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- PDB-6k5t: Complex of SUMO1 and phosphorylated hcmv protein IE2 -

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Basic information

Entry
Database: PDB / ID: 6k5t
TitleComplex of SUMO1 and phosphorylated hcmv protein IE2
Components
  • 12-mer from Viral transcription factor IE2
  • Small ubiquitin-related modifier 1
KeywordsPROTEIN BINDING/TRANSCRIPTION / Complex / VIRAL PROTEIN / 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 / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / PML body organization ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / DNA-templated viral transcription / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / negative regulation of action potential / small protein activating enzyme binding / regulation of calcium ion transmembrane transport / bidirectional double-stranded viral DNA replication / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / 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 / Maturation of nucleoprotein / negative regulation of protein import into nucleus / transcription factor binding / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / potassium channel regulator activity / nuclear pore / Regulation of IFNG signaling / SUMOylation of DNA damage response and repair proteins / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / 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 / nuclear body / protein stabilization / nuclear speck / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription / host cell nucleus / nucleolus / enzyme binding / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Herpesvirus intermediate/early protein 2/3 / Herpes virus intermediate/early protein 2/3 / Cytomegalovirus IE1/IE2 / Cytomegalovirus IE1 protein / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Viral transcription factor IE2 / Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human cytomegalovirus
MethodSOLUTION NMR / simulated annealing
AuthorsTripathi, V. / Chatterjee, K.S.
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 31, 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
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small ubiquitin-related modifier 1
B: 12-mer from Viral transcription factor IE2


Theoretical massNumber of molelcules
Total (without water)10,3392
Polymers10,3392
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1360 Å2
ΔGint-10 kcal/mol
Surface area5850 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 1 / SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain ...SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein SMT3C / Smt3C / Ubiquitin-like protein UBL1


Mass: 8970.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 / Production host: Escherichia coli (E. coli) / References: UniProt: P63165
#2: Protein/peptide 12-mer from 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
Has protein modificationY

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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-IDContentsDetailsLabelSolvent system
solution10.3 mM [U-13C; U-15N] SUMO1, 3 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2OPBS, pH 7.415N_sample90% H2O/10% D2O
solution21 mM [U-13C; U-15N] SUMO1, 1.5 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2OPBS, pH 7.413C15N_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 mMSUMO1[U-13C; U-15N]1
3 mMPhosphorylated SIM from viral protein IE2natural abundance1
1 mMSUMO1[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: Codition_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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