9DQB | pdb_00009dqb

Cryo-EM structure of a double-loaded SUMO E1-E2-SUMO1 complex.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structures reveal the molecular mechanism of SUMO E1-E2 thioester transfer.

Nayak, A.Nayak, D.Jia, L.Ruben, E.A.Viswanadhapalli, S.Dos Santos Bury, P.Nassar, K.M.Yu, C.H.Tumanova, A.A.Stratton, C.M.Ebadi, P.Ivanov, D.N.Sung, P.Vadlamudi, R.K.Wasmuth, E.V.Olsen, S.K.

(2025) Nat Struct Mol Biol 32: 2441-2453

  • DOI: https://doi.org/10.1038/s41594-025-01681-8
  • Primary Citation of Related Structures:  
    9DQB, 9DRJ

  • PubMed Abstract: 

    Post-translational modification of proteins by SUMO (small ubiquitin-like modifier) regulates fundamental cellular processes and occurs through the sequential interactions and activities of three enzymes: E1, E2 and E3. SUMO E1 activates SUMO in a two-step process involving adenylation and thioester bond formation, followed by transfer of SUMO to its dedicated E2 enzyme, UBC9. This process is termed E1-E2 thioester transfer (or transthioesterification). Despite its fundamental importance, the molecular basis for SUMO E1-UBC9 thioester transfer and the molecular rules governing SUMO E1-UBC9 specificity are poorly understood. Here we present cryo-EM reconstructions of human SUMO E1 in complex with UBC9, SUMO1 adenylate and SUMO1 thioester intermediate. Our structures reveal drastic conformational changes that accompany thioester transfer, providing insights into the molecular recognition of UBC9 by SUMO E1 and delineating the rules that govern SUMO E1-UBC9 specificity. Collectively, our structural, biochemical and cell-based studies elucidate the molecular mechanisms by which SUMOylation exerts its essential biological functions.


  • Organizational Affiliation
    • Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SUMO-conjugating enzyme UBC9A [auth C]178Homo sapiensMutation(s): 6 
Gene Names: UBE2IUBC9UBCE9
EC: 2.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63279 (Homo sapiens)
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Go to UniProtKB:  P63279
PHAROS:  P63279
GTEx:  ENSG00000103275 
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UniProt GroupP63279
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 1B [auth D]117Homo sapiensMutation(s): 0 
Gene Names: SUMO1SMT3CSMT3H3UBL1OK/SW-cl.43
UniProt & NIH Common Fund Data Resources
Find proteins for P63165 (Homo sapiens)
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PHAROS:  P63165
GTEx:  ENSG00000116030 
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UniProt GroupP63165
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 1C [auth G]117Homo sapiensMutation(s): 1 
Gene Names: SUMO1SMT3CSMT3H3UBL1OK/SW-cl.43
UniProt & NIH Common Fund Data Resources
Find proteins for P63165 (Homo sapiens)
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PHAROS:  P63165
GTEx:  ENSG00000116030 
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UniProt GroupP63165
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
SUMO-activating enzyme subunit 1D [auth A]366Homo sapiensMutation(s): 0 
Gene Names: SAE1AOS1SUA1UBLE1A
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Find proteins for Q9UBE0 (Homo sapiens)
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PHAROS:  Q9UBE0
GTEx:  ENSG00000142230 
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UniProt GroupQ9UBE0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
SUMO-activating enzyme subunit 2E [auth B]548Homo sapiensMutation(s): 0 
Gene Names: UBA2SAE2UBLE1BHRIHFB2115
EC: 2.3.2
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Find proteins for Q9UBT2 (Homo sapiens)
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Go to UniProtKB:  Q9UBT2
PHAROS:  Q9UBT2
GTEx:  ENSG00000126261 
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UniProt GroupQ9UBT2
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references
  • Version 1.2: 2025-12-24
    Changes: Data collection, Database references