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- PDB-9dqb: Cryo-EM structure of a double-loaded SUMO E1-E2-SUMO1 complex. -

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Basic information

Entry
Database: PDB / ID: 9dqb
TitleCryo-EM structure of a double-loaded SUMO E1-E2-SUMO1 complex.
Components
  • (SUMO-activating enzyme subunit ...) x 2
  • (Small ubiquitin-related modifier ...) x 2
  • SUMO-conjugating enzyme UBC9
KeywordsLIGASE / Sumo1(a) / Sumo1(t) / sae1 / ubc9 / uba2
Function / homology
Function and homology information


SUMO activating enzyme complex / SUMO activating enzyme activity / SUMO ligase complex / SUMO conjugating enzyme activity / transferase complex / RING-like zinc finger domain binding / SUMOylation of nuclear envelope proteins / HLH domain binding / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors ...SUMO activating enzyme complex / SUMO activating enzyme activity / SUMO ligase complex / SUMO conjugating enzyme activity / transferase complex / RING-like zinc finger domain binding / SUMOylation of nuclear envelope proteins / HLH domain binding / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / ubiquitin activating enzyme activity / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / nuclear stress granule / negative regulation of action potential / negative regulation of transcription initiation by RNA polymerase II / import into nucleus / mitotic nuclear membrane reassembly / positive regulation of protein sumoylation / small protein activating enzyme binding / regulation of calcium ion transmembrane transport / synaptonemal complex / SUMO binding / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / negative regulation of protein import into nucleus / SUMOylation of DNA methylation proteins / Maturation of nucleoprotein / nuclear export / ATP-dependent protein binding / XY body / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / regulation of cardiac muscle cell contraction / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / transcription factor binding / roof of mouth development / Maturation of nucleoprotein / : / SUMOylation of ubiquitinylation proteins / ubiquitin-like protein conjugating enzyme binding / ubiquitin-specific protease binding / cellular response to cadmium ion / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / ubiquitin-like protein ligase binding / nuclear pore / protein sumoylation / potassium channel regulator activity / Regulation of IFNG signaling / transporter activator activity / postsynaptic cytosol / SUMOylation of DNA damage response and repair proteins / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / presynaptic cytosol / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / protein modification process / transcription coregulator binding / Meiotic synapsis / SUMOylation of chromatin organization proteins / SUMOylation of intracellular receptors / Regulation of endogenous retroelements by KRAB-ZFP proteins / Maturation of DENV proteins / chromosome segregation / regulation of protein stability / positive regulation of protein-containing complex assembly / PML body / PKR-mediated signaling / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / enzyme activator activity / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nuclear envelope / cellular response to heat / transferase activity / nuclear membrane / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Dengue Virus-Host Interactions / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / nuclear body / nuclear speck / protein stabilization / positive regulation of cell migration / protein heterodimerization activity / cell division / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA repair / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / glutamatergic synapse / magnesium ion binding / enzyme binding
Similarity search - Function
SUMO-activating enzyme subunit 2, C-terminal domain / SUMO-activating enzyme subunit 2 C-terminus / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Small ubiquitin-related modifier 1, Ubl domain / Ubiquitin-activating enzyme E1, Cys active site ...SUMO-activating enzyme subunit 2, C-terminal domain / SUMO-activating enzyme subunit 2 C-terminus / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Small ubiquitin-related modifier 1, Ubl domain / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / : / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Small ubiquitin-related modifier 1 / SUMO-conjugating enzyme UBC9 / SUMO-activating enzyme subunit 1 / SUMO-activating enzyme subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsJia, L. / Nayak, D. / Ruben, E.A. / Nayak, A. / Wasmuth, E.V. / Olsen, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Cryo-EM structures reveal the molecular mechanism of SUMO E1-E2 thioester transfer.
Authors: Anindita Nayak / Digant Nayak / Lijia Jia / Eliza A Ruben / Suryavathi Viswanadhapalli / Priscila Dos Santos Bury / Khaled Mohamed Nassar / Corey H Yu / Anna A Tumanova / Caleb M Stratton / ...Authors: Anindita Nayak / Digant Nayak / Lijia Jia / Eliza A Ruben / Suryavathi Viswanadhapalli / Priscila Dos Santos Bury / Khaled Mohamed Nassar / Corey H Yu / Anna A Tumanova / Caleb M Stratton / Pirouz Ebadi / Dmitri N Ivanov / Patrick Sung / Ratna K Vadlamudi / Elizabeth V Wasmuth / Shaun K Olsen /
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 ...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.
History
DepositionSep 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: SUMO-conjugating enzyme UBC9
D: Small ubiquitin-related modifier 1
G: Small ubiquitin-related modifier 1
A: SUMO-activating enzyme subunit 1
B: SUMO-activating enzyme subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,1807
Polymers148,7675
Non-polymers4132
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 1 types, 1 molecules C

#1: Protein SUMO-conjugating enzyme UBC9 / RING-type E3 SUMO transferase UBC9 / SUMO-protein ligase / Ubiquitin carrier protein 9 / Ubiquitin ...RING-type E3 SUMO transferase UBC9 / SUMO-protein ligase / Ubiquitin carrier protein 9 / Ubiquitin carrier protein I / Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / p18


Mass: 20255.172 Da / Num. of mol.: 1 / Mutation: F22A,G23Q,V25S,A129K,C138S,K153R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Production host: Escherichia coli (E. coli)
References: UniProt: P63279, Transferases; Acyltransferases; Aminoacyltransferases

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Small ubiquitin-related modifier ... , 2 types, 2 molecules DG

#2: Protein Small ubiquitin-related modifier 1 / SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain ...SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein SMT3C / Smt3C / Ubiquitin-like protein UBL1


Mass: 13320.909 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 / Production host: Escherichia coli (E. coli) / References: UniProt: P63165
#3: Protein Small ubiquitin-related modifier 1 / SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain ...SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein SMT3C / Smt3C / Ubiquitin-like protein UBL1


Mass: 13288.844 Da / Num. of mol.: 1 / Mutation: C52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 / Production host: Escherichia coli (E. coli) / References: UniProt: P63165

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SUMO-activating enzyme subunit ... , 2 types, 2 molecules AB

#4: Protein SUMO-activating enzyme subunit 1 / Ubiquitin-like 1-activating enzyme E1A


Mass: 40671.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAE1, AOS1, SUA1, UBLE1A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBE0
#5: Protein SUMO-activating enzyme subunit 2 / Anthracycline-associated resistance ARX / Ubiquitin-like 1-activating enzyme E1B / Ubiquitin-like ...Anthracycline-associated resistance ARX / Ubiquitin-like 1-activating enzyme E1B / Ubiquitin-like modifier-activating enzyme 2


Mass: 61230.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA2, SAE2, UBLE1B, HRIHFB2115 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UBT2, Transferases; Acyltransferases; Aminoacyltransferases

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Double-loaded SUMO E1-E2-SUMO1 complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113479 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039333
ELECTRON MICROSCOPYf_angle_d0.7512605
ELECTRON MICROSCOPYf_dihedral_angle_d6.8151258
ELECTRON MICROSCOPYf_chiral_restr0.0461395
ELECTRON MICROSCOPYf_plane_restr0.0041639

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