7PVN: Human UBA6

Crystal Structure of Human UBA6 in Complex with ATP. Determined by X-ray diffraction at 2.71 Å resolution. Released 31 Aug 2022.

Method: X-ray diffraction
Resolution: 2.71 Å
Organism: Homo sapiens
Chains: 2
Atoms: 16,110
Mol. weight: 239.78 kDa
Ligands: ATP, MG, CA
Released: 31 Aug 2022

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

Secondary structure: helices and β-sheets

7PVN contains 117 α-helices and 94 β-strands across 2 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: 57 helices, 48 β-strands

Element	Residues	Length	Sheet
α-helix	41-51	11
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	98-103	6
α-helix	109-114	6
β-strand	117	1	2
α-helix	118-129	12
β-strand	134-138	5	1
α-helix	149-153	5
β-strand	156-159	4	1
α-helix	164-176	13
α-helix	180-181	2
β-strand	182-189	8	1
β-strand	190	1	3
β-strand	192-198	7	1
β-strand	203-205	3	4
α-helix	211-214	4
β-strand	215-217	3	5
β-strand	218-221	4	6
β-strand	228-231	4	6
β-strand	244-251	8	5
α-helix	254-256	3
β-strand	260-262	3	5
β-strand	264-267	4	6
β-strand	270-272	3	6
α-helix	280-282	3
β-strand	284-290	7	5
α-helix	291-294	4
β-strand	295-297	3	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
α-helix	411-413	3
β-strand	416-417	2	1
β-strand	420	1	1
α-helix	422-426	5
α-helix	433-436	4
α-helix	444-450	7
α-helix	452-459	8
β-strand	462-466	5	7
α-helix	470-482	13
β-strand	492-496	5	7
β-strand	500	1	8
α-helix	504-507	4
α-helix	514-516	3
β-strand	520	1	8
α-helix	521-532	12
β-strand	538-541	4	7
α-helix	547-549	3
α-helix	555-560	6
β-strand	563-566	4	7
α-helix	571-584	14
β-strand	588-594	7	7
β-strand	595	1	9
β-strand	597-603	7	7
β-strand	608	1	10
α-helix	611-613	3
α-helix	624-628	5
α-helix	634-646	13
α-helix	647-651	5
α-helix	652-662	11
α-helix	666-675	10
α-helix	682-690	9
α-helix	696-708	13
α-helix	709-713	5
α-helix	714-721	8
α-helix	752-768	17
α-helix	775-778	4
α-helix	780-789	10
α-helix	796-798	3
α-helix	819-833	15
α-helix	858-873	16
α-helix	875-877	3
α-helix	880-888	9
α-helix	890-892	3
β-strand	893	1	9
α-helix	895-913	19
β-strand	922-927	6	7
β-strand	932-937	6	7
α-helix	938-939	2
β-strand	940	1	10
α-helix	941-942	2
β-strand	944	1	11
β-strand	952	1	11
β-strand	958-961	4	12
β-strand	967	1	13
α-helix	968-979	12
β-strand	985-988	4	14
β-strand	991-994	4	14
α-helix	1001-1006	6
β-strand	1008	1	13
α-helix	1009-1012	4
β-strand	1021-1024	4	12
β-strand	1025-1028	4	14
β-strand	1038-1039	2	14
β-strand	1043-1046	4	12

Chain B: 60 helices, 46 β-strands

Element	Residues	Length	Sheet
α-helix	41-51	11
α-helix	53-60	8
β-strand	63-66	4	15
α-helix	71-83	13
β-strand	87-91	5	15
β-strand	95	1	16
α-helix	96	1
α-helix	100-103	4
α-helix	109-114	6
β-strand	117	1	16
α-helix	118-129	12
β-strand	134-138	5	15
α-helix	149-153	5
β-strand	156-160	5	15
α-helix	164-176	13
α-helix	180-181	2
β-strand	182-189	8	15
β-strand	190	1	17
β-strand	192-198	7	15
β-strand	203-205	3	18
α-helix	211-214	4
β-strand	215-217	3	19
β-strand	218-221	4	20
β-strand	229-231	3	20
β-strand	244-251	8	19
α-helix	254-256	3
β-strand	260-262	3	19
β-strand	264-267	4	20
β-strand	270-272	3	20
α-helix	280-282	3
β-strand	284-291	8	19
β-strand	295-297	3	18
α-helix	302-307	6
β-strand	311-312	2	15
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	17
α-helix	388-407	20
α-helix	411-413	3
β-strand	416-417	2	15
β-strand	420	1	15
α-helix	422-426	5
α-helix	433-436	4
α-helix	444-450	7
α-helix	452-459	8
β-strand	462-466	5	21
α-helix	470-482	13
β-strand	492-496	5	21
β-strand	500	1	22
α-helix	504-507	4
α-helix	514-516	3
β-strand	520	1	22
α-helix	521-532	12
β-strand	538-541	4	21
α-helix	547-550	4
α-helix	555-560	6
β-strand	563-566	4	21
α-helix	571-584	14
β-strand	588-594	7	21
β-strand	597-603	7	21
β-strand	608	1	23
α-helix	611-613	3
α-helix	617-619	3
α-helix	621-623	3
α-helix	624-628	5
α-helix	634-646	13
α-helix	647-651	5
α-helix	652-662	11
α-helix	666-675	10
α-helix	682-690	9
α-helix	696-708	13
α-helix	709-713	5
α-helix	714-721	8
α-helix	752-768	17
α-helix	775-778	4
α-helix	780-789	10
α-helix	818-834	17
α-helix	840-842	3
α-helix	858-873	16
α-helix	875-877	3
α-helix	880-888	9
α-helix	890-892	3
α-helix	895-913	19
β-strand	922-927	6	21
β-strand	932-937	6	21
α-helix	938-939	2
β-strand	940	1	23
α-helix	941-942	2
β-strand	944-945	2	24
β-strand	951-952	2	24
β-strand	958-961	4	25
β-strand	967	1	26
α-helix	968-979	12
β-strand	983-988	6	27
β-strand	991-994	4	27
α-helix	1001-1006	6
β-strand	1008	1	26
α-helix	1009-1013	5
β-strand	1021-1024	4	25
β-strand	1025-1028	4	27
α-helix	1036-1037	2
β-strand	1038-1039	2	27
β-strand	1043-1046	4	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme 6	A, B	protein	1052	Homo sapiens	A0AVT1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7PVN_1 Ubiquitin-like modifier-activating enzyme 6 (chains A, B)
MEGSEPVAAHQGEEASCSSWGTGSTNKNLPIMSTASVEIDDALYSRQRYVLGDTAMQKMA
KSHVFLSGMGGLGLEIAKNLVLAGIKAVTIHDTEKCQAWDLGTNFFLSEDDVVNKRNRAE
AVLKHIAELNPYVHVTSSSVPFNETTDLSFLDKYQCVVLTEMKLPLQKKINDFCRSQCPP
IKFISADVHGIWSRLFCDFGDEFEVLDTTGEEPKEIFISNITQANPGIVTCLENHPHKLE
TGQFLTFREINGMTGLNGSIQQITVISPFSFSIGDTTELEPYLHGGIAVQVKTPKTVFFE
SLERQLKHPKCLIVDFSNPEAPLEIHTAMLALDQFQEKYSRKPNVGCQQDSEELLKLATS
ISETLEEKPDVNADIVHWLSWTAQGFLSPLAAAVGGVASQEVLKAVTGKFSPLCQWLYLE
AADIVESLGKPECEEFLPRGDRYDALRACIGDTLCQKLQNLNIFLVGCGAIGCEMLKNFA
LLGVGTSKEKGMITVTDPDLIEKSNLNRQFLFRPHHIQKPKSYTAADATLKINSQIKIDA
HLNKVCPTTETIYNDEFYTKQDVIITALDNVEARRYVDSRCLANLRPLLDSGTMGTKGHT
EVIVPHLTESYNSHRDPPEEEIPFATLKSFPAAIEHTIQWARDKFESSFSHKPSLFNKFW
QTYSSAEEVLQKIQSGHSLEGCFQVIKLLSRRPRNWSQCVELARLKFEKYFNHKALQLLH
CFPLDIRLKDGSLFWQSPKRPPSPIKFDLNEPLHLSFLQNAAKLYATVYCIPFAEEDLSA
DALLNILSEVKIQEFKPSNKVVQTDETARKPDHVPISSEDERNAIFQLEKAILSNEATKS
DLQMAVLSFEKDDDHNGHIDFITAASNLRAKMYSIEPADRFKTKRIAGKIIPAIATTTAT
VSGLVALEMIKVTGGYPFEAYKNCFLNLAIPIVVFTETTEVRKTKIRNGISFTIWDRWTV
HGKEDFTLLDFINAVKEKYGIEPTMVVQGVKMLYVPVMPGHAKRLKLTMHKLVKPTTEKK
YVDLTVSFAPDIDGDEDLPGPPVRYYFSHDTD

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
MG	Magnesium ion	Mg	2
CA	Calcium ion	Ca	3

Water and common crystallization additives (GOL, CL) are not listed.

Primary citation

Structures of UBA6 explain its dual specificity for ubiquitin and FAT10. Truongvan, N., Li, S., Misra, M. et al. Nat Commun (2022) 13:4789-4789. DOI 10.1038/s41467-022-32040-6 · PubMed

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

7SOL 2.25 Å, Crystal Structures of the bispecific ubiquitin/FAT10 activating enzyme, Uba6
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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