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- PDB-1u4a: Solution structure of human SUMO-3 C47S -

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Basic information

Entry
Database: PDB / ID: 1u4a
TitleSolution structure of human SUMO-3 C47S
ComponentsUbiquitin-like protein SMT3A
KeywordsPROTEIN BINDING / beta beta alpha beta beta alpha beta fold
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) / SUMOylation of immune response proteins / regulation of protein localization to nucleus / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation ...SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of immune response proteins / regulation of protein localization to nucleus / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / PML body / kinetochore / Formation of Incision Complex in GG-NER / protein tag activity / nucleoplasm / nucleus / cytoplasm
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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDing, H. / Xu, Y. / Dai, H. / Tang, Y. / Wu, J. / Shi, Y.
CitationJournal: Biochemistry / Year: 2005
Title: Solution Structure of Human SUMO-3 C47S and Its Binding Surface for Ubc9
Authors: Ding, H. / Xu, Y. / Chen, Q. / Dai, H. / Tang, Y. / Wu, J. / Shi, Y.
History
DepositionJul 23, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-like protein SMT3A


Theoretical massNumber of molelcules
Total (without water)10,1181
Polymers10,1181
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin-like protein SMT3A / Small ubiquitin-like modifier protein 3


Mass: 10118.255 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain / Mutation: C47S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: brain / Gene: SUMO3 / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P55854

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1312D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM 15N-labeled protein25mM phosphate buffer, 75mM Nacl 90% H2O, 10% D2O
20.6mM 13C,15N-labeled protein25mM phosphate buffer, 75mM Nacl 90% H2O, 10% D2O
Sample conditionsIonic strength: 25mM phosphate buffer, 75mM Nacl / pH: 6.25 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2F. Delaglioprocessing
Sparky3T.D.Goddard , D.G.Knellerprocessing
CNS1.1A.T.Brunger ,D.D.Adanis etalstructure solution
CSI1David S. Wishartdata analysis
MOLMOL2k.2Koradistructure solution
MOLMOL2k.2Koradirefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1540 restraints, 1406 are NOE-derived distance constraints, 78 dihedral angle restraints, 56 distance restraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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