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- PDB-6kna: Viral Ubiquitin from Autographa californica Nucleo Polyhedrosis Virus -

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Basic information

Entry
Database: PDB / ID: 6kna
TitleViral Ubiquitin from Autographa californica Nucleo Polyhedrosis Virus
ComponentsViral ubiquitin
KeywordsVIRAL PROTEIN / STRUCTURE FROM CYANA 2.1
Function / homology
Function and homology information


symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / host cell nucleus
Similarity search - Function
Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Viral ubiquitin / viral Ubiquitin
Similarity search - Component
Biological speciesAutographa californica multiple nucleopolyhedrovirus
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNegi, H. / Reddy, P.P. / Das, R.
CitationJournal: Biochem.J. / Year: 2020
Title: A novel polyubiquitin chain linkage formed by viral Ubiquitin is resistant to host deubiquitinating enzymes.
Authors: Negi, H. / Reddy, P.P. / Vengayil, V. / Patole, C. / Laxman, S. / Das, R.
History
DepositionAug 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jun 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 1.3May 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

Downloads & links

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Assembly

Deposited unit
A: Viral ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,5021
Polymers8,5021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Viral ubiquitin


Mass: 8501.804 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica multiple nucleopolyhedrovirus
Gene: Ac-v-ubi, LO84_035 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N7CSW3, UniProt: P16709*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
121isotropic13D HNCA
131isotropic13D HN(CA)CB
141isotropic13D HNCO
151isotropic13D CBCA(CO)NH
181isotropic13D HN(CO)CA
171isotropic13D H(CCO)NH
161isotropic13D C(CO)NH
191isotropic13D (H)CCH-TOCSY
1121isotropic13D (H)CCH-COSY
1101isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.7 mM [U-99% 13C; U-99% 15N] Viral Ubiquitin protein, 90% H2O/10% D2O
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.7 mM / Component: Viral Ubiquitin protein / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 25 mM / Label: conditions_1 / pH: 5.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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