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- PDB-1faf: NMR STRUCTURE OF THE N-TERMINAL J DOMAIN OF MURINE POLYOMAVIRUS T... -

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Basic information

Entry
Database: PDB / ID: 1faf
TitleNMR STRUCTURE OF THE N-TERMINAL J DOMAIN OF MURINE POLYOMAVIRUS T ANTIGENS.
ComponentsLARGE T ANTIGEN
KeywordsVIRAL PROTEIN / J DOMAIN / HPD MOTIF / ANTI-PARALLEL HAIRPIN OF HELICES
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA 3'-5' helicase / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / isomerase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA replication / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA 3'-5' helicase / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / isomerase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA replication / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / host cell nucleus / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / DnaJ domain / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus ...Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / DnaJ domain / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / DnaJ molecular chaperone homology domain / Chaperone J-domain superfamily / DnaJ domain / Helix Hairpins / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Large T antigen / Large T antigen
Similarity search - Component
Biological speciesMurine polyomavirus
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING IN CARTESIAN SPACE
AuthorsBerjanskii, M.V. / Riley, M.I. / Xie, A. / Semenchenko, V. / Folk, W.R. / Van Doren, S.R.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: NMR structure of the N-terminal J domain of murine polyomavirus T antigens. Implications for DnaJ-like domains and for mutations of T antigens.
Authors: Berjanskii, M.V. / Riley, M.I. / Xie, A. / Semenchenko, V. / Folk, W.R. / Van Doren, S.R.
History
DepositionJul 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LARGE T ANTIGEN


Theoretical massNumber of molelcules
Total (without water)9,1761
Polymers9,1761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)47 / 100STRUCTURES WITH FAVORABLE NON-BOND ENERGY,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #12

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Components

#1: Protein LARGE T ANTIGEN


Mass: 9175.588 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine polyomavirus / Genus: Polyomavirus / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P03074, UniProt: P03073*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY- HSQC
121100MS MIXING
1313D 13C-SEPARATED FSCT-HSMQC -NOESY
141100MS MIXING
1513D 13C-SEPARATED NOESY- HMQC
161100MS MIXING
1713D 13C-SEPARATED NOESY- CTHSQC
181200MS MIXING
191HNCA-J
1101HACAHB-COSY
1111HNHB
1121H-D EXCHANGE DETECTED BY 15N HSQC

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Sample preparation

DetailsContents: 1.7 MM PYJ U-15N; 25 MM PHOSPHATE BUFFER, 100MM KCL
Sample conditionsIonic strength: 25mM_PHOSPHATE/100mM_KCL / pH: 6 / Pressure: 1 atm / Temperature: 303.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionClassification
XwinNMR1.3structure solution
SYBYL TRIAD6.3structure solution
CNS1structure solution
CNS1refinement
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING IN CARTESIAN SPACE
Software ordinal: 1
NMR ensembleConformer selection criteria: STRUCTURES WITH FAVORABLE NON-BOND ENERGY,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 100 / Conformers submitted total number: 47

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