9DRJ: SUMO E1-E2-SUMO1 complex

Cryo-EM structure of a SUMO E1-E2-SUMO1 complex. Determined by electron microscopy at 2.7 Å resolution. Released 1 Oct 2025.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,540
Mol. weight: 133.65 kDa
Ligands: ZN, AMP
Released: 1 Oct 2025

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

Secondary structure: helices and β-sheets

9DRJ contains 58 α-helices and 43 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: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	13-26	14
α-helix	28-35	8
β-strand	38-42	5	1
α-helix	46-58	13
β-strand	62-66	5	1
β-strand	70	1	2
β-strand	90	1	2
α-helix	91-102	12
β-strand	107-111	5	1
α-helix	120-123	4
β-strand	128-132	5	1
α-helix	136-148	13
β-strand	152-159	8	1
β-strand	162-168	7	1
β-strand	171-177	7	3
β-strand	206-212	7	3
α-helix	216-219	4
α-helix	227-235	9
α-helix	239-253	15
α-helix	259-261	3
α-helix	262-279	18
α-helix	284-286	3
α-helix	289-293	5
α-helix	300-319	20
β-strand	321	1	3
α-helix	323-325	3
β-strand	328-332	5	1
β-strand	337-341	5	1

Chain B: 32 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	9-17	9
β-strand	19-23	5	1
α-helix	27-39	13
β-strand	43-48	6	1
β-strand	51	1	4
α-helix	54-58	5
α-helix	65-67	3
β-strand	71	1	4
α-helix	72-83	12
β-strand	88-93	6	1
α-helix	103-106	4
β-strand	111-114	4	1
α-helix	119-132	14
β-strand	136-142	7	1
β-strand	145-151	7	1
α-helix	172-176	5
α-helix	182-197	16
α-helix	208-209	2
α-helix	223-229	7
α-helix	240-247	8
α-helix	251-256	6
α-helix	257-261	5
α-helix	262-268	7
α-helix	270-273	4
α-helix	277-279	3
α-helix	284-289	6
α-helix	308-310	3
α-helix	315-335	21
α-helix	337-339	3
α-helix	340-342	3
α-helix	349-365	17
α-helix	373-380	8
α-helix	383-385	3
α-helix	388-406	19
α-helix	410-412	3
β-strand	414-418	5	1
β-strand	427-433	7	1
α-helix	434-438	5
β-strand	451-454	4	5
α-helix	456-458	3
β-strand	460	1	6
α-helix	461-465	5
α-helix	466-470	5
β-strand	478-482	5	5
β-strand	488-491	4	5
β-strand	505	1	6
α-helix	506-509	4
β-strand	516-521	6	5
β-strand	527-534	8	5
β-strand	544-547	4	5

Chain C: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-18	16
β-strand	25-30	6	5
α-helix	31	1
β-strand	36-46	11	5
α-helix	47-48	2
β-strand	57-63	7	5
β-strand	74-77	4	5
β-strand	86	1	7
β-strand	91	1	5
β-strand	92	1	7
α-helix	95-97	3
α-helix	109-121	13
α-helix	133-138	6
α-helix	141-154	14

Chain D: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	8
β-strand	33-38	6	8
α-helix	45-55	11
β-strand	62-66	5	8
β-strand	69-70	2	8
α-helix	71-72	2
α-helix	77-80	4
β-strand	86-92	7	8
α-helix	93-94	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SUMO-activating enzyme subunit 1	A	protein	346	Homo sapiens	Q9UBE0 (AlphaFold model)
SUMO-activating enzyme subunit 2	B	protein	548	Homo sapiens	Q9UBT2 (AlphaFold model)
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)

Sequence of entity 1 (A), FASTA

>9DRJ_1 SUMO-activating enzyme subunit 1 (chains A)
MVEKEEAGGGISEEEAAQYDRQIRLWGLEAQKRLRASRVLLVGLKGLGAEIAKNLILAGV
KGLTMLDHEQVTPEDPGAQFLIRTGSVGRNRAEASLERAQNLNPMVDVKVDTEDIEKKPE
SFFTQFDAVCLTCCSRDVIVKVDQICHKNSIKFFTGDVFGYHGYTFANLGEHEFVEEKTK
VAKVSQGVEDGPDTKRAKLDSSETTMVKKKVVFCPVKEALEVDWSSEKAKAALKRTTSDY
FLLQVLLKFRTDKGRDPSSDTYEEDSELLLQIRNDVLDSLGISPDLLPEDFVRYCFSEMA
PVCAVVGGILAQEIVKALSQRDPPHNNFFFFDGMKGNGIVECLGPK

Sequence of entity 2 (B), FASTA

>9DRJ_2 SUMO-activating enzyme subunit 2 (chains B)
MALSRGLPRELAEAVAGGRVLVVGAGGIGCELLKNLVLTGFSHIDLIDLDTIDVSNLNRQ
FLFQKKHVGRSKAQVAKESVLQFYPKANIVAYHDSIMNPDYNVEFFRQFILVMNALDNRA
ARNHVNRMCLAADVPLIESGTAGYLGQVTTIKKGVTECYECHPKPTQRTFPGCTIRNTPS
EPIHCIVWAKYLFNQLFGEEDADQEVSPDRADPEAAWEPTEAEARARASNEDGDIKRIST
KEWAKSTGYDPVKLFTKLFKDDIRYLLTMDKLWRKRKPPVPLDWAEVQSQGEETNASDQQ
NEPQLGLKDQQVLDVKSYARLFSKSIETLRVHLAEKGDGAELIWDKDDPSAMDFVTSAAN
LRMHIFSMNMKSRFDIKSMAGNIIPAIATTNAVIAGLIVLEGLKILSGKIDQCRTIFLNK
QPNPRKKLLVPCALDPPNPNCYVCASKPEVTVRLNVHKVTVLTLQDKIVKEKFAMVAPDV
QIEDGKGTILISSEEGETEANNHKKLSEFGIRNGSRLQADDFLQDYTLLINILHSEDLGK
DVEFEVVG

Sequence of entity 3 (C), FASTA

>9DRJ_3 SUMO-conjugating enzyme UBC9 (chains C)
MGSSHHHHHHSSGLVPRGSHMSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMN
WECAIPGKKGTPWEGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEED
KDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYSQNRVEYEKRVRAQAKKFAPS

Sequence of entity 4 (D), FASTA

>9DRJ_4 Small ubiquitin-related modifier 1 (chains D)
MGSSHHHHHHSSGLVPRGSHMSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKM
TTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	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 Q9UBE0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9QN5 1.97 Å, Crystal structure of human SUMO E1 with small unit cell parameters in the P1 21 1 space…
6XOG 1.98 Å, Structure of SUMO1-ML786519 adduct bound to SAE
6XOI 2.0 Å, Structure of SUMO1-ML00752641 adduct bound to SAE
8VY5 2.01 Å, Crystal structure of human SAE1
6XOH 2.23 Å, Structure of SUMO1-ML00789344 adduct bound to SAE
1Y8Q 2.25 Å, Sumo E1 activating enzyme SAE1-SAE2-MG-ATP complex
3KYC 2.45 Å, Human SUMO E1 complex with a SUMO1-AMP mimic
6CWY 2.46 Å, Crystal structure of SUMO E1 in complex with an allosteric inhibitor
9IF6 2.51 Å, Crystal structure of human SUMO E1 with large unit cell parameters in the P1 21 1 space…
3KYD 2.61 Å, Human SUMO E1~SUMO1-AMP tetrahedral intermediate mimic
1Y8R 2.75 Å, Sumo E1 activating enzyme SAE1-SAE2-SUMO1-MG-ATP complex
6CWZ 3.1 Å, Crystal structure of apo SUMO E1

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