9YKW: Ubiquitin-like modifier-activating enzyme 6

Cryo-EM structure of double-loaded human UBA6-UBE2Z-Ub(t)/Ub(a) thioester mimetic complex. Determined by electron microscopy at 3.86 Å resolution. Released 12 Aug 2026.

Method: Electron microscopy
Resolution: 3.86 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,794
Mol. weight: 162.2 kDa
Ligands: IHP
Released: 12 Aug 2026

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

Secondary structure: helices and β-sheets

9YKW contains 72 α-helices and 64 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: 53 helices, 45 β-strands

Element	Residues	Length	Sheet
α-helix	46-48	3
α-helix	53-59	7
β-strand	63-67	5	1
α-helix	72-83	12
β-strand	87-91	5	1
β-strand	95	1	2
α-helix	98-101	4
α-helix	110-113	4
β-strand	117	1	2
α-helix	118-122	5
α-helix	124-127	4
β-strand	134-136	3	1
α-helix	149-153	5
β-strand	156-160	5	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
α-helix	212-215	4
β-strand	216-217	2	5
β-strand	218-221	4	6
β-strand	227-231	5	6
α-helix	232	1
β-strand	244-251	8	5
β-strand	259-262	4	5
β-strand	264-267	4	6
β-strand	270-273	4	6
α-helix	280-282	3
β-strand	284-290	7	5
β-strand	295-298	4	4
α-helix	302-306	5
α-helix	311-313	3
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	417-420	4	1
α-helix	422-425	4
α-helix	433-436	4
α-helix	444-449	6
α-helix	452-459	8
β-strand	462-465	4	7
α-helix	473-482	10
β-strand	492-496	5	7
β-strand	500	1	8
β-strand	520	1	8
α-helix	521-532	12
β-strand	538-541	4	7
α-helix	547-551	5
α-helix	555-560	6
β-strand	563-566	4	7
α-helix	572-584	13
β-strand	588-594	7	7
β-strand	597-603	7	7
β-strand	608	1	9
α-helix	611-613	3
α-helix	616-619	4
α-helix	624-629	6
α-helix	634-646	13
α-helix	647-651	5
α-helix	652-662	11
α-helix	670-674	5
α-helix	684-690	7
α-helix	696-707	12
α-helix	708-712	5
α-helix	713-721	9
α-helix	752-768	17
α-helix	780-786	7
α-helix	858-872	15
α-helix	880-888	9
α-helix	895-913	19
β-strand	922-927	6	7
β-strand	932-937	6	7
β-strand	940	1	9
β-strand	944	1	10
β-strand	952	1	10
β-strand	958-961	4	11
β-strand	967	1	12
α-helix	968-978	11
β-strand	985-987	3	13
β-strand	992-994	3	13
α-helix	1002-1005	4
β-strand	1008	1	12
α-helix	1009-1013	5
β-strand	1021-1024	4	11
β-strand	1025-1027	3	13
β-strand	1028	1	14
α-helix	1037	1
β-strand	1038	1	14
α-helix	1039	1
α-helix	1041-1042	2
β-strand	1043-1046	4	11

Chain B: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	15
β-strand	12-16	5	15
β-strand	22	1	16
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	15
β-strand	48-50	3	15
β-strand	55	1	16
β-strand	66-70	5	15
β-strand	74	1	17

Chain C: 15 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	101-113	13
α-helix	115-116	2
β-strand	121-123	3	18
β-strand	131-136	6	18
α-helix	137-138	2
β-strand	147-153	7	18
α-helix	162-163	2
β-strand	164-167	4	18
α-helix	171-173	3
β-strand	186	1	18
β-strand	189	1	17
α-helix	206-216	11
α-helix	222-224	3
α-helix	236-249	14
α-helix	250-254	5
α-helix	255-258	4
α-helix	265-267	3
α-helix	268-278	11
α-helix	280-287	8
α-helix	313-315	3
α-helix	316-322	7

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	19
β-strand	12-15	4	19
α-helix	23-33	11
α-helix	38-40	3
β-strand	44-45	2	7
β-strand	48-49	2	7
β-strand	65-67	3	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	B, D	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 Z	C	protein	262	Homo sapiens	Q9H832 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9YKW_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, D), FASTA

>9YKW_2 Ubiquitin (chains B, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (C), FASTA

>9YKW_3 Ubiquitin-conjugating enzyme E2 Z (chains C)
GERTAPQSLLRIKRDIMSIYKEPPPGMFVVPDTVDMTKIHALITGPFDTPYEGGFFLFVF
RCPPDYPIHPPRVKLMTTGNNTVRFNPNFKRNGRVCLSILGTWTGPAWSPAQSISSVLIS
IQSLMTENPYHNEPGFEQERHPGDSKNYNECIRHETIRVAVCDMMEGKSPSPEPLRGVME
KSFLEYYDFYEVACKDRLHLQGQTMQDPFGEKRGHFDYQSLLMRLGLIRQKVLERLHNEN
AEMDSDSSSSGTETDLHGSLRV

Ligands and cofactors

ID	Name	Formula	Copies
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
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

Browse structure collections

About this viewer

MolViewer shows 9YKW directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.