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- PDB-1a5r: STRUCTURE DETERMINATION OF THE SMALL UBIQUITIN-RELATED MODIFIER S... -

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Entry
Database: PDB / ID: 1a5r
TitleSTRUCTURE DETERMINATION OF THE SMALL UBIQUITIN-RELATED MODIFIER SUMO-1, NMR, 10 STRUCTURES
ComponentsSUMO-1
KeywordsTARGETING PROTEIN / SUMO-1 / POST-TRANSLATIONAL PROTEIN MODIFICATION / UBIQUITIN-LIKE PROTEINS
Function / homology
Function and homology information


protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of potassium ion transmembrane transporter activity / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of potassium ion transmembrane transporter activity / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / small protein activating enzyme binding / negative regulation of action potential / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / regulation of calcium ion transmembrane transport / XY body / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of DNA binding / Maturation of nucleoprotein / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / cellular response to cadmium ion / ubiquitin-specific protease binding / transcription factor binding / roof of mouth development / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / postsynaptic cytosol / potassium channel regulator activity / Regulation of IFNG signaling / nuclear pore / presynaptic cytosol / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / negative regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to heat / nuclear membrane / protein stabilization / nuclear speck / nuclear body / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / enzyme binding / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBayer, P. / Arndt, A. / Metzger, S. / Mahajan, R. / Melchior, F. / Jaenicke, R. / Becker, J.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Structure determination of the small ubiquitin-related modifier SUMO-1.
Authors: Bayer, P. / Arndt, A. / Metzger, S. / Mahajan, R. / Melchior, F. / Jaenicke, R. / Becker, J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: A Small Ubiquitin-Related Polypeptide Involved in Targeting Rangap1 to Nuclear Pore Complex Protein Ranbp2
Authors: Mahajan, R. / Delphin, C. / Guan, T. / Gerace, L. / Melchior, F.
#2: Journal: J.Biol.Chem. / Year: 1997
Title: Preferential Modification of Nuclear Proteins by a Novel Ubiquitin-Like Molecule
Authors: Kamitani, T. / Nguyen, H.P. / Yeh, E.T.
#3: Journal: J.Cell Biol. / Year: 1996
Title: A Novel Ubiquitin-Like Modification Modulates the Partitioning of the Ran-Gtpase-Activating Protein Rangap1 between the Cytosol and the Nuclear Pore Complex
Authors: Matunis, M.J. / Coutavas, E. / Blobel, G.
History
DepositionFeb 18, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 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: SUMO-1


Theoretical massNumber of molelcules
Total (without water)11,7191
Polymers11,7191
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 / 30ENERGY
Representative

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Components

#1: Protein SUMO-1 / PIC1 / GMP1 / UBL1 / SENTRIN


Mass: 11719.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P63165

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121NOESY
131CLEAN-TOCSY
141GS-15N-HSQC
15115N-NOESY-HMQC
16115N-TOCSY-HMQC

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Sample preparation

DetailsContents: H2O
Sample conditionsIonic strength: 100 mM / pH: 7 / Pressure: STANDARD / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
NDEEstructure solution
X-PLOR 3.851 PRE-RELEASE VERSIONVERSIONstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: ENERGY / Conformers calculated total number: 30 / Conformers submitted total number: 10

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