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- PDB-2asq: Solution Structure of SUMO-1 in Complex with a SUMO-binding Motif... -

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Basic information

Entry
Database: PDB / ID: 2asq
TitleSolution Structure of SUMO-1 in Complex with a SUMO-binding Motif (SBM)
Components
  • Protein inhibitor of activated STAT2
  • Small ubiquitin-related modifier 1
KeywordsPROTEIN BINDING / Protein-Peptide Complex / SUMO-1 / Small Ubiquitin-like Modifier 1 / SUMO-Binding Motif / SBM / Protein Inhibitor of Activated STAT / PIASx
Function / homology
Function and homology information


SUMO ligase activity / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / negative regulation of action potential / negative regulation of transcription initiation by RNA polymerase II / negative regulation of androgen receptor signaling pathway ...SUMO ligase activity / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / negative regulation of action potential / negative regulation of transcription initiation by RNA polymerase II / negative regulation of androgen receptor signaling pathway / small protein activating enzyme binding / regulation of calcium ion transmembrane transport / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / SUMOylation of DNA methylation proteins / negative regulation of protein import into nucleus / Maturation of nucleoprotein / 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 / roof of mouth development / Maturation of nucleoprotein / SUMOylation of ubiquitinylation proteins / 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 / presynaptic cytosol / endoplasmic reticulum unfolded protein response / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / SUMOylation of intracellular receptors / Maturation of DENV proteins / regulation of protein stability / positive regulation of protein-containing complex assembly / PML body / PKR-mediated signaling / Activation of anterior HOX genes in hindbrain development during early embryogenesis / transcription coregulator activity / Formation of Incision Complex in GG-NER / protein tag activity / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to heat / nuclear membrane / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / nuclear speck / protein stabilization / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA repair / regulation of transcription by RNA polymerase II / nucleolus / chromatin / negative regulation of transcription by RNA polymerase II / glutamatergic synapse / enzyme binding / DNA binding / DNA-templated transcription / RNA binding / nucleoplasm / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
PINIT domain / PINIT domain superfamily / PINIT domain / PINIT domain profile. / MIZ/SP-RING zinc finger / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / Small ubiquitin-related modifier 1, Ubl domain / SAP domain superfamily / SAP motif profile. ...PINIT domain / PINIT domain superfamily / PINIT domain / PINIT domain profile. / MIZ/SP-RING zinc finger / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / Small ubiquitin-related modifier 1, Ubl domain / SAP domain superfamily / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
E3 SUMO-protein ligase PIAS2 / Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSong, J. / Zhang, Z. / Hu, W. / Chen, Y.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Small Ubiquitin-like Modifier (SUMO) Recognition of a SUMO Binding Motif: A reversal of the bound orientation
Authors: Song, J. / Zhang, Z. / Hu, W. / Chen, Y.
History
DepositionAug 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: Small ubiquitin-related modifier 1
B: Protein inhibitor of activated STAT2


Theoretical massNumber of molelcules
Total (without water)13,9852
Polymers13,9852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
Representative

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Components

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


Mass: 11149.545 Da / Num. of mol.: 1 / Fragment: Structured Region of SUMO-1 (residues 21-97)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1 / Plasmid: PET11a+ (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(Novagen) / References: UniProt: P63165
#2: Protein/peptide Protein inhibitor of activated STAT2 / Protein inhibitor of activated STAT x / Msx-interacting zinc finger protein / Miz1 / DAB2- ...Protein inhibitor of activated STAT x / Msx-interacting zinc finger protein / Miz1 / DAB2-interacting protein / DIP / Androgen receptor-interacting protein 3 / ARIP3 / PIAS-NY protein


Mass: 2835.079 Da / Num. of mol.: 1 / Fragment: SUMO-binding Motif in PIASx
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIAS2, PIASX / Plasmid: PET31a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)plysS (Novagen) / References: UniProt: O75928

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
121HNCA-J
2323D 13C-separated NOESY
242HNCA-J
151(H)CCH-TOCSY
262CC(co)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM 15N,13C-enriched PIASx-P peptide and unlabeled SUMO-1; 20mM phosphate buffer pH6.8; 92% H2O, 8% D2O, 17oC92% H2O, 8% D2O
21 mM 15N,13C-enriched SUMO-1 and unlabeled PIASx-P peptide; 20mM phosphate buffer pH6.8; 92% H2O, 8% D2O, 17oC92% H2O, 8% D2O

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.1Brukercollection
NMRPipe1.1Delaglio, Frankprocessing
HADDOCK1.3Bonvin, Alexandrerefinement
Felix2000Accelrysdata analysis
NMRView5One Moon Scientificdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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