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- PDB-1wz0: Solution Structure of Human SUMO-2 (SMT3B), a Ubiquitin-like Protein -

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Basic information

Entry
Database: PDB / ID: 1wz0
TitleSolution Structure of Human SUMO-2 (SMT3B), a Ubiquitin-like Protein
ComponentsUbiquitin-like protein SMT3B
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SUMO-2 / ubiquitin-like molecule / Sentrin2 / NPPFSA / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMO transferase activity / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation ...SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMO transferase activity / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / postsynaptic cytosol / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / hippocampal mossy fiber to CA3 synapse / Regulation of endogenous retroelements by KRAB-ZFP proteins / SUMOylation of intracellular receptors / PML body / GABA-ergic synapse / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / ubiquitin protein ligase binding / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsZhao, C. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of Human SUMO-2 (SMT3B), a Ubiquitin-like Protein
Authors: Zhao, C. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionFeb 21, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-like protein SMT3B


Theoretical massNumber of molelcules
Total (without water)11,5021
Polymers11,5021
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 / 100target function, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin-like protein SMT3B / Sentrin 2 / HSMT3


Mass: 11501.726 Da / Num. of mol.: 1 / Fragment: ubiquitin-like molecule
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free synthesis / Gene: SMT3B / Plasmid: P040510-09 / References: UniProt: P61956

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.21mM protein U-15N, 13C; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 7 / Pressure: ambient / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.921Kobayashi, N.data analysis
CYANA1.0.8Guentert, P.structure solution
CYANA1.0.8Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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