9QIA: UBA6-UbDha-BIRC6 trapped ternary complex

Structure of UBA6-UbDha-BIRC6 trapped ternary complex (cluster 2). Determined by electron microscopy at 4.38 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 4.38 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,428
Mol. weight: 173.27 kDa
Ligands: AMP, IHP
Released: 29 Oct 2025

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

Secondary structure: helices and β-sheets

9QIA contains 83 α-helices and 70 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: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	4525-4532	8
α-helix	4533-4535	3
β-strand	4537-4540	4	1
β-strand	4543-4545	3	2
β-strand	4551-4553	3	2
α-helix	4560-4565	6
α-helix	4573-4585	13
β-strand	4591	1	3
β-strand	4596	1	3
β-strand	4597-4602	6	1
β-strand	4608-4614	7	1
α-helix	4615-4616	2
β-strand	4625-4631	7	1
β-strand	4642-4645	4	1
β-strand	4659	1	4
β-strand	4664	1	1
β-strand	4665	1	4
α-helix	4668-4670	3
α-helix	4688-4694	7
α-helix	4695-4699	5
α-helix	4704-4707	4
α-helix	4712-4714	3
α-helix	4718-4735	18
α-helix	4736-4742	7
α-helix	4743-4745	3
α-helix	4752-4761	10
α-helix	4763-4779	17
α-helix	4787-4809	23
α-helix	4811-4813	3

Chain B: 60 helices, 45 β-strands

Element	Residues	Length	Sheet
α-helix	41-51	11
α-helix	53-59	7
β-strand	63-67	5	5
α-helix	71-83	13
β-strand	87-91	5	5
β-strand	95	1	6
α-helix	99-102	4
α-helix	109-114	6
β-strand	117	1	6
α-helix	118-127	10
β-strand	134-138	5	5
α-helix	149-153	5
β-strand	156-159	4	5
α-helix	164-175	12
α-helix	180-181	2
β-strand	182-189	8	5
β-strand	192-198	7	5
β-strand	203-205	3	7
α-helix	211-213	3
β-strand	215	1	8
β-strand	218-222	5	9
β-strand	227-231	5	9
α-helix	232	1
β-strand	244-248	5	8
α-helix	254-256	3
β-strand	260-262	3	8
β-strand	264-267	4	9
β-strand	270-273	4	9
α-helix	280-282	3
β-strand	287-291	5	8
β-strand	295-297	3	7
α-helix	302-307	6
α-helix	321-339	19
α-helix	342-344	3
α-helix	348-364	17
α-helix	373-381	9
α-helix	388-407	20
α-helix	411-413	3
β-strand	416-417	2	5
β-strand	420	1	5
α-helix	422-426	5
α-helix	433-436	4
α-helix	444-449	6
α-helix	452-458	7
β-strand	462-466	5	10
α-helix	470-482	13
β-strand	492-496	5	10
β-strand	500	1	11
α-helix	505-508	4
α-helix	514-516	3
β-strand	520	1	11
α-helix	521-530	10
β-strand	538-541	4	10
α-helix	548-551	4
α-helix	555-560	6
β-strand	563-566	4	10
α-helix	571-582	12
β-strand	588-594	7	10
β-strand	597-603	7	10
β-strand	608	1	12
α-helix	611-613	3
α-helix	618-621	4
α-helix	624	1
α-helix	625-629	5
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	13
β-strand	733	1	13
α-helix	752-768	17
α-helix	775-778	4
α-helix	780-787	8
α-helix	793-795	3
α-helix	821-833	13
α-helix	840-842	3
α-helix	845-847	3
α-helix	858-872	15
α-helix	880-888	9
α-helix	890-892	3
α-helix	895-914	20
β-strand	923-927	5	10
β-strand	932-936	5	10
α-helix	937-939	3
β-strand	940	1	12
α-helix	941	1
β-strand	944-945	2	14
β-strand	951-952	2	14
β-strand	958-961	4	15
β-strand	967	1	16
α-helix	968-979	12
β-strand	985-988	4	17
β-strand	991-994	4	17
α-helix	1002-1006	5
β-strand	1008	1	16
α-helix	1009-1013	5
β-strand	1021-1024	4	15
β-strand	1025-1028	4	17
α-helix	1036-1037	2
β-strand	1038-1039	2	17
β-strand	1043-1046	4	15

Chain C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	18
β-strand	13	1	18
α-helix	23-33	11
β-strand	42-45	4	19
β-strand	48-49	2	19
α-helix	50-51	2
α-helix	57-59	3
β-strand	67	1	18
β-strand	68-70	3	19

Chain E: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	20
β-strand	12-16	5	20
β-strand	22	1	21
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	20
β-strand	48-49	2	20
β-strand	55	1	21
α-helix	56-59	4
β-strand	65-70	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6	A	protein	325	Homo sapiens	Q9NR09
Ubiquitin-like modifier-activating enzyme 6	B	protein	1054	Homo sapiens	A0AVT1 (AlphaFold model)
Polyubiquitin-C	C, E	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9QIA_1 Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6 (chains A)
GPANQEKKLGEYSKKAAMKPKPLSVLKSLEEKYVAVMKKLQFDTFEMVSEDEDGKLGFKV
NYHYMSQVKNANDANSAARARRLAQEAVTLSTSLPLSSSSSVFVRCDEERLDIMKVLITG
PADTPYANGCFEFDVYFPQDYPSSPPLVNLETTGGHSVRFNPNLYNDGKVCLSILNTWHG
RPEEKWNPQTSSFLQVLVSVQSLILVAEPYFNEPGYERSRGTPSGTQSSREYDGNIRQAT
VKWAMLEQIRNPSPCFKEVIHKHFYLKRVEIMAQCEEWIADIQQYSSDKRVGRTMSHHAA
ALKRHTAQLREELLKLPCPEGLDPD

Sequence of entity 2 (B), FASTA

>9QIA_2 Ubiquitin-like modifier-activating enzyme 6 (chains B)
GPMEGSEPVAAHQGEEASCSSWGTGSTNKNLPIMSTASVEIDDALYSRQRYVLGDTAMQK
MAKSHVFLSGMGGLGLEIAKNLVLAGIKAVTIHDTEKCQAWDLGTNFFLSEDDVVNKRNR
AEAVLKHIAELNPYVHVTSSSVPFNETTDLSFLDKYQCVVLTEMKLPLQKKINDFCRSQC
PPIKFISADVHGIWSRLFCDFGDEFEVLDTTGEEPKEIFISNITQANPGIVTCLENHPHK
LETGQFLTFREINGMTGLNGSIQQITVISPFSFSIGDTTELEPYLHGGIAVQVKTPKTVF
FESLERQLKHPKCLIVDFSNPEAPLEIHTAMLALDQFQEKYSRKPNVGCQQDSEELLKLA
TSISETLEEKPDVNADIVHWLSWTAQGFLSPLAAAVGGVASQEVLKAVTGKFSPLCQWLY
LEAADIVESLGKPECEEFLPRGDRYDALRACIGDTLCQKLQNLNIFLVGCGAIGCEMLKN
FALLGVGTSKEKGMITVTDPDLIEKSNLNRQFLFRPHHIQKPKSYTAADATLKINSQIKI
DAHLNKVCPTTETIYNDEFYTKQDVIITALDNVEARRYVDSRCLANLRPLLDSGTMGTKG
HTEVIVPHLTESYNSHRDPPEEEIPFSTLKSFPAAIEHTIQWARDKFESSFSHKPSLFNK
FWQTYSSAEEVLQKIQSGHSLEGCFQVIKLLSRRPRNWSQCVELARLKFEKYFNHKALQL
LHCFPLDIRLKDGSLFWQSPKRPPSPIKFDLNEPLHLSFLQNAAKLYATVYCIPFAEEDL
SADALLNILSEVKIQEFKPSNKVVQTDETARKPDHVPISSEDERNAIFQLEKAILSNEAT
KSDLQMAVLSFEKDDDHNGHIDFITAASNLRAKMYSIEPADRFKTKRIAGKIIPAIATTT
ATVSGLVALEMIKVTGGYPFEAYKNCFLNLAIPIVVFTETTEVRKTKIRNGISFTIWDRW
TVHGKEDFTLLDFINAVKEKYGIEPTMVVQGVKMLYVPVMPGHAKRLKLTMHKLVKPTTE
KKYVDLTVSFAPDIDGDEDLPGPPVRYYFSHDTD

Sequence of entity 3 (C, E), FASTA

>9QIA_3 Polyubiquitin-C (chains C, E)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGA

Ligands and cofactors

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

Primary citation

UBA6 specificity for ubiquitin E2 conjugating enzymes reveals a priority mechanism of BIRC6. Riechmann, C., Ellison, C.J., Anderson, J.W. et al. Nat Struct Mol Biol (2026) 33:464-478. DOI 10.1038/s41594-025-01717-z · PubMed

Other PDB entries of the same protein (UniProt Q9NR09), best resolution first:

8E2E 1.98 Å, Cryo-EM structure of helical arch of BIRC6 (from local refinement 1)
3CEG 2.01 Å, Crystal structure of the UBC domain of baculoviral IAP repeat-containing protein 6
8E2D 2.07 Å, Cryo-EM structure of BIRC6 (consensus)
8E2H 2.3 Å, Cryo-EM structure of C-terminal arm of BIRC6 (from local refinement 4)
8E2F 2.47 Å, Cryo-EM structure of N-terminal arm of BIRC6 (from local refinement 2)
8E2G 2.99 Å, Cryo-EM structure of N-terminal arm (aa68-966) of BIRC6 (from local refinement 3)
8ATO 3.0 Å, Structure of the giant inhibitor of apoptosis, BIRC6 bound to the regulator SMAC
8E2I 3.04 Å, Cryo-EM structure of BIRC6/Smac
9QH5 3.09 Å, Consensus structure of UBA6-UbDha-BIRC6 trapped ternary complex (doubly loaded)
8E2K 3.21 Å, Cryo-EM structure of BIRC6/HtrA2-S306A
8ATM 3.3 Å, Structure of the giant inhibitor of apoptosis, BIRC6 (composite map)
8ATU 3.3 Å, Cryo-EM structure of human BIRC6

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