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- PDB-6jxw: Complex of SUMO2 bound SLS4 from ICP0. -

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Basic information

Entry
Database: PDB / ID: 6jxw
TitleComplex of SUMO2 bound SLS4 from ICP0.
Components
  • SLS4-SIM from Ubiquitin E3 ligase ICP0
  • Small ubiquitin-related modifier 2
KeywordsPROTEIN BINDING/PEPTIDE / SUMOylation / PROTEIN BINDING-PEPTIDE complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host exit from mitosis / release from viral latency / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / suppression by virus of host type I interferon production / viral tegument / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / response to type I interferon ...symbiont-mediated perturbation of host exit from mitosis / release from viral latency / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / suppression by virus of host type I interferon production / viral tegument / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / response to type I interferon / SUMOylation of RNA binding proteins / SUMO transferase activity / symbiont-mediated disruption of host cell PML body / ubiquitin-like protein ligase binding / 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 / RING-type E3 ubiquitin transferase / PML body / protein tag activity / Formation of Incision Complex in GG-NER / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / 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 / host cell cytoplasm / ubiquitin protein ligase binding / host cell nucleus / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
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 ...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-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ICP0 / Small ubiquitin-related modifier 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 1 (Herpes simplex virus type 1)
MethodSOLUTION NMR / simulated annealing
AuthorsHembram, D.S.S. / Negi, H. / Shet, D. / Das, R.
Funding support India, 1items
OrganizationGrant numberCountry
Other government4120 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
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small ubiquitin-related modifier 2
B: SLS4-SIM from Ubiquitin E3 ligase ICP0


Theoretical massNumber of molelcules
Total (without water)13,0462
Polymers13,0462
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1250 Å2
ΔGint-4 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 2 / SUMO-2 / HSMT3 / SMT3 homolog 2 / SUMO-3 / Sentrin-2 / Ubiquitin-like protein SMT3B / Smt3B


Mass: 10886.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO2 / Production host: Escherichia coli (E. coli) / References: UniProt: P61956
#2: Protein/peptide SLS4-SIM from Ubiquitin E3 ligase ICP0


Mass: 2159.383 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Human herpesvirus 1 (Herpes simplex virus type 1)
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
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
132isotropic13D CBCA(CO)NH
142isotropic13D HN(CA)CB
152isotropic13D HNCO
162isotropic13D HN(CA)CO
172isotropic13D (H)CCH-TOCSY
183isotropic13D 1H-15N NOESY
194isotropic12D 1H-1H TOCSY
1104isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-98% 15N] SUMO2, 2.0 mM SLS4-SIM from Ubiquitin E3 ligase ICP0, 90% H2O/10% D2O15N-sample90% H2O/10% D2O
solution20.5 mM [U-100% 13C; U-100% 15N] SUMO2, 2.0 mM SLS4-SIM from Ubiquitin E3 ligase ICP0, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
solution30.5 mM [U-15N; U-2H] SUMO2, 2.0 mM SLS4-SIM from Ubiquitin E3 ligase ICP0, 90% H2O/10% D2O15N_2H_sample90% H2O/10% D2O
solution42.0 mM [U-15N; U-2H] SUMO2, 0.5 mM SLS4-SIM from Ubiquitin E3 ligase ICP0, 90% H2O/10% D2O15N_2H_1_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMSUMO2[U-98% 15N]1
2.0 mMSLS4-SIM from Ubiquitin E3 ligase ICP0natural abundance1
0.5 mMSUMO2[U-100% 13C; U-100% 15N]2
2.0 mMSLS4-SIM from Ubiquitin E3 ligase ICP0natural abundance2
0.5 mMSUMO2[U-15N; U-2H]3
2.0 mMSLS4-SIM from Ubiquitin E3 ligase ICP0natural abundance3
2.0 mMSUMO2[U-15N; U-2H]4
0.5 mMSLS4-SIM from Ubiquitin E3 ligase ICP0natural abundance4
Sample conditionsIonic 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
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
HADDOCKBonvinstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 5
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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