[English] 日本語
Yorodumi
- PDB-2kqs: Phosphorylation of SUMO-interacting motif by CK2 enhances Daxx SU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kqs
TitlePhosphorylation of SUMO-interacting motif by CK2 enhances Daxx SUMO binding activity
Components
  • Death domain-associated protein 6
  • Small ubiquitin-related modifier 1
KeywordsTRANSCRIPTION / APOPTOSIS / SUMO / SIM / Daxx / Nucleus / Phosphoprotein / Ubl conjugation pathway / Transcription regulation
Function / homology
Function and homology information


cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / SUMO-modified protein reader activity / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / 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 ...cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / SUMO-modified protein reader activity / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / 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 / cellular response to sodium arsenite / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / 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 / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / transcription regulator inhibitor activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / nuclear androgen receptor binding / negative regulation of protein import into nucleus / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / protein kinase activator activity / negative regulation of DNA binding / ubiquitin-like protein ligase binding / androgen receptor signaling pathway / SUMOylation of DNA replication proteins / transcription factor binding / SUMOylation of transcription factors / protein sumoylation / regulation of protein ubiquitination / chromosome, centromeric region / extrinsic apoptotic signaling pathway via death domain receptors / potassium channel regulator activity / positive regulation of protein kinase activity / cellular response to unfolded protein / SUMOylation of DNA damage response and repair proteins / Regulation of IFNG signaling / nuclear pore / JNK cascade / cellular response to copper ion / Inhibition of DNA recombination at telomere / heat shock protein binding / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / molecular condensate scaffold 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 / HCMV Early Events / protein tag activity / transcription corepressor activity / regulation of protein localization / nucleosome assembly / Regulation of TP53 Degradation / p53 binding / 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 / histone binding / regulation of gene expression / regulation of apoptotic process / nuclear membrane / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / nuclear body / protein stabilization / nuclear speck / chromatin remodeling / positive regulation of protein phosphorylation / negative regulation of gene expression / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription / nucleolus / protein kinase binding / enzyme binding / protein homodimerization activity / RNA binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
Daxx, N-terminal Rassf1C-interacting domain / Daxx, N-terminal domain superfamily / Daxx, histone-binding domain / Daxx, histone-binding domain superfamily / Daxx N-terminal Rassf1C-interacting domain / Death domain-associated protein 6, histone binding domain / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...Daxx, N-terminal Rassf1C-interacting domain / Daxx, N-terminal domain superfamily / Daxx, histone-binding domain / Daxx, histone-binding domain superfamily / Daxx N-terminal Rassf1C-interacting domain / Death domain-associated protein 6, histone binding domain / Small ubiquitin-related modifier 1, Ubl 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 / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 1 / Death domain-associated protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsNaik, M.T. / Huang, T.H. / Shih, H.
CitationJournal: Mol.Cell / Year: 2011
Title: Structural and functional roles of Daxx SIM phosphorylation in SUMO paralog-selective binding and apoptosis modulation.
Authors: Chang, C.C. / Naik, M.T. / Huang, Y.S. / Jeng, J.C. / Liao, P.H. / Kuo, H.Y. / Ho, C.C. / Hsieh, Y.L. / Lin, C.H. / Huang, N.J. / Naik, N.M. / Kung, C.C. / Lin, S.Y. / Chen, R.H. / Chang, K. ...Authors: Chang, C.C. / Naik, M.T. / Huang, Y.S. / Jeng, J.C. / Liao, P.H. / Kuo, H.Y. / Ho, C.C. / Hsieh, Y.L. / Lin, C.H. / Huang, N.J. / Naik, N.M. / Kung, C.C. / Lin, S.Y. / Chen, R.H. / Chang, K.S. / Huang, T.H. / Shih, H.M.
History
DepositionNov 17, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 21, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Small ubiquitin-related modifier 1
B: Death domain-associated protein 6


Theoretical massNumber of molelcules
Total (without water)13,5892
Polymers13,5892
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)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

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


Mass: 11293.674 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 Death domain-associated protein 6 / Daxx / hDaxx / Fas death domain-associated protein / ETS1-associated protein 1 / EAP1


Mass: 2295.456 Da / Num. of mol.: 1 / Fragment: UNP residues 721-741 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human)
Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UER7

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: This entry describes the solution structure of complex between Small Ubiquitin like Modifier -1 (SUMO-1) and the synthetic peptide derived from the C-terminal SUMO Interacting Motif (SIM) of ...Details: This entry describes the solution structure of complex between Small Ubiquitin like Modifier -1 (SUMO-1) and the synthetic peptide derived from the C-terminal SUMO Interacting Motif (SIM) of Death Associated Protein -6.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HNCO
1713D 1H-15N TOCSY
1813D (H)CCH-COSY
1913D CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11223D 1H-15N NOESY - F1 filtered
11323D 1H-13C NOESY - F1 filtered
11423D HNHA
11542D 1H-15N HSQC - IPAP

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.27-0.5mM [U-100% 15N] SUMO1-1, 0-1.7mM DAXX20-2, 10mM potassium phosphate-3, 100mM potassium chloride-4, 2mM DTT-5, 0.1mM EDTA-6, 0.001% sodium azide-7, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] SUMO1-8, 2mM DAXX20-9, 10mM potassium phosphate-10, 100mM potassium chloride-11, 2mM DTT-12, 0.1mM EDTA-13, 0.001% sodium azide-14, 90% H2O/10% D2O90% H2O/10% D2O
32 mM SUMO1-15, 0.5mM [U-100% 13C; U-100% 15N] DAXX20-16, 10mM potassium phosphate-17, 100mM potassium chloride-18, 2mM DTT-19, 0.1mM EDTA-20, 0.001% sodium azide-21, 90% H2O/10% D2O90% H2O/10% D2O
40.5mM [U-100% 13C; U-100% 15N] SUMO1-22, 0.5mM [U-100% 13C; U-100% 15N] DAXX20-23, 10mM potassium phosphate-24, 100mM potassium chloride-25, 2mM DTT-26, 0.1mM EDTA-27, 0.001% sodium azide-28, 0.0066 w/v Pf1 phage-29, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMSUMO1-1[U-100% 15N]0.27-0.51
mMDAXX20-20-1.71
10 mMpotassium phosphate-31
100 mMpotassium chloride-41
2 mMDTT-51
0.1 mMEDTA-61
0.001 %sodium azide-71
0.5 mMSUMO1-8[U-100% 13C; U-100% 15N]2
2 mMDAXX20-92
10 mMpotassium phosphate-102
100 mMpotassium chloride-112
2 mMDTT-122
0.1 mMEDTA-132
0.001 %sodium azide-142
2 mMSUMO1-153
0.5 mMDAXX20-16[U-100% 13C; U-100% 15N]3
10 mMpotassium phosphate-173
100 mMpotassium chloride-183
2 mMDTT-193
0.1 mMEDTA-203
0.001 %sodium azide-213
0.5 mMSUMO1-22[U-100% 13C; U-100% 15N]4
0.5 mMDAXX20-23[U-100% 13C; U-100% 15N]4
10 mMpotassium phosphate-244
100 mMpotassium chloride-254
2 mMDTT-264
0.1 mMEDTA-274
0.001 %sodium azide-284
0.0066 w/vPf1 phage-294
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 290 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.2BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENstructure solution
CNS1.2BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENrefinement
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
TopSpin2.1Bruker Biospinprocessing
TopSpin2.1Bruker Biospincollection
Sparky3.113Goddardpeak picking
Sparky3.113Goddardchemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2087 / NOE intraresidue total count: 690 / NOE long range total count: 692 / NOE medium range total count: 303 / NOE sequential total count: 520 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 22 / Protein phi angle constraints total count: 109 / Protein psi angle constraints total count: 109
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Representative conformer: 1

+
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://pdbjlvh1.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