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- PDB-6jxv: SUMO1 bound to phosphorylated SLS4-SIM peptide from ICP0 -

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Basic information

Entry
Database: PDB / ID: 6jxv
TitleSUMO1 bound to phosphorylated SLS4-SIM peptide from ICP0
Components
  • Phosphorylated SLS4-SIM from ubiquitin E3 ligase ICP0
  • Small ubiquitin-related modifier
KeywordsPROTEIN BINDING/PEPTIDE / SUMOylation / Phosphorylation / PROTEIN BINDING-PEPTIDE complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host exit from mitosis / release from viral latency / positive regulation of ATPase-coupled calcium transmembrane transporter activity / 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 / suppression by virus of host type I interferon production / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity ...symbiont-mediated perturbation of host exit from mitosis / release from viral latency / positive regulation of ATPase-coupled calcium transmembrane transporter activity / 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 / suppression by virus of host type I interferon production / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / viral tegument / 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 / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / response to type I interferon / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / symbiont-mediated disruption of host cell PML body / negative regulation of protein import into nucleus / transcription factor binding / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / 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 / RING-type E3 ubiquitin transferase / regulation of protein stability / negative regulation of DNA-binding transcription factor activity / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / protein tag activity / ubiquitin protein ligase 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / nuclear membrane / host cell cytoplasm / 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
Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type ...Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Small ubiquitin-related modifier / E3 ubiquitin-protein ligase ICP0 / Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human alphaherpesvirus 1 strain 17
MethodSOLUTION NMR / simulated annealing
AuthorsHembram, D.S.S. / Negi, H. / Shet, D. / Das, R.
Funding support India, 1items
OrganizationGrant numberCountry
India
CitationJournal: J.Mol.Biol. / Year: 2020
Title: The Viral SUMO-Targeted Ubiquitin Ligase ICP0 is Phosphorylated and Activated by Host Kinase Chk2.
Authors: Hembram, D.S.S. / Negi, H. / Biswas, P. / Tripathi, V. / Bhushan, L. / Shet, D. / Kumar, V. / Das, R.
History
DepositionApr 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small ubiquitin-related modifier
B: Phosphorylated SLS4-SIM from ubiquitin E3 ligase ICP0


Theoretical massNumber of molelcules
Total (without water)13,8942
Polymers13,8942
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1350 Å2
ΔGint-7 kcal/mol
Surface area5670 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 / SUMO


Mass: 11575.005 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A024R3Z2, UniProt: P63165*PLUS
#2: Protein/peptide Phosphorylated SLS4-SIM from ubiquitin E3 ligase ICP0


Mass: 2319.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human alphaherpesvirus 1 strain 17 / References: UniProt: P08393*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
121isotropic13D half-filtered NOESY
131isotropic13D HNCO
141isotropic13D HNCA
151isotropic13D (H)CCH-TOCSY
161isotropic13D HN(CO)CA
171isotropic13D CBCA(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM [U-13C; U-15N] SUMO1, 1.2 mM Phosphorylated SLS4, 90% H2O/10% D2O13C,15N_sample90% H2O/10% D2O
solution20.5 mM [U-15N] SUMO1, 2.0 mM Phosphorylated SLS4, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMSUMO1[U-13C; U-15N]1
1.2 mMPhosphorylated SLS4natural abundance1
0.5 mMSUMO1[U-15N]2
2.0 mMPhosphorylated SLS4natural abundance2
Sample conditionsDetails: PBS buffer, pH 7.4 / Ionic strength: 137 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
SparkyGoddardchemical shift assignment
HADDOCKBonvinstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
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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