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- EMDB-47110: Cryo-EM structure of a double-loaded SUMO E1-E2-SUMO1 complex. -

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Entry
Database: EMDB / ID: EMD-47110
TitleCryo-EM structure of a double-loaded SUMO E1-E2-SUMO1 complex.
Map data
Sample
  • Complex: Double-loaded SUMO E1-E2-SUMO1 complex
    • Protein or peptide: SUMO-conjugating enzyme UBC9
    • Protein or peptide: Small ubiquitin-related modifier 1
    • Protein or peptide: Small ubiquitin-related modifier 1
    • Protein or peptide: SUMO-activating enzyme subunit 1
    • Protein or peptide: SUMO-activating enzyme subunit 2
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: ZINC ION
KeywordsSumo1(a) / Sumo1(t) / sae1 / ubc9 / uba2 / LIGASE
Function / homology
Function and homology information


SUMO activating enzyme activity / SUMO activating enzyme complex / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / transferase complex / SUMOylation of nuclear envelope proteins ...SUMO activating enzyme activity / SUMO activating enzyme complex / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / transferase complex / SUMOylation of nuclear envelope proteins / HLH domain binding / ubiquitin activating enzyme activity / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of delayed rectifier potassium channel activity / PML body organization / negative regulation of DNA binding / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / nuclear stress granule / Vitamin D (calciferol) metabolism / SUMO binding / mitotic nuclear membrane reassembly / synaptonemal complex / positive regulation of protein sumoylation / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / XY body / regulation of calcium ion transmembrane transport / ATP-dependent protein binding / Maturation of nucleoprotein / nuclear export / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / regulation of cardiac muscle cell contraction / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / positive regulation of protein targeting to mitochondrion / Maturation of nucleoprotein / ubiquitin-like protein conjugating enzyme binding / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / transcription factor binding / ubiquitin-specific protease binding / cellular response to cadmium ion / roof of mouth development / SUMOylation of transcription factors / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / potassium channel regulator activity / Regulation of IFNG signaling / postsynaptic cytosol / nuclear pore / transporter activator activity / negative regulation of DNA-binding transcription factor activity / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / Meiotic synapsis / SUMOylation of chromatin organization proteins / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / chromosome segregation / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / enzyme activator activity / PML body / modulation of chemical synaptic transmission / PKR-mediated signaling / regulation of protein stability / protein modification process / Schaffer collateral - CA1 synapse / Formation of Incision Complex in GG-NER / protein tag activity / nuclear envelope / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to heat / transferase activity / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / protein stabilization / nuclear speck / nuclear body / positive regulation of cell migration / protein heterodimerization activity / cell division / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsJia L / Nayak D / Ruben EA / Nayak A / Wasmuth EV / Olsen SK
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47110.png

Downloads & links

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Map

FileDownload / File: emd_47110.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 256 pix.
= 222.72 Å		0.87 Å/pix.
x 256 pix.
= 222.72 Å		0.87 Å/pix.
x 256 pix.
= 222.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.113
Minimum - Maximum-0.57131517 - 0.91119117
Average (Standard dev.)0.0001664105 (±0.02159713)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 222.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47110_msk_1.map
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Half map: #1

Fileemd_47110_half_map_1.map
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Half map: #2

Fileemd_47110_half_map_2.map
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Sample components

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Entire : Double-loaded SUMO E1-E2-SUMO1 complex

EntireName: Double-loaded SUMO E1-E2-SUMO1 complex
Components
  • Complex: Double-loaded SUMO E1-E2-SUMO1 complex
    • Protein or peptide: SUMO-conjugating enzyme UBC9
    • Protein or peptide: Small ubiquitin-related modifier 1
    • Protein or peptide: Small ubiquitin-related modifier 1
    • Protein or peptide: SUMO-activating enzyme subunit 1
    • Protein or peptide: SUMO-activating enzyme subunit 2
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Double-loaded SUMO E1-E2-SUMO1 complex

SupramoleculeName: Double-loaded SUMO E1-E2-SUMO1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: SUMO-conjugating enzyme UBC9

MacromoleculeName: SUMO-conjugating enzyme UBC9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Aminoacyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.255172 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MSGIALSRLA QERKAWRKDH PAQFSAVPTK NPDGTMNLMN WECAIPGKKG TPWEGGLFKL RMLFKDDYP SSPPKCKFEP PLFHPNVYPS GTVCLSILEE DKDWRPAITI KQILLGIQEL LNEPNIQDPK QAEAYTIYSQ N RVEYEKRV RAQARKFAPS

UniProtKB: SUMO-conjugating enzyme UBC9

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Macromolecule #2: Small ubiquitin-related modifier 1

MacromoleculeName: Small ubiquitin-related modifier 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.320909 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MSDQEAKPST EDLGDKKEGE YIKLKVIGQD SSEIHFKVKM TTHLKKLKES YCQRQGVPMN SLRFLFEGQ RIADNHTPKE LGMEEEDVIE VYQEQTGG

UniProtKB: Small ubiquitin-related modifier 1

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Macromolecule #3: Small ubiquitin-related modifier 1

MacromoleculeName: Small ubiquitin-related modifier 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.288844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MSDQEAKPST EDLGDKKEGE YIKLKVIGQD SSEIHFKVKM TTHLKKLKES YAQRQGVPMN SLRFLFEGQ RIADNHTPKE LGMEEEDVIE VYQEQTGG

UniProtKB: Small ubiquitin-related modifier 1

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Macromolecule #4: SUMO-activating enzyme subunit 1

MacromoleculeName: SUMO-activating enzyme subunit 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.671137 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MVEKEEAGGG ISEEEAAQYD RQIRLWGLEA QKRLRASRVL LVGLKGLGAE IAKNLILAGV KGLTMLDHE QVTPEDPGAQ FLIRTGSVGR NRAEASLERA QNLNPMVDVK VDTEDIEKKP ESFFTQFDAV CLTCCSRDVI V KVDQICHK ...String:
MGSSHHHHHH SSGLVPRGSH MVEKEEAGGG ISEEEAAQYD RQIRLWGLEA QKRLRASRVL LVGLKGLGAE IAKNLILAGV KGLTMLDHE QVTPEDPGAQ FLIRTGSVGR NRAEASLERA QNLNPMVDVK VDTEDIEKKP ESFFTQFDAV CLTCCSRDVI V KVDQICHK NSIKFFTGDV FGYHGYTFAN LGEHEFVEEK TKVAKVSQGV EDGPDTKRAK LDSSETTMVK KKVVFCPVKE AL EVDWSSE KAKAALKRTT SDYFLLQVLL KFRTDKGRDP SSDTYEEDSE LLLQIRNDVL DSLGISPDLL PEDFVRYCFS EMA PVCAVV GGILAQEIVK ALSQRDPPHN NFFFFDGMKG NGIVECLGPK

UniProtKB: SUMO-activating enzyme subunit 1

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Macromolecule #5: SUMO-activating enzyme subunit 2

MacromoleculeName: SUMO-activating enzyme subunit 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Aminoacyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.230844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALSRGLPRE LAEAVAGGRV LVVGAGGIGC ELLKNLVLTG FSHIDLIDLD TIDVSNLNRQ FLFQKKHVGR SKAQVAKESV LQFYPKANI VAYHDSIMNP DYNVEFFRQF ILVMNALDNR AARNHVNRMC LAADVPLIES GTAGYLGQVT TIKKGVTECY E CHPKPTQR ...String:
MALSRGLPRE LAEAVAGGRV LVVGAGGIGC ELLKNLVLTG FSHIDLIDLD TIDVSNLNRQ FLFQKKHVGR SKAQVAKESV LQFYPKANI VAYHDSIMNP DYNVEFFRQF ILVMNALDNR AARNHVNRMC LAADVPLIES GTAGYLGQVT TIKKGVTECY E CHPKPTQR TFPGCTIRNT PSEPIHCIVW AKYLFNQLFG EEDADQEVSP DRADPEAAWE PTEAEARARA SNEDGDIKRI ST KEWAKST GYDPVKLFTK LFKDDIRYLL TMDKLWRKRK PPVPLDWAEV QSQGEETNAS DQQNEPQLGL KDQQVLDVKS YAR LFSKSI ETLRVHLAEK GDGAELIWDK DDPSAMDFVT SAANLRMHIF SMNMKSRFDI KSMAGNIIPA IATTNAVIAG LIVL EGLKI LSGKIDQCRT IFLNKQPNPR KKLLVPCALD PPNPNCYVCA SKPEVTVRLN VHKVTVLTLQ DKIVKEKFAM VAPDV QIED GKGTILISSE EGETEANNHK KLSEFGIRNG SRLQADDFLQ DYTLLINILH SEDLGKDVEF EVVG

UniProtKB: SUMO-activating enzyme subunit 2

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Macromolecule #6: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3kyc

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 113479
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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