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- PDB-6k5r: Complex of SUMO2 with Phosphorylated viral SIM IE2 -

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Basic information

Entry
Database: PDB / ID: 6k5r
TitleComplex of SUMO2 with Phosphorylated viral SIM IE2
Components
  • ASP-THR-ALA-GLY-CYS-ILE-VAL-ILE-SEP-ASP-SEP-GLU
  • Small ubiquitin-related modifier 3
KeywordsPROTEIN BINDING/TRANSCRIPTION / complex / PROTEIN BINDING-TRANSCRIPTION complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / DNA-templated viral transcription / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / bidirectional double-stranded viral DNA replication / SUMOylation of immune response proteins / regulation of protein localization to nucleus / negative regulation of DNA binding / ubiquitin-like protein ligase binding ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / DNA-templated viral transcription / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / bidirectional double-stranded viral DNA replication / SUMOylation of immune response proteins / regulation of protein localization to nucleus / negative regulation of DNA binding / ubiquitin-like protein ligase binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / SUMOylation of DNA replication proteins / protein sumoylation / SUMOylation of transcription factors / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / PML body / kinetochore / protein tag activity / Formation of Incision Complex in GG-NER / host cell nucleus / regulation of DNA-templated transcription / DNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Herpesvirus intermediate/early protein 2/3 / Herpes virus intermediate/early protein 2/3 / Cytomegalovirus IE1/IE2 / Cytomegalovirus IE1 protein / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Viral transcription factor IE2 / Small ubiquitin-related modifier 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Human cytomegalovirus
MethodSOLUTION NMR / simulated annealing
AuthorsChatterjee, K.S. / Das, R.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Casein kinase-2-mediated phosphorylation increases the SUMO-dependent activity of the cytomegalovirus transactivator IE2.
Authors: Tripathi, V. / Chatterjee, K.S. / Das, R.
History
DepositionMay 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small ubiquitin-related modifier 3
B: ASP-THR-ALA-GLY-CYS-ILE-VAL-ILE-SEP-ASP-SEP-GLU


Theoretical massNumber of molelcules
Total (without water)10,2612
Polymers10,2612
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1170 Å2
ΔGint-8 kcal/mol
Surface area5970 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Small ubiquitin-related modifier 3 / Small Ubiquitin like Modifier 2 / SUMO-3 / SMT3 homolog 1 / SUMO-2 / Ubiquitin-like protein SMT3A / Smt3A


Mass: 8892.013 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO3, SMT3A, SMT3H1 / Production host: Escherichia coli (E. coli) / References: UniProt: P55854
#2: Protein/peptide ASP-THR-ALA-GLY-CYS-ILE-VAL-ILE-SEP-ASP-SEP-GLU / Viral transcription factor IE2 / IE2 / Protein UL122


Mass: 1369.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human cytomegalovirus (strain AD169) / References: UniProt: P19893

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
133isotropic12D 1H-1H TOCSY
143isotropic12D 1H-1H NOESY
152isotropic13D half filtered NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.3 mM [U-15N] SUMO2, 3 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution21 mM [U-13C; U-15N] SUMO2, 1.5 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution33 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2OPhosphorylated SIM from viral protein IE290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMSUMO2[U-15N]1
3 mMPhosphorylated SIM from viral protein IE2natural abundance1
1 mMSUMO2[U-13C; U-15N]2
1.5 mMPhosphorylated SIM from viral protein IE2natural abundance2
3 mMPhosphorylated SIM from viral protein IE2natural abundance3
Sample conditionsIonic strength: 162.7 mM / Label: condition_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
HADDOCKBonvinstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
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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