UBE1L activating enzyme bound to ISG15 and UBE2L6. Determined by electron microscopy at 3.5 Å resolution. Released 13 Dec 2023.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,589
Mol. weight: 147.37 kDa
Ligands: AMP
Released: 13 Dec 2023

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

Secondary structure: helices and β-sheets

8OIF contains 41 α-helices and 53 β-strands across 3 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: 34 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	34-38	5	1
α-helix	43-54	12
β-strand	58-62	5	1
α-helix	65	1
β-strand	66	1	2
α-helix	67	1
α-helix	69-71	3
β-strand	86	1	2
α-helix	87-99	13
β-strand	105-106	2	1
α-helix	116-118	3
β-strand	121-125	5	1
α-helix	131-142	12
β-strand	145-152	8	1
β-strand	153	1	3
β-strand	155-161	7	1
β-strand	166-168	3	4
α-helix	175-177	3
β-strand	178-179	2	5
β-strand	180	1	6
β-strand	195	1	6
β-strand	208-210	3	5
β-strand	226-227	2	5
β-strand	253-255	3	5
β-strand	260-262	3	4
α-helix	267-270	4
β-strand	276	1	1
α-helix	282-304	23
α-helix	307-309	3
α-helix	313-323	11
α-helix	343-352	10
β-strand	356	1	3
α-helix	358-374	17
α-helix	381-383	3
β-strand	386-389	4	1
α-helix	416-419	4
α-helix	424-432	9
β-strand	434-438	5	7
α-helix	442-454	13
β-strand	463-467	5	7
α-helix	474-479	6
α-helix	485-487	3
α-helix	492-503	12
β-strand	509-512	4	7
α-helix	526-531	6
β-strand	535-537	3	7
α-helix	543-555	13
β-strand	559-565	7	7
β-strand	568-574	7	7
α-helix	580-582	3
α-helix	586-591	6
α-helix	612-614	3
α-helix	854-871	18
β-strand	883-887	5	7
α-helix	888-890	3
β-strand	892-896	5	7
α-helix	899-903	5
β-strand	904-906	3	8
β-strand	909-911	3	8
β-strand	917-919	3	9
β-strand	927	1	10
α-helix	928-938	11
β-strand	945-948	4	11
β-strand	951-955	5	11
α-helix	960-966	7
β-strand	970	1	10
α-helix	971-978	8
α-helix	982-984	3
β-strand	989-992	4	9
β-strand	993-995	3	11
α-helix	1006-1007	2
β-strand	1008-1011	4	9

Chain I: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	82-87	6	12
β-strand	93-98	6	12
β-strand	103	1	13
α-helix	104-115	12
β-strand	122-125	4	12
β-strand	130	1	12
β-strand	136	1	13
α-helix	137-140	4
β-strand	147-152	6	12

Chain L: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-16	12
β-strand	23-26	4	14
β-strand	36-39	4	14
β-strand	51-53	3	14
β-strand	56	1	15
α-helix	65-66	2
β-strand	67	1	15
β-strand	70	1	14
β-strand	79	1	16
β-strand	85	1	16
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-146	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme 7	A	protein	1014	Homo sapiens	P41226 (AlphaFold model)
Ubiquitin-like protein ISG15	I	protein	157	Homo sapiens	P05161 (AlphaFold model)
Ubiquitin/ISG15-conjugating enzyme E2 L6	L	protein	155	Homo sapiens	O14933 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8OIF_1 Ubiquitin-like modifier-activating enzyme 7 (chains A)
GSMDALDASKLLDEELYSRQLYVLGSPAMQRIQGARVLVSGLQGLGAEVAKNLVLMGVGS
LTLHDPHPTCWSDLAAQFLLSEQDLERSRAEASQELLAQLNRAVQVVVHTGDITEDLLLD
FQVVVLTAAKLEEQLKVGTLCHKHGVCFLAADTRGLVGQLFCDFGEDFTVQDPTEAEPLT
AAIQHISQGSPGILTLRKGANTHYFRDGDLVTFSGIEGMVELNDCDPRSIHVREDGSLEI
GDTTTFSRYLRGGAITEVKRPKTVRHKSLDTALLQPHVVAQSSQEVHHAHCLHQAFCALH
KFQHLHGRPPQPWDPVDAETVVGLARDLEPLKRTEEEPLEEPLDEALVRTVALSSAGVLS
PMVAMLGAVAAQEVLKAISRKFMPLDQWLYFDALDCLPEDGELLPSPEDCALRGSRYDGQ
IAVFGAGFQEKLRRQHYLLVGAGAIGCELLKVFALVGLGAGNSGGLTVVDMDHIERSNLS
RQFLFRSQDVGRPKAEVAAAAARGLNPDLQVIPLTYPLDPTTEHIYGDNFFSRVDGVAAA
LDSFQARRYVAARCTHYLKPLLEAGTSGTWGSATVFMPHVTEAYRAPASAAASEDAPYPV
CTVRYFPSTAEHTLQWARHEFEELFRLSAETINHHQQAHTSLADMDEPQTLTLLKPVLGV
LRVRPQNWQDCVAWALGHWKLCFHYGIKQLLRHFPPNKVLEDGTPFWSGPKQCPQPLEFD
TNQDTHLLYVLAAANLYAQMHGLPGSQDWTALRELLKLLPQPDPQQMAPIFASNLELASA
SAEFGPEQQKELNKALEVWSVGPPLKPLMFEKDDDSNFHVDFVVAAASLRCQNYGIPPVN
RAQSKRIVGQIIPAIATTTAAVAGLLGLELYKVVSGPRPRSAFRHSYLHLAENYLIRYMP
FAPAIQTFHHLKWTSWDRLKVPAGQPERTLESLLAHLQEQHGLRVRILLHGSALLYAAGW
SPEKQAQHLPLRVTELVQQLTGQAPAPGQRVLVLELSCEGDDEDTAFPPLHYEL

Sequence of entity 2 (I), FASTA

>8OIF_2 Ubiquitin-like protein ISG15 (chains I)
MGWDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPL
ASQGLGPGSTVLLVVDKSDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDD
LFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGG

Sequence of entity 3 (L), FASTA

>8OIF_3 Ubiquitin/ISG15-conjugating enzyme E2 L6 (chains L)
GPMMASMRVVKELEDLQKKPPPYLRNLSSDDANVLVWHALLLPDQPPYHLKAFNLRISFP
PEYPFKPPMIKFTTKIYHPNVDENGQICLPIISSENWKPSTKTSQVLEALNVLVNRPNIR
EPLRMDLADLLTQNPELFRKNAEEFTLRFGVDRPS

Ligands and cofactors

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

Primary citation

Insights into the ISG15 transfer cascade by the UBE1L activating enzyme. Wallace, I., Baek, K., Prabu, J.R. et al. Nat Commun (2023) 14:7970-7970. DOI 10.1038/s41467-023-43711-3 · PubMed

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

8SE9 3.2 Å, Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex…
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…
8WWX Ube1L acts akin to a mitt, that mediates UbcH8 binding and orchestrates "E1-E2"…

Browse structure collections

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