7SOL: Ubiquitin-like modifier-activating enzyme 6

Crystal Structures of the bispecific ubiquitin/FAT10 activating enzyme, Uba6. Determined by X-ray diffraction at 2.25 Å resolution. Released 2 Nov 2022.

Method: X-ray diffraction
Resolution: 2.25 Å
Organisms: Homo sapiens, Triticum aestivum
Chains: 4
Atoms: 17,964
Mol. weight: 250.26 kDa
Ligands: AMP, IHP
Released: 2 Nov 2022

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

Secondary structure: helices and β-sheets

7SOL contains 132 α-helices and 118 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: 64 helices, 50 β-strands

Element	Residues	Length	Sheet
α-helix	45-51	7
α-helix	53-59	7
β-strand	63-67	5	1
α-helix	71-83	13
β-strand	87-91	5	1
β-strand	95	1	2
α-helix	98-102	5
α-helix	109-113	5
β-strand	117	1	2
α-helix	118-127	10
β-strand	134-138	5	1
α-helix	148-153	6
β-strand	156-159	4	1
α-helix	164-175	12
α-helix	180-181	2
β-strand	182-189	8	1
β-strand	190	1	3
β-strand	192-198	7	1
β-strand	202-205	4	4
β-strand	207	1	5
α-helix	211-214	4
β-strand	215-217	3	6
β-strand	218-221	4	7
β-strand	228-231	4	7
β-strand	244-248	5	6
β-strand	251	1	8
β-strand	260-262	3	6
β-strand	264-267	4	7
β-strand	270-272	3	7
α-helix	280-282	3
β-strand	284	1	8
β-strand	287-291	5	6
α-helix	292-294	3
β-strand	295-298	4	4
α-helix	302-307	6
β-strand	311	1	1
α-helix	321-339	19
α-helix	342-344	3
α-helix	348-364	17
α-helix	369-371	3
α-helix	373-382	10
β-strand	386	1	3
α-helix	388-407	20
β-strand	409	1	5
α-helix	411-413	3
β-strand	416-417	2	1
β-strand	420	1	1
α-helix	422-424	3
α-helix	426-428	3
α-helix	433-436	4
α-helix	444-450	7
α-helix	452-459	8
β-strand	462-466	5	9
α-helix	470-482	13
β-strand	492-496	5	9
α-helix	499	1
β-strand	500	1	10
α-helix	501	1
α-helix	514-516	3
β-strand	520	1	10
α-helix	521-532	12
β-strand	538-541	4	9
α-helix	547-549	3
α-helix	555-560	6
β-strand	563-566	4	9
α-helix	571-583	13
β-strand	588-594	7	9
β-strand	597-603	7	9
β-strand	608	1	11
α-helix	611-613	3
α-helix	616-620	5
α-helix	624-628	5
α-helix	634-646	13
α-helix	647-651	5
α-helix	652-663	12
α-helix	666-674	9
α-helix	682-690	9
α-helix	696-708	13
α-helix	709-713	5
α-helix	714-721	8
β-strand	727	1	12
β-strand	733	1	12
α-helix	752-768	17
α-helix	775-778	4
α-helix	780-788	9
α-helix	790-795	6
α-helix	814-817	4
α-helix	818-833	16
α-helix	840-842	3
α-helix	845-847	3
α-helix	858-872	15
α-helix	875-877	3
α-helix	880-887	8
α-helix	890-892	3
α-helix	895-913	19
α-helix	918-920	3
β-strand	923-927	5	9
β-strand	932-936	5	9
α-helix	939	1
β-strand	940	1	11
α-helix	941	1
β-strand	944-947	4	13
β-strand	950-952	3	13
β-strand	958-961	4	14
β-strand	967	1	15
α-helix	968-979	12
β-strand	983-988	6	14
β-strand	991-994	4	14
α-helix	1001-1006	6
β-strand	1008	1	15
α-helix	1009-1013	5
β-strand	1021-1028	8	14
α-helix	1036-1037	2
β-strand	1038-1046	9	14

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	-5--2	4
β-strand	0-6	7	16
β-strand	12-18	7	16
β-strand	22	1	17
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	16
β-strand	48-49	2	16
β-strand	55	1	17
α-helix	57-59	3
β-strand	66-70	5	16
β-strand	75	1	9

Chain C: 62 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	63-67	5	18
α-helix	71-83	13
β-strand	87-91	5	18
β-strand	95	1	19
α-helix	98-102	5
α-helix	109-113	5
β-strand	117	1	19
α-helix	118-129	12
β-strand	134-138	5	18
α-helix	148-153	6
β-strand	156-160	5	18
α-helix	164-175	12
α-helix	180-181	2
β-strand	182-189	8	18
β-strand	190	1	20
β-strand	192-198	7	18
β-strand	202-205	4	21
α-helix	211-214	4
β-strand	215-217	3	22
β-strand	218-221	4	23
β-strand	228-231	4	23
α-helix	232	1
β-strand	244-248	5	22
β-strand	251	1	24
α-helix	254-256	3
β-strand	260-262	3	22
β-strand	264-267	4	23
β-strand	270-272	3	23
α-helix	280-282	3
β-strand	284	1	24
β-strand	287-291	5	22
α-helix	292-294	3
β-strand	295-298	4	21
α-helix	302-305	4
β-strand	311	1	18
α-helix	321-339	19
α-helix	342-344	3
α-helix	348-364	17
α-helix	369-371	3
α-helix	373-382	10
β-strand	386	1	20
α-helix	388-407	20
β-strand	416-417	2	18
β-strand	420	1	18
α-helix	422-424	3
α-helix	426-428	3
α-helix	433-436	4
α-helix	444-450	7
α-helix	452-459	8
β-strand	462-466	5	25
α-helix	470-482	13
β-strand	492-496	5	25
α-helix	499	1
β-strand	500	1	26
α-helix	501	1
α-helix	514-516	3
β-strand	520	1	26
α-helix	521-532	12
β-strand	538-541	4	25
α-helix	547-549	3
α-helix	555-560	6
β-strand	563-566	4	25
α-helix	571-583	13
β-strand	588-594	7	25
β-strand	597-603	7	25
β-strand	608	1	27
α-helix	611-613	3
α-helix	616-618	3
β-strand	622-624	3	28
α-helix	627-628	2
α-helix	634-646	13
α-helix	647-651	5
α-helix	652-662	11
α-helix	666-674	9
α-helix	682-690	9
α-helix	696-708	13
α-helix	709-713	5
α-helix	714-721	8
β-strand	727	1	29
β-strand	733	1	29
α-helix	744-747	4
α-helix	752-768	17
α-helix	780-786	7
α-helix	793-795	3
α-helix	820-833	14
α-helix	840-842	3
α-helix	845-847	3
α-helix	858-872	15
α-helix	875-877	3
α-helix	880-887	8
β-strand	890-892	3	28
α-helix	895-913	19
α-helix	918-920	3
β-strand	923-927	5	25
β-strand	932-936	5	25
α-helix	939	1
β-strand	940	1	27
α-helix	941	1
β-strand	944-945	2	30
α-helix	946	1
β-strand	951-952	2	30
β-strand	958-961	4	31
β-strand	967	1	32
α-helix	968-979	12
β-strand	985-988	4	33
β-strand	991-994	4	33
α-helix	1002-1006	5
β-strand	1008	1	32
α-helix	1009-1013	5
β-strand	1021-1024	4	31
β-strand	1025-1028	4	33
α-helix	1036-1037	2
β-strand	1038-1039	2	33
β-strand	1043-1046	4	31

Chain D: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	0-6	7	34
β-strand	12-18	7	34
β-strand	22	1	35
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	34
β-strand	48-49	2	34
β-strand	55	1	35
β-strand	66-70	5	34
β-strand	75	1	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme 6	A, C	protein	1020	Homo sapiens	A0AVT1 (AlphaFold model)
Ubiquitin	B, D	protein	83	Triticum aestivum	P69326 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7SOL_1 Ubiquitin-like modifier-activating enzyme 6 (chains A, C)
GAMGVEIDDALYSRQRYVLGDTAMQKMAKSHVFLSGMGGLGLEIAKNLVLAGIKAVTIHD
TEKCQAWDLGTNFFLSEDDVVNKRNRAEAVLKHIAELNPYVHVTSSSVPFNETTDLSFLD
KYQCVVLTEMKLPLQKKINDFCRSQCPPIKFISADVHGIWSRLFCDFGDEFEVLDTTGEE
PKEIFISNITQANPGIVTCLENHPHKLETGQFLTFREINGMTGLNGSIQQITVISPFSFS
IGDTTELEPYLHGGIAVQVKTPKTVFFESLERQLKHPKCLIVDFSNPEAPLEIHTAMLAL
DQFQEKYSRKPNVGCQQDSEELLKLATSISETLEEKPDVNADIVHWLSWTAQGFLSPLAA
AVGGVASQEVLKAVTGKFSPLCQWLYLEAADIVESLGKPECEEFLPRGDRYDALRACIGD
TLCQKLQNLNIFLVGCGAIGCEMLKNFALLGVGTSKEKGMITVTDPDLIEKSNLNRQFLF
RPHHIQKPKSYTAADATLKINSQIKIDAHLNKVCPTTETIYNDEFYTKQDVIITALDNVE
ARRYVDSRCLANLRPLLDSGTMGTKGHTEVIVPHLTESYNSHRDPPEEEIPFATLKSFPA
AIEHTIQWARDKFESSFSHKPSLFNKFWQTYSSAEEVLQKIQSGHSLEGCFQVIKLLSRR
PRNWSQCVELARLKFEKYFNHKALQLLHCFPLDIRLKDGSLFWQSPKRPPSPIKFDLNEP
LHLSFLQNAAKLYATVYCIPFAEEDLSADALLNILSEVKIQEFKPSNKVVQTDETARKPD
HVPISSEDERNAIFQLEKAILSNEATKSDLQMAVLSFEKDDDHNGHIDFITAASNLRAKM
YSIEPADRFKTKRIAGKIIPAIATTTATVSGLVALEMIKVTGGYPFEAYKNCFLNLAIPI
VVFTETTEVRKTKIRNGISFTIWDRWTVHGKEDFTLLDFINAVKEKYGIEPTMVVQGVKM
LYVPVMPGHAKRLKLTMHKLVKPTTEKKYVDLTVSFAPDIDGDEDLPGPPVRYYFSHDTD

Sequence of entity 2 (B, D), FASTA

>7SOL_2 Ubiquitin (chains B, D)
MHHHHHHMQIFVRTLTGRTITLEVESSDTIDNVRARIQDREGIPPDQQRLIFAGRQLEDG
RTLADYNIQRESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	2
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1

Primary citation

Crystal structures reveal catalytic and regulatory mechanisms of the dual-specificity ubiquitin/FAT10 E1 enzyme Uba6. Yuan, L., Gao, F., Lv, Z. et al. Nat Commun (2022) 13:4880-4880. DOI 10.1038/s41467-022-32613-5 · PubMed

Other PDB entries of the same protein (UniProt A0AVT1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7PVN 2.71 Å, Crystal Structure of Human UBA6 in Complex with ATP
9YKV 2.73 Å, Cryo-EM structure of double-loaded human UBA6-UBE2Z-FAT10(t)/FAT10(a) thioester mimetic…
28MJ 2.77 Å, Cryo-EM structure of UBA6 in complex with FAT10 in the pre-adenylation state.
28MO 3.01 Å, Cryo-EM structure of UBA6-UbDha-UBE2Z trapped ternary complex (singly loaded)
28MQ 3.04 Å, Cryo-EM structure of UBA6-FAT10Dha-UBE2Z trapped ternary complex
9QH5 3.09 Å, Consensus structure of UBA6-UbDha-BIRC6 trapped ternary complex (doubly loaded)
28MP 3.12 Å, Cryo-EM structure of UBA6-UbDha-UBE2Z trapped ternary complex (doubly loaded)
9YLF 3.14 Å, Cryo-EM structure of single-loaded human UBA6-UBE2Z/Ub(a) adenylate complex.
9YLB 3.24 Å, Cryo-EM structure of single-loaded human UBA6-UBE2Z/FAT10(a) adenylate complex.
7PYV 3.27 Å, Crystal structure of human UBA6 in complex with the ubiquitin-like modifier FAT10
9QIC 3.29 Å, Consensus structure of UBA6
9XGB 3.3 Å, UBA6-BIRC6 ubc-ubt

Browse structure collections

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