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- PDB-1vyx: Solution structure of the KSHV K3 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 1vyx
TitleSolution structure of the KSHV K3 N-terminal domain
ComponentsORF K3
KeywordsZINC-BINDING PROTEIN / RING DOMAIN / CROSS-BRACE MOTIF
Function / homology
Function and homology information


: / symbiont-mediated suppression of host adaptive immune response / host cell endoplasmic reticulum / RING-type E3 ubiquitin transferase / endocytosis involved in viral entry into host cell / transferase activity / ubiquitin-dependent protein catabolic process / symbiont-mediated perturbation of host ubiquitin-like protein modification / membrane => GO:0016020 / protein ubiquitination ...: / symbiont-mediated suppression of host adaptive immune response / host cell endoplasmic reticulum / RING-type E3 ubiquitin transferase / endocytosis involved in viral entry into host cell / transferase activity / ubiquitin-dependent protein catabolic process / symbiont-mediated perturbation of host ubiquitin-like protein modification / membrane => GO:0016020 / protein ubiquitination / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell plasma membrane / zinc ion binding
Similarity search - Function
RING-variant domain / Zinc finger RING-CH-type profile. / Zinc finger, RING-CH-type / The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase MIR1
Similarity search - Component
Biological speciesHUMAN HERPESVIRUS 8
MethodSOLUTION NMR / XPLOR3.8
AuthorsDodd, R.B. / Allen, M.D. / Brown, S.E. / Sanderson, C.M. / Duncan, L.M. / lehner, P.J. / Bycroft, M. / Read, R.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Solution Structure of the Kaposi'S Sarcoma-Associated Herpesvirus K3 N-Terminal Domain Reveals a Novel E2-Binding C4Hc3-Type Ring Domain
Authors: Dodd, R.B. / Allen, M.D. / Brown, S.E. / Sanderson, C.M. / Duncan, L.M. / Lehner, P.J. / Bycroft, M. / Read, R.J.
History
DepositionMay 7, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 2, 2018Group: Data collection / Experimental preparation
Category: pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions ...pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_sample_details / pdbx_nmr_spectrometer
Item: _pdbx_nmr_exptl_sample_conditions.ionic_strength_units / _pdbx_nmr_exptl_sample_conditions.label ..._pdbx_nmr_exptl_sample_conditions.ionic_strength_units / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pressure / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_spectrometer.model
Revision 1.5May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORF K3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9643
Polymers6,8331
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)28 / 30NO VIOLATIONS GREATER THAN 0.25A, NO ANGLE VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein ORF K3 / K3RING


Mass: 6832.696 Da / Num. of mol.: 1 / Fragment: RING FINGER, RESIDUES 1-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN HERPESVIRUS 8 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P90495
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY
141HN(CA)CB
151CBCA(CO)NH
161HNCO
171HN(CA)CO
18113C-HSQC
191HNHB
NMR detailsText: THE STRUCTURE WAS DETERMINED USING STANDAR TRIPLE- RESONANCE METHODS ON 13C-15N-LABELLED K3-RING DOMAIN

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Sample preparation

DetailsType: solution
Contents: 50 MM POTASSIUM PHOSPHATE (PH 6.0), CONTAINING 50 MM NACL
Label: sample_1
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMPotassium phosphatenatural abundance1
50 mMNaClnatural abundance2
Sample conditionsIonic strength: 100.0 mM / Label: sample_1 / pH: 6.0 / Pressure: ambient atm / Temperature: 298.0 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
XwinNMRstructure solution
ANSIGstructure solution
X-PLORstructure solution
RefinementMethod: XPLOR3.8 / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: NO VIOLATIONS GREATER THAN 0.25A, NO ANGLE VIOLATIONS
Conformers calculated total number: 30 / Conformers submitted total number: 28

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