[English] 日本語
Yorodumi
- PDB-2las: Molecular Determinants of Paralogue-Specific SUMO-SIM Recognition -

+
Open data


ID or keywords:

Loading...

-
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 / : / SUMOylation of nuclear envelope proteins / annulate lamellae / 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 / : / SUMOylation of nuclear envelope proteins / annulate lamellae / 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 / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of DNA binding / negative regulation of action potential / nuclear stress granule / PML body organization / 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 immune response proteins / Transport of the SLBP Dependant Mature mRNA / SUMOylation of DNA methylation proteins / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / NLS-bearing protein import into nucleus / regulation of calcium ion transmembrane transport / Transport of Mature mRNA Derived from an Intronless Transcript / XY body / Maturation of nucleoprotein / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / nuclear export / Nuclear import of Rev protein / Transferases; Acyltransferases; Aminoacyltransferases / regulation of cardiac muscle cell contraction / SUMO transferase activity / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / kinase activator activity / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / centrosome localization / nucleocytoplasmic transport / Maturation of nucleoprotein / 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 / SUMOylation of transcription factors / ubiquitin-like protein ligase binding / roof of mouth development / SUMOylation of DNA replication proteins / protein sumoylation / Regulation of HSF1-mediated heat shock response / potassium channel regulator activity / mRNA transport / Regulation of IFNG signaling / postsynaptic cytosol / nuclear pore / : / transporter activator activity / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Transcriptional and post-translational regulation of MITF-M expression and activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / SUMOylation of transcription cofactors / response to amphetamine / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / HCMV Late Events / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / PKR-mediated signaling / PML body / regulation of protein stability / small GTPase binding / ISG15 antiviral mechanism / protein tag activity / Formation of Incision Complex in GG-NER / HCMV Early Events / Separation of Sister Chromatids / Signaling by ALK fusions and activated point mutants / nuclear envelope / protein folding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process
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 / PH-like domain superfamily / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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

-
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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more