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- PDB-2las: Molecular Determinants of Paralogue-Specific SUMO-SIM Recognition -

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Basic information

Entry
Database: PDB / ID: 2las
TitleMolecular Determinants of Paralogue-Specific SUMO-SIM Recognition
Components
  • M-IR2_peptide
  • Small ubiquitin-related modifier 1
KeywordsTRANSCRIPTION / RanBP2 / post-translational modification
Function / homology
Function and homology information


cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / negative regulation of potassium ion transmembrane transporter activity / SUMO ligase activity / protein localization to nuclear pore / annulate lamellae / : / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors ...cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / negative regulation of potassium ion transmembrane transporter activity / SUMO ligase activity / protein localization to nuclear pore / annulate lamellae / : / 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) / 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 / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / small protein activating enzyme binding / nuclear inclusion body / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / NLS-bearing protein import into nucleus / SUMOylation of SUMOylation proteins / XY body / regulation of calcium ion transmembrane transport / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Maturation of nucleoprotein / Nuclear import of Rev protein / nuclear export / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / kinase activator activity / Transferases; Acyltransferases; Aminoacyltransferases / regulation of cardiac muscle cell contraction / SUMO transferase activity / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Maturation of nucleoprotein / centrosome localization / regulation of gluconeogenesis / Viral Messenger RNA Synthesis / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / 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 / Regulation of HSF1-mediated heat shock response / mRNA transport / potassium channel regulator activity / Regulation of IFNG signaling / postsynaptic cytosol / transporter activator activity / nuclear pore / negative regulation of DNA-binding transcription factor activity / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / Resolution of Sister Chromatid Cohesion / response to amphetamine / SUMOylation of chromatin organization proteins / HCMV Late Events / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / PML body / PKR-mediated signaling / regulation of protein stability / small GTPase binding / ISG15 antiviral mechanism / Formation of Incision Complex in GG-NER / protein tag activity / HCMV Early Events / Separation of Sister Chromatids / Signaling by ALK fusions and activated point mutants / nuclear envelope / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding
Similarity search - Function
Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Small ubiquitin-related modifier 1, Ubl domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like ...Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Small ubiquitin-related modifier 1, Ubl domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / PH-like domain superfamily / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
E3 SUMO-protein ligase RanBP2 / Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsNamanja, A. / Li, Y. / Su, Y. / Wong, S. / Lu, J. / Colson, L. / Wu, C. / Li, S. / Chen, Y.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Insights into High Affinity Small Ubiquitin-like Modifier (SUMO) Recognition by SUMO-interacting Motifs (SIMs) Revealed by a Combination of NMR and Peptide Array Analysis.
Authors: Namanja, A.T. / Li, Y.J. / Su, Y. / Wong, S. / Lu, J. / Colson, L.T. / Wu, C. / Li, S.S. / Chen, Y.
History
DepositionMar 20, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Apr 27, 2016Group: Structure summary
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small ubiquitin-related modifier 1
B: M-IR2_peptide


Theoretical massNumber of molelcules
Total (without water)13,1922
Polymers13,1922
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 / 200all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: 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: 11575.005 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OK/SW-cl.43, SMT3C, SMT3H3, SUMO1, UBL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63165
#2: Protein/peptide M-IR2_peptide


Mass: 1616.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49792*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(COCA)CB
1313D HN(CA)CB
1413D HNCA
1513D HN(CO)CA
1623D 15N-edited NOESYHSQC
1722D 1H-1H TOCSY
1822D 1H-1H NOESY
1932D 1H-13C HSQC aliphatic
11032D 1H-13C HSQC aromatic
11132D 1H-1H TOCSY
11232D 1H-1H TOCSY
11332D 1H-13C HSQC-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N; U-2H] SUMO1, 1.0 mM M-IR2 peptide, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-15N]; perdeuterated SUMO1, 0.6 mM M-IR2 peptide, 90% H2O/10% D2O90% H2O/10% D2O
30.6 mM [U-15N; U-2H] SUMO1, 0.4 mM M-IR2 peptide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMSUMO1-1[U-13C; U-15N; U-2H]1
1.0 mMM-IR2 peptide-21
0.5 mMSUMO1-3[U-15N]; perdeuterated2
0.6 mMM-IR2 peptide-42
0.6 mMSUMO1-5[U-15N; U-2H]3
0.4 mMM-IR2 peptide-63
Sample conditionsIonic strength: 0 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Brukercollection
TopSpin2.1Brukerprocessing
Sparky3.113Goddardchemical shift assignment
HADDOCK2Bonvinstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readdata analysis
HADDOCKBonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 200 / Conformers submitted total number: 10

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