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- PDB-2mp2: Solution structure of SUMO dimer in complex with SIM2-3 from RNF4 -

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Basic information

Entry
Database: PDB / ID: 2mp2
TitleSolution structure of SUMO dimer in complex with SIM2-3 from RNF4
Components
  • (Small ubiquitin-related modifier 3) x 2
  • E3 ubiquitin-protein ligase RNF4
KeywordsPROTEIN BINDING / SUMO / dimer / SIM / RNF4 / Complex
Function / homology
Function and homology information


regulation of spindle assembly / regulation of kinetochore assembly / microtubule end / SUMO polymer binding / Processing of DNA double-strand break ends / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / cellular response to hydroxyurea / Antigen processing: Ubiquitination & Proteasome degradation ...regulation of spindle assembly / regulation of kinetochore assembly / microtubule end / SUMO polymer binding / Processing of DNA double-strand break ends / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / cellular response to hydroxyurea / Antigen processing: Ubiquitination & Proteasome degradation / protein K6-linked ubiquitination / cellular response to testosterone stimulus / SUMOylation of immune response proteins / response to arsenic-containing substance / regulation of protein localization to nucleus / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / negative regulation of protein localization to chromatin / nuclear androgen receptor binding / negative regulation of DNA binding / ubiquitin-like protein ligase binding / protein K63-linked ubiquitination / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / nucleosome binding / protein autoubiquitination / protein K48-linked ubiquitination / SUMOylation of DNA damage response and repair proteins / TBP-class protein binding / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / nuclear estrogen receptor binding / SUMOylation of intracellular receptors / RING-type E3 ubiquitin transferase / cellular response to gamma radiation / PML body / kinetochore / Formation of Incision Complex in GG-NER / ubiquitin-protein transferase activity / protein tag activity / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
RNF4, RING finger, HC subclass / : / Ring finger domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. ...RNF4, RING finger, HC subclass / : / Ring finger domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 3 / E3 ubiquitin-protein ligase RNF4
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsXu, Y. / Plechanovov, A. / Simpson, P. / Marchant, J. / Leidecker, O. / Sebastian, K. / Hay, R.T. / Matthews, S.J.
CitationJournal: Nat Commun / Year: 2014
Title: Structural insight into SUMO chain recognition and manipulation by the ubiquitin ligase RNF4.
Authors: Xu, Y. / Plechanovova, A. / Simpson, P. / Marchant, J. / Leidecker, O. / Kraatz, S. / Hay, R.T. / Matthews, S.J.
History
DepositionMay 9, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small ubiquitin-related modifier 3
B: Small ubiquitin-related modifier 3
C: E3 ubiquitin-protein ligase RNF4


Theoretical massNumber of molelcules
Total (without water)22,4163
Polymers22,4163
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 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Small ubiquitin-related modifier 3 / SUMO-3 / SMT3 homolog 1 / SUMO-2 / Ubiquitin-like protein SMT3B / Smt3B


Mass: 9350.436 Da / Num. of mol.: 1 / Fragment: UNP residues 12-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMT3B, SMT3H1, SUMO3 / Plasmid: pHIS-TEV-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55854
#2: Protein Small ubiquitin-related modifier 3 / SUMO-3 / SMT3 homolog 1 / SUMO-2 / Ubiquitin-like protein SMT3B / Smt3B


Mass: 10351.586 Da / Num. of mol.: 1 / Fragment: UNP residues 2-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMT3B, SMT3H1, SUMO3 / Plasmid: pHIS-TEV-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55854
#3: Protein/peptide E3 ubiquitin-protein ligase RNF4 / RING finger protein 4


Mass: 2713.941 Da / Num. of mol.: 1 / Fragment: UNP residues 45-69 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9QZS2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC
1442D 1H-15N HSQC
1533D HN(CA)CB
1633D CBCA(CO)NH
1733D (H)CCH-TOCSY
1833D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-99% 13C; U-99% 15N] SUMO 1, 0.3 mM SUMO 2, 1.0 mM RNF4, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM SUMO 1, 0.3 mM [U-99% 13C; U-99% 15N] SUMO 2, 1.0 mM RNF4, 90% H2O/10% D2O90% H2O/10% D2O
30.3 mM [U-99% 13C; U-99% 15N] SUMO 1, 0.3 mM SUMO 2, 90% H2O/10% D2O90% H2O/10% D2O
40.3 mM SUMO 1, 0.3 mM [U-99% 13C; U-99% 15N] SUMO 2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMSUMO 1-1[U-99% 13C; U-99% 15N]1
0.3 mMSUMO 2-21
1.0 mMRNF4-31
0.3 mMSUMO 1-42
0.3 mMSUMO 2-5[U-99% 13C; U-99% 15N]2
1.0 mMRNF4-62
0.3 mMSUMO 1-7[U-99% 13C; U-99% 15N]3
0.3 mMSUMO 2-83
0.3 mMSUMO 1-94
0.3 mMSUMO 2-10[U-99% 13C; U-99% 15N]4
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIALinge, O'Donoghue and Nilgesstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
TopSpinBruker Biospincollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2200
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 10

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