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- PDB-2rnn: Solution Structure of the N-terminal SAP Domain of SUMO E3 Ligase... -

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Basic information

Entry
Database: PDB / ID: 2rnn
TitleSolution Structure of the N-terminal SAP Domain of SUMO E3 Ligases from Saccharomyces cerevisiae
ComponentsE3 SUMO-protein ligase SIZ1
KeywordsLIGASE / SUMO ligase / DNA binding / sumoylation / Metal-binding / Nucleus / Phosphoprotein / Ubl conjugation pathway / Zinc-finger
Function / homology
Function and homology information


DNA double-strand break attachment to nuclear envelope / SUMO ligase activity / SUMOylation of transcription factors / septin ring / cellular bud neck / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / SUMOylation of chromatin organization proteins ...DNA double-strand break attachment to nuclear envelope / SUMO ligase activity / SUMOylation of transcription factors / septin ring / cellular bud neck / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / SUMOylation of chromatin organization proteins / protein sumoylation / negative regulation of protein ubiquitination / chromosome segregation / transcription coregulator activity / chromatin / regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
E3 SUMO-protein ligase SIZ1, plant / 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. / SAP domain superfamily / SAP domain ...E3 SUMO-protein ligase SIZ1, plant / 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. / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 SUMO-protein ligase SIZ1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSuzuki, R. / Shindo, H. / Tase, A. / Yamazaki, T.
CitationJournal: Proteins / Year: 2009
Title: Solution structures and DNA binding properties of the N-terminal SAP domains of SUMO E3 ligases from Saccharomyces cerevisiae and Oryza sativa.
Authors: Suzuki, R. / Shindo, H. / Tase, A. / Kikuchi, Y. / Shimizu, M. / Yamazaki, T.
History
DepositionJan 30, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 SUMO-protein ligase SIZ1


Theoretical massNumber of molelcules
Total (without water)13,2421
Polymers13,2421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein E3 SUMO-protein ligase SIZ1 / SAP and Miz-finger domain-containing protein 1 / Ubiquitin-like protein ligase 1


Mass: 13242.145 Da / Num. of mol.: 1 / Fragment: residues (UNP 1-111)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIZ1, ULL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04195, Ligases

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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 1H-15N NOESY
1322D 1H-15N HSQC
1423D HNCO
1523D HNCA
1623D CBCA(CO)NH
1723D 13C-edited 1H-15N NOESY
1832D 1H-13C HSQC
1933D (H)CCH-TOCSY
11034D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.55 mM [U-15N] Siz1, 20 mM potassium phosphate, 300 mM sodium chloride, 3 mM DTT, 92% H2O/8% D2O92% H2O/8% D2O
20.6 mM [U-13C; U-15N] Siz1, 20 mM potassium phosphate, 300 mM sodium chloride, 3 mM DTT, 92% H2O/8% D2O92% H2O/8% D2O
30.69 mM [U-13C; U-15N] Siz1, 20 mM potassium phosphate, 300 mM sodium chloride, 3 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.55 mMSiz1[U-15N]1
20 mMpotassium phosphate1
300 mMsodium chloride1
3 mMDTT1
0.6 mMSiz1[U-13C; U-15N]2
20 mMpotassium phosphate2
300 mMsodium chloride2
3 mMDTT2
0.69 mMSiz1[U-13C; U-15N]3
20 mMpotassium phosphate3
300 mMsodium chloride3
3 mMDTT3
Sample conditionspH: 6.1 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Bruker Biospincollection
NMRPipereleased at Feb 10, 2006Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOS2003.027.13.05Cornilescu, Delaglio and Baxdata analysis
Sparky3.113Goddardpeak picking
Sparky3.113Goddardchemical shift assignment
PIPP4.3.6Garrettpeak picking
PIPP4.3.6Garrettchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
AQUA3.2Rullmann, Doreleijers and Kapteindata analysis
ProcheckNMR3.5.4Laskowski and MacArthurdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2009 / NOE intraresidue total count: 586 / NOE long range total count: 283 / NOE medium range total count: 528 / NOE sequential total count: 612 / Hydrogen bond constraints total count: 106 / Protein chi angle constraints total count: 37 / Protein other angle constraints total count: 9 / Protein phi angle constraints total count: 73 / Protein psi angle constraints total count: 78
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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