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

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Basic information

Entry
Database: PDB / ID: 6jxu
TitleSUMO1 bound to SLS4-SIM peptide from ICP0
Components
  • Small ubiquitin-related modifier
  • viral protein
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 / negative regulation of potassium ion transmembrane transporter activity / positive regulation of ATPase-coupled calcium transmembrane transporter activity / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) ...symbiont-mediated perturbation of host exit from mitosis / release from viral latency / negative regulation of potassium ion transmembrane transporter activity / positive regulation of ATPase-coupled calcium transmembrane transporter activity / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of delayed rectifier potassium channel activity / PML body organization / viral tegument / negative regulation of DNA binding / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / nuclear stress granule / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / response to type I interferon / regulation of calcium ion transmembrane transport / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / symbiont-mediated disruption of host cell PML body / Maturation of nucleoprotein / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / transcription factor binding / ubiquitin-specific protease binding / cellular response to cadmium ion / ubiquitin-like protein ligase binding / roof of mouth development / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / potassium channel regulator activity / Regulation of IFNG signaling / postsynaptic cytosol / transporter activator activity / nuclear pore / negative regulation of DNA-binding transcription factor activity / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / Formation of Incision Complex in GG-NER / protein tag activity / PML body / PKR-mediated signaling / RING-type E3 ubiquitin transferase / regulation of protein stability / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / ubiquitin protein ligase activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of protein localization / cellular response to heat / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / nuclear membrane / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / protein stabilization / nuclear speck / nuclear body / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription / nucleolus / host cell nucleus / glutamatergic synapse / enzyme binding / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / 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 / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type
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 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
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
B: viral protein


Theoretical massNumber of molelcules
Total (without water)12,9022
Polymers12,9022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR titration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1150 Å2
ΔGint-4 kcal/mol
Surface area5620 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 viral protein


Mass: 1327.422 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
323isotropic12D 1H-13C HSQC
333isotropic13D CBCA(CO)NH
343isotropic13D HN(CA)CB
353isotropic13D HNCO
363isotropic13D HN(CA)CO
272isotropic13D 1H-15N NOESY
284isotropic12D NOESY
494isotropic12D TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-98% 15N] SUMO1, 2.0 mM SLS4-SIM from Ubiquitin E3 Ligase, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.5 mM [U-15N; U-2H] SUMO1, 2.0 mM SLS4-SIM from Ubiquitin E3 Ligase, 90% H2O/10% D2O15N_2H_sample90% H2O/10% D2O
solution30.5 mM [U-13C; U-15N] SUMO1, 2.0 mM SLS4-SIM from Ubiquitin E3 Ligase, 90% H2O/10% D2O13C,15N_sample90% H2O/10% D2O
solution42.0 mM [U-15N; U-2H] SUMO1, 0.5 mM SLS4-SIM from Ubiquitin E3 Ligase, 90% H2O/10% D2O15N_2H_1_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMSUMO1[U-98% 15N]1
2.0 mMSLS4-SIM from Ubiquitin E3 Ligasenatural abundance1
0.5 mMSUMO1[U-15N; U-2H]2
2.0 mMSLS4-SIM from Ubiquitin E3 Ligasenatural abundance2
0.5 mMSUMO1[U-13C; U-15N]3
2.0 mMSLS4-SIM from Ubiquitin E3 Ligasenatural abundance3
2.0 mMSUMO1[U-15N; U-2H]4
0.5 mMSLS4-SIM from Ubiquitin E3 Ligasenatural abundance4
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1137 mM15N_sample7.41 atm298 K
2137 mM15N_2H_sample7.41 atm298 K
3137 mM13C_15N_sample7.41 atm298 K
4137 mM15N_2H_1_sample7.41 atm298 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
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddardchemical shift assignment
HADDOCKBonvinstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 6
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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