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- PDB-8odr: Mimetic of UBC9-SUMO1 -

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Basic information

Entry
Database: PDB / ID: 8odr
TitleMimetic of UBC9-SUMO1
Components
  • SUMO-conjugating enzyme UBC9
  • Small ubiquitin-related modifier 1
KeywordsLIGASE / UBC9 / SUMO1 / CONJUGATION / UBIQUITIN-LIKE
Function / homology
Function and homology information


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 / negative regulation of delayed rectifier potassium channel activity ...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 / negative regulation of delayed rectifier potassium channel activity / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly / synaptonemal complex / small protein activating enzyme binding / negative regulation of action potential / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / regulation of calcium ion transmembrane transport / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / nuclear export / Transferases; Acyltransferases; Aminoacyltransferases / regulation of cardiac muscle cell contraction / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of DNA binding / Maturation of nucleoprotein / cellular response to cadmium ion / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / transcription factor binding / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / roof of mouth development / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / postsynaptic cytosol / potassium channel regulator activity / transporter activator activity / Regulation of IFNG signaling / nuclear pore / 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 / Meiotic synapsis / negative regulation of DNA-binding transcription factor activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / chromosome segregation / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / Formation of Incision Complex in GG-NER / protein tag activity / modulation of chemical synaptic transmission / protein modification process / PML body / PKR-mediated signaling / regulation of protein stability / Schaffer collateral - CA1 synapse / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear envelope / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / regulation of protein localization / cellular response to heat / 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 / cell division / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Small ubiquitin-related modifier 1, Ubl domain / 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 ...Small ubiquitin-related modifier 1, Ubl domain / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsCoste, F. / Goffinont, S. / Suskiewicz, M.J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101078837European Union
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural insights into the regulation of the human E2∼SUMO conjugate through analysis of its stable mimetic.
Authors: Goffinont, S. / Coste, F. / Prieu-Serandon, P. / Mance, L. / Gaudon, V. / Garnier, N. / Castaing, B. / Suskiewicz, M.J.
History
DepositionMar 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUMO-conjugating enzyme UBC9
B: Small ubiquitin-related modifier 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5763
Polymers29,4802
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.280, 53.575, 100.259
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#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: 19002.867 Da / Num. of mol.: 1 / Mutation: K14R, A129K
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
#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: 10476.812 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: LiSO4, Tris pH8.5, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.85→47.25 Å / Num. obs: 6755 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 64.3 Å2 / CC1/2: 0.982 / Rpim(I) all: 0.106 / Net I/σ(I): 5
Reflection shellResolution: 2.85→3 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 949 / CC1/2: 0.682 / Rpim(I) all: 0.506 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→47.25 Å / SU ML: 0.3751 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2579 702 10.45 %
Rwork0.2212 6013 -
obs0.2252 6715 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.45 Å2
Refinement stepCycle: LAST / Resolution: 2.85→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 5 0 1788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00241834
X-RAY DIFFRACTIONf_angle_d0.50422501
X-RAY DIFFRACTIONf_chiral_restr0.0408271
X-RAY DIFFRACTIONf_plane_restr0.0044331
X-RAY DIFFRACTIONf_dihedral_angle_d13.2091660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.070.35711230.35031183X-RAY DIFFRACTION99.77
3.07-3.380.331450.2751177X-RAY DIFFRACTION99.92
3.38-3.870.26961490.23431177X-RAY DIFFRACTION100
3.87-4.870.25171330.18441205X-RAY DIFFRACTION99.93
4.87-47.250.20781520.19621271X-RAY DIFFRACTION99.86

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