9DQB: Double-loaded SUMO E1-E2-SUMO1 complex

Cryo-EM structure of a double-loaded SUMO E1-E2-SUMO1 complex. Determined by electron microscopy at 3.6 Å resolution. Released 1 Oct 2025.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 5
Atoms: 9,154
Mol. weight: 149.18 kDa
Ligands: AMP, ZN
Released: 1 Oct 2025

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

Secondary structure: helices and β-sheets

9DQB contains 58 α-helices and 51 β-strands across 5 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: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	13-18	6
α-helix	20-35	16
β-strand	38-42	5	6
α-helix	46-58	13
β-strand	62-66	5	6
β-strand	70	1	7
α-helix	83	1
β-strand	90	1	7
α-helix	91-102	12
β-strand	107-111	5	6
α-helix	120-123	4
β-strand	128-131	4	6
α-helix	136-148	13
β-strand	152-159	8	6
β-strand	162-168	7	6
β-strand	172-177	6	8
β-strand	206-211	6	8
α-helix	216-219	4
α-helix	227-233	7
α-helix	239-253	15
α-helix	259-261	3
α-helix	262-280	19
α-helix	284-286	3
α-helix	291-295	5
α-helix	300-319	20
α-helix	323-326	4
β-strand	328-332	5	6
β-strand	337-341	5	6

Chain B: 27 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	9-17	9
β-strand	19-23	5	6
α-helix	27-39	13
β-strand	43-47	5	6
β-strand	51	1	9
α-helix	55-58	4
α-helix	65-67	3
β-strand	71	1	9
α-helix	72-80	9
β-strand	88-92	5	6
α-helix	103-107	5
β-strand	111-114	4	6
α-helix	119-132	14
β-strand	136-142	7	6
β-strand	143	1	10
β-strand	145-151	7	6
α-helix	182-196	15
α-helix	219-222	4
α-helix	223-228	6
α-helix	240-246	7
α-helix	251-256	6
α-helix	257-261	5
α-helix	262-267	6
α-helix	270-273	4
α-helix	277-278	2
α-helix	284-289	6
α-helix	315-335	21
α-helix	349-365	17
α-helix	373-380	8
β-strand	386	1	10
α-helix	388-406	19
β-strand	414-418	5	6
β-strand	427-433	7	6
α-helix	435-438	4
β-strand	449-454	6	1
β-strand	460	1	11
α-helix	461-463	3
α-helix	464-470	7
β-strand	481-482	2	1
β-strand	488-489	2	1
α-helix	495-498	4
α-helix	499-501	3
β-strand	505	1	11
β-strand	516-519	4	1
β-strand	528-534	7	1
α-helix	536-538	3
β-strand	544-546	3	1

Chain C: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-18	16
β-strand	25-30	6	1
β-strand	36-46	11	1
β-strand	57-63	7	1
α-helix	72-73	2
β-strand	74-77	4	1
β-strand	86	1	2
β-strand	91	1	1
β-strand	92	1	2
α-helix	95-97	3
α-helix	109-121	13
α-helix	132-139	8
α-helix	141-154	14

Chain D: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	3
β-strand	33-38	6	3
α-helix	44-55	12
α-helix	59-61	3
β-strand	62-66	5	3
β-strand	69-70	2	3
α-helix	71-72	2
α-helix	77-80	4
α-helix	82-83	2
β-strand	86-92	7	3

Chain G: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	22-23	2	4
α-helix	24	1
β-strand	25-27	3	5
β-strand	33-34	2	5
β-strand	37-38	2	4
α-helix	45-54	10
β-strand	63-66	4	5
β-strand	69-70	2	5
α-helix	71-72	2
α-helix	77-80	4
β-strand	87-91	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SUMO-conjugating enzyme UBC9	C	protein	178	Homo sapiens	P63279 (AlphaFold model)
Small ubiquitin-related modifier 1	D	protein	117	Homo sapiens	P63165 (AlphaFold model)
Small ubiquitin-related modifier 1	G	protein	117	Homo sapiens	P63165 (AlphaFold model)
SUMO-activating enzyme subunit 1	A	protein	366	Homo sapiens	Q9UBE0 (AlphaFold model)
SUMO-activating enzyme subunit 2	B	protein	548	Homo sapiens	Q9UBT2 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>9DQB_1 SUMO-conjugating enzyme UBC9 (chains C)
MGSSHHHHHHSSGLVPRGSHMSGIALSRLAQERKAWRKDHPAQFSAVPTKNPDGTMNLMN
WECAIPGKKGTPWEGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEED
KDWRPAITIKQILLGIQELLNEPNIQDPKQAEAYTIYSQNRVEYEKRVRAQARKFAPS

Sequence of entity 2 (D), FASTA

>9DQB_2 Small ubiquitin-related modifier 1 (chains D)
MGSSHHHHHHSSGLVPRGSHMSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKM
TTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG

Sequence of entity 3 (G), FASTA

>9DQB_3 Small ubiquitin-related modifier 1 (chains G)
MGSSHHHHHHSSGLVPRGSHMSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKM
TTHLKKLKESYAQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG

Sequence of entity 4 (A), FASTA

>9DQB_4 SUMO-activating enzyme subunit 1 (chains A)
MGSSHHHHHHSSGLVPRGSHMVEKEEAGGGISEEEAAQYDRQIRLWGLEAQKRLRASRVL
LVGLKGLGAEIAKNLILAGVKGLTMLDHEQVTPEDPGAQFLIRTGSVGRNRAEASLERAQ
NLNPMVDVKVDTEDIEKKPESFFTQFDAVCLTCCSRDVIVKVDQICHKNSIKFFTGDVFG
YHGYTFANLGEHEFVEEKTKVAKVSQGVEDGPDTKRAKLDSSETTMVKKKVVFCPVKEAL
EVDWSSEKAKAALKRTTSDYFLLQVLLKFRTDKGRDPSSDTYEEDSELLLQIRNDVLDSL
GISPDLLPEDFVRYCFSEMAPVCAVVGGILAQEIVKALSQRDPPHNNFFFFDGMKGNGIV
ECLGPK

Sequence of entity 5 (B), FASTA

>9DQB_5 SUMO-activating enzyme subunit 2 (chains B)
MALSRGLPRELAEAVAGGRVLVVGAGGIGCELLKNLVLTGFSHIDLIDLDTIDVSNLNRQ
FLFQKKHVGRSKAQVAKESVLQFYPKANIVAYHDSIMNPDYNVEFFRQFILVMNALDNRA
ARNHVNRMCLAADVPLIESGTAGYLGQVTTIKKGVTECYECHPKPTQRTFPGCTIRNTPS
EPIHCIVWAKYLFNQLFGEEDADQEVSPDRADPEAAWEPTEAEARARASNEDGDIKRIST
KEWAKSTGYDPVKLFTKLFKDDIRYLLTMDKLWRKRKPPVPLDWAEVQSQGEETNASDQQ
NEPQLGLKDQQVLDVKSYARLFSKSIETLRVHLAEKGDGAELIWDKDDPSAMDFVTSAAN
LRMHIFSMNMKSRFDIKSMAGNIIPAIATTNAVIAGLIVLEGLKILSGKIDQCRTIFLNK
QPNPRKKLLVPCALDPPNPNCYVCASKPEVTVRLNVHKVTVLTLQDKIVKEKFAMVAPDV
QIEDGKGTILISSEEGETEANNHKKLSEFGIRNGSRLQADDFLQDYTLLINILHSEDLGK
DVEFEVVG

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	1
ZN	Zinc ion	Zn	1

Primary citation

Cryo-EM structures reveal the molecular mechanism of SUMO E1-E2 thioester transfer. Nayak, A., Nayak, D., Jia, L. et al. Nat Struct Mol Biol (2025) 32:2441-2453. DOI 10.1038/s41594-025-01681-8 · PubMed

Other PDB entries of the same protein (UniProt P63279 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5F6E 1.12 Å, Crystal Structure of human Ubc9 (K48A/K49A/E54A)
5F6Y 1.14 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole)
2GRR 1.3 Å, Crystal Structure of human RanGAP1-Ubc9-D127S
5F6V 1.49 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol from…
5F6U 1.55 Å, Crystal Structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 8 (JSS190B146)
5F6D 1.55 Å, Crystal structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 6
5F6X 1.56 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole…
5F6W 1.7 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol)
2GRO 1.7 Å, Crystal Structure of human RanGAP1-Ubc9-N85Q
2GRQ 1.7 Å, Crystal Structure of human RanGAP1-Ubc9-D127A
9GLR 1.72 Å, Crystal Structure of Human UBC9 C93E
2GRN 1.8 Å, Crystal Structure of human RanGAP1-Ubc9

Browse structure collections

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