9YKV: Ubiquitin-like modifier-activating enzyme 6

Cryo-EM structure of double-loaded human UBA6-UBE2Z-FAT10(t)/FAT10(a) thioester mimetic complex. Determined by electron microscopy at 2.73 Å resolution. Released 12 Aug 2026.

Method: Electron microscopy
Resolution: 2.73 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,923
Mol. weight: 182.58 kDa
Ligands: AMP, POP, IHP
Released: 12 Aug 2026

Explore 9YKV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YKV contains 74 α-helices and 79 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: 55 helices, 52 β-strands

Element	Residues	Length	Sheet
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	96	1
α-helix	99-102	4
α-helix	110-114	5
β-strand	117	1	2
α-helix	118-121	4
α-helix	123-127	5
β-strand	134-138	5	1
α-helix	149-153	5
β-strand	156-159	4	1
α-helix	164-176	13
β-strand	182-189	8	1
β-strand	190	1	3
β-strand	192-198	7	1
β-strand	202-205	4	4
α-helix	212-215	4
β-strand	216-217	2	5
β-strand	218	1	6
β-strand	228-230	3	7
β-strand	231	1	6
β-strand	244-250	7	5
β-strand	257	1	5
β-strand	261-262	2	5
β-strand	264-267	4	7
β-strand	270-272	3	7
β-strand	285-290	6	5
β-strand	295-298	4	4
α-helix	304-306	3
α-helix	311	1
β-strand	312	1	1
α-helix	313	1
β-strand	315	1	8
α-helix	321-339	19
α-helix	342-344	3
α-helix	348-357	10
α-helix	361-364	4
α-helix	373-381	9
β-strand	386	1	3
α-helix	388-407	20
α-helix	411-413	3
β-strand	417	1	1
α-helix	422-426	5
α-helix	433-435	3
α-helix	444-450	7
α-helix	452-459	8
β-strand	462-466	5	8
α-helix	470-482	13
β-strand	492-496	5	8
β-strand	500	1	9
α-helix	503-505	3
α-helix	514-516	3
β-strand	520	1	9
α-helix	521-532	12
β-strand	538-541	4	8
α-helix	547-549	3
α-helix	555-560	6
β-strand	563-566	4	8
α-helix	571-584	14
β-strand	588-594	7	8
β-strand	595	1	10
β-strand	597-603	7	8
β-strand	608	1	11
α-helix	611-613	3
α-helix	616-619	4
α-helix	621-623	3
α-helix	624-626	3
α-helix	634-645	12
α-helix	646-650	5
α-helix	652-662	11
α-helix	669-672	4
α-helix	684-690	7
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	781-783	3
α-helix	784-788	5
α-helix	858-872	15
α-helix	876-878	3
α-helix	880-888	9
α-helix	890-892	3
β-strand	893	1	10
α-helix	895-913	19
β-strand	922-927	6	8
β-strand	932-937	6	8
β-strand	940	1	11
β-strand	944-946	3	13
β-strand	950-952	3	13
β-strand	958-961	4	14
β-strand	967	1	15
α-helix	968-978	11
β-strand	985-988	4	16
β-strand	991-994	4	16
β-strand	1008	1	15
α-helix	1010-1013	4
α-helix	1016-1018	3
β-strand	1021-1024	4	14
β-strand	1025-1028	4	16
α-helix	1036-1037	2
β-strand	1038-1039	2	16
β-strand	1043-1046	4	14

Chain B: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	97-98	2
α-helix	101-113	13
α-helix	115-116	2
β-strand	119-123	5	17
β-strand	130-136	7	17
β-strand	137	1	18
α-helix	138	1
β-strand	144	1	18
β-strand	147-153	7	17
β-strand	164-167	4	17
β-strand	181	1	19
β-strand	186	1	17
β-strand	187	1	19
β-strand	189	1	20
α-helix	190-192	3
α-helix	206-216	11
α-helix	221-224	4
α-helix	236-249	14
α-helix	250-254	5
α-helix	255-257	3
α-helix	265-276	12
α-helix	279-284	6
α-helix	290-292	3
α-helix	295	1
β-strand	296	1	21
α-helix	297	1
β-strand	307	1	21
α-helix	310-325	16

Chain C: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	88-93	6	22
β-strand	101-106	6	22
β-strand	111	1	23
α-helix	112-123	12
α-helix	127-129	3
β-strand	132-134	3	22
β-strand	137-138	2	22
β-strand	144	1	23
β-strand	155-158	4	22

Chain D: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	90-94	5	24
β-strand	102-104	3	24
β-strand	111	1	25
α-helix	112-115	4
β-strand	131-134	4	24
β-strand	137-138	2	24
β-strand	144	1	25
β-strand	155-159	5	24
β-strand	163	1	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme 6	A	protein	1016	Homo sapiens	A0AVT1 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 Z	B	protein	262	Homo sapiens	Q9H832 (AlphaFold model)
Ubiquitin D	C, D	protein	165	Homo sapiens	A0A1U9X8S9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9YKV_1 Ubiquitin-like modifier-activating enzyme 6 (chains A)
VEIDDALYSRQRYVLGDTAMQKMAKSHVFLSGMGGLGLEIAKNLVLAGIKAVTIHDTEKC
QAWDLGTNFFLSEDDVVNKRNRAEAVLKHIAELNPYVHVTSSSVPFNETTDLSFLDKYQC
VVLTEMKLPLQKKINDFCRSQCPPIKFISADVHGIWSRLFCDFGDEFEVLDTTGEEPKEI
FISNITQANPGIVTCLENHPHKLETGQFLTFREINGMTGLNGSIQQITVISPFSFSIGDT
TELEPYLHGGIAVQVKTPKTVFFESLERQLKHPKCLIVDFSNPEAPLEIHTAMLALDQFQ
EKYSRKPNVGCQQDSEELLKLATSISETLEEKPDVNADIVHWLSWTAQGFLSPLAAAVGG
VASQEVLKAVTGKFSPLCQWLYLEAADIVESLGKPECEEFLPRGDRYDALRACIGDTLCQ
KLQNLNIFLVGCGAIGCEMLKNFALLGVGTSKEKGMITVTDPDLIEKSNLNRQFLFRPHH
IQKPKSYTAADATLKINSQIKIDAHLNKVCPTTETIYNDEFYTKQDVIITALDNVEARRY
VDSRCLANLRPLLDSGTMGTKGHTEVIVPHLTESYNSHRDPPEEEIPFCTLKSFPAAIEH
TIQWARDKFESSFSHKPSLFNKFWQTYSSAEEVLQKIQSGHSLEGCFQVIKLLSRRPRNW
SQCVELARLKFEKYFNHKALQLLHCFPLDIRLKDGSLFWQSPKRPPSPIKFDLNEPLHLS
FLQNAAKLYATVYCIPFAEEDLSADALLNILSEVKIQEFKPSNKVVQTDETARKPDHVPI
SSEDERNAIFQLEKAILSNEATKSDLQMAVLSFEKDDDHNGHIDFITAASNLRAKMYSIE
PADRFKTKRIAGKIIPAIATTTATVSGLVALEMIKVTGGYPFEAYKNCFLNLAIPIVVFT
ETTEVRKTKIRNGISFTIWDRWTVHGKEDFTLLDFINAVKEKYGIEPTMVVQGVKMLYVP
VMPGHAKRLKLTMHKLVKPTTEKKYVDLTVSFAPDIDGDEDLPGPPVRYYFSHDTD

Sequence of entity 2 (B), FASTA

>9YKV_2 Ubiquitin-conjugating enzyme E2 Z (chains B)
GERTAPQSLLRIKRDIMSIYKEPPPGMFVVPDTVDMTRIHALITGPFDTPYEGGFFLFVF
RCPPDYPIHPPRVRLMTTGNNTVRFNPNFKRNGRVCLSILGTWTGPAWSPAQSISSVLIS
IQSLMTENPYHNEPGFEQERHPGDSKNYNECIRHETIRVAVCDMMEGKSPSPEPLRGVME
KSFLEYYDFYEVACKDRLHLQGQTMQDPFGEKRGHFDYQSLLMRLGLIRQKVLERLHNEN
AEMDSDSSSSGTETDLHGSLRV

Sequence of entity 3 (C, D), FASTA

>9YKV_3 Ubiquitin D (chains C, D)
MAPNASTLTVHVRSEEWDLMTFDANPYDSVKKIKEHVRSKTKVPVQDQVLLLGSKILKPR
RSLSSYGIDKEKTIHLTLKVVKPSDEELPLFLVESGDEAKRHLLQVRRSSSVAQVKAMIE
TKTGIIPETQIVTLNGKRLEDGKMMADYGIRKGNLLFLASYSIGG

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	1
POP	Pyrophosphate 2-	H2 O7 P2	1
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1

Primary citation

Cryo-EM structures of UBA6 reveal mechanisms of E1-E2 specificity and dual FAT10/ubiquitin thioester transfer. Nayak, D., Jia, L., Dos Santos Bury, P. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-69882-3 · 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
7PVN 2.71 Å, Crystal Structure of Human UBA6 in Complex with ATP
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

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