9YLF: Ubiquitin-like modifier-activating enzyme 6

Cryo-EM structure of single-loaded human UBA6-UBE2Z/Ub(a) adenylate complex. Determined by electron microscopy at 3.14 Å resolution. Released 12 Aug 2026.

Method: Electron microscopy
Resolution: 3.14 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,302
Mol. weight: 153.88 kDa
Ligands: IHP, AMP
Released: 12 Aug 2026

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

Secondary structure: helices and β-sheets

9YLF contains 69 α-helices and 67 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: 52 helices, 51 β-strands

Element	Residues	Length	Sheet
α-helix	45-50	6
α-helix	53-60	8
β-strand	63-67	5	1
α-helix	72-83	12
β-strand	87-91	5	1
β-strand	95	1	2
α-helix	98-103	6
α-helix	111-114	4
β-strand	117	1	2
α-helix	118-129	12
β-strand	134-138	5	1
α-helix	149-152	4
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	202-205	4	4
β-strand	207	1	5
α-helix	212-215	4
β-strand	216-217	2	6
β-strand	218-222	5	7
β-strand	227-231	5	7
β-strand	244-251	8	6
β-strand	257	1	6
β-strand	260-262	3	6
β-strand	263-267	5	7
β-strand	270-273	4	7
α-helix	280-282	3
β-strand	284-290	7	6
β-strand	295-298	4	4
α-helix	302-307	6
α-helix	311	1
β-strand	312	1	1
α-helix	313	1
α-helix	321-339	19
α-helix	342-344	3
α-helix	348-364	17
α-helix	369-371	3
α-helix	373-381	9
β-strand	386	1	3
α-helix	388-407	20
β-strand	409	1	5
α-helix	411-413	3
β-strand	417	1	1
β-strand	420	1	1
α-helix	422-426	5
α-helix	433-435	3
α-helix	444-450	7
α-helix	452-459	8
β-strand	462-465	4	8
α-helix	470-482	13
β-strand	492-496	5	8
β-strand	500	1	9
α-helix	503-506	4
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	588-593	6	8
β-strand	597-603	7	8
β-strand	608	1	10
α-helix	611-613	3
α-helix	624-629	6
α-helix	634-646	13
α-helix	647-651	5
α-helix	652-662	11
α-helix	669-674	6
α-helix	682-690	9
α-helix	696-708	13
α-helix	709-713	5
α-helix	714-721	8
β-strand	727	1	11
β-strand	733	1	11
α-helix	752-768	17
α-helix	780-787	8
α-helix	858-872	15
α-helix	880-887	8
α-helix	895-913	19
β-strand	922-927	6	8
β-strand	932-937	6	8
α-helix	938-939	2
β-strand	940	1	10
α-helix	941-942	2
β-strand	944-946	3	12
β-strand	950-952	3	12
β-strand	958-961	4	13
β-strand	967	1	14
α-helix	968-978	11
β-strand	983-988	6	15
β-strand	991-994	4	15
α-helix	1003-1005	3
β-strand	1008	1	14
α-helix	1009-1013	5
β-strand	1021-1024	4	13
β-strand	1025-1028	4	15
α-helix	1036-1037	2
β-strand	1038-1039	2	15
β-strand	1043-1046	4	13

Chain C: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	99	1	16
α-helix	101-113	13
α-helix	115-116	2
β-strand	119-123	5	17
β-strand	130-136	7	17
α-helix	137-138	2
β-strand	147-153	7	17
β-strand	157	1	16
α-helix	162-163	2
β-strand	164-167	4	17
β-strand	181	1	18
β-strand	186	1	17
β-strand	187	1	18
α-helix	199-200	2
α-helix	206-215	10
α-helix	221-224	4
α-helix	226-228	3
α-helix	236-249	14
α-helix	250-255	6
α-helix	256-257	2
α-helix	268-289	22
α-helix	312-315	4
α-helix	316-322	7

Chain D: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	12-15	4	19
β-strand	22	1	20
α-helix	23-33	11
β-strand	42-45	4	19
β-strand	48-49	2	19
α-helix	50-51	2
β-strand	55	1	20
α-helix	56-59	4
β-strand	66-70	5	19

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	C	protein	262	Homo sapiens	Q9H832 (AlphaFold model)
Ubiquitin	D	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9YLF_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 (C), FASTA

>9YLF_2 Ubiquitin-conjugating enzyme E2 Z (chains C)
GERTAPQSLLRIKRDIMSIYKEPPPGMFVVPDTVDMTKIHALITGPFDTPYEGGFFLFVF
RCPPDYPIHPPRVKLMTTGNNTVRFNPNFARNGKVCLSILGTWTGPAWSPAQSISSVLIS
IQSLMTENPYHNEPGFEQERHPGDSKNYNECIRHETIRVAVCDMMEGKSPSPEPLRGVME
KSFLEYYDFYEVACKDRLHLQGQTMQDPFGEKRGHFDYQSLLMRLGLIRQKVLERLHNEN
AEMDSDSSSSGTETDLHGSLRV

Sequence of entity 3 (D), FASTA

>9YLF_3 Ubiquitin (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

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