- 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
Title
Solution Structure of SUMO-1 in Complex with a SUMO-binding Motif (SBM)
Components
Protein inhibitor of activated STAT2
Small ubiquitin-related modifier 1
Keywords
PROTEIN 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 / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / PML body organization ...SUMO ligase activity / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of androgen receptor signaling pathway / negative regulation of action potential / small protein activating enzyme binding / septin ring / regulation of calcium ion transmembrane transport / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / transcription factor binding / SUMOylation of transcription factors / protein sumoylation / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / Regulation of IFNG signaling / nuclear pore / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / transcription coregulator activity / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / Formation of Incision Complex in GG-NER / Activation of anterior HOX genes in hindbrain development during early embryogenesis / protein tag activity / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear membrane / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / protein stabilization / nuclear speck / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / regulation of transcription by RNA polymerase II / enzyme binding / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function
Smallubiquitin-relatedmodifier1 / 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
ProteininhibitorofactivatedSTAT2 / 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
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D 13C-separated NOESY
1
2
1
HNCA-J
2
3
2
3D 13C-separated NOESY
2
4
2
HNCA-J
1
5
1
(H)CCH-TOCSY
2
6
2
CC(co)NH
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1 mM 15N,13C-enriched PIASx-P peptide and unlabeled SUMO-1; 20mM phosphate buffer pH6.8; 92% H2O, 8% D2O, 17oC
92% H2O, 8% D2O
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1 mM 15N,13C-enriched SUMO-1 and unlabeled PIASx-P peptide; 20mM phosphate buffer pH6.8; 92% H2O, 8% D2O, 17oC
92% H2O, 8% D2O
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz
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Processing
NMR software
Name
Version
Developer
Classification
XwinNMR
1.1
Bruker
collection
NMRPipe
1.1
Delaglio, Frank
processing
HADDOCK
1.3
Bonvin, Alexandre
refinement
Felix
2000
Accelrys
dataanalysis
NMRView
5
OneMoonScientific
dataanalysis
Refinement
Method: simulated annealing / Software ordinal: 1
NMR ensemble
Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 10 / Conformers submitted total number: 10
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