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- PDB-4hly: The complex crystal structure of the DNA binding domain of vIRF-1... -

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Basic information

Entry
Database: PDB / ID: 4hly
TitleThe complex crystal structure of the DNA binding domain of vIRF-1 from the oncogenic KSHV with DNA
Components
  • 5'-D(*GP*CP*GP*TP*CP*GP*AP*GP*AP*CP*GP*C)-3'
  • K9
KeywordsDNA BINDING PROTEIN/DNA / helix-turn-helix / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


: / protein sequestering activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / transcription cis-regulatory region binding / DNA-binding transcription factor activity / protein domain specific binding / host cell nucleus
Similarity search - Function
Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / SMAD-like domain superfamily / SMAD/FHA domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / SMAD-like domain superfamily / SMAD/FHA domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / VIRF-1 / K9
Similarity search - Component
Biological speciesHuman herpesvirus 8
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.48 Å
AuthorsHew, K. / Venkatachalam, R.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: The crystal structure of the DNA-binding domain of vIRF-1 from the oncogenic KSHV reveals a conserved fold for DNA binding and reinforces its role as a transcription factor.
Authors: Hew, K. / Dahlroth, S.L. / Venkatachalam, R. / Nasertorabi, F. / Lim, B.T. / Cornvik, T. / Nordlund, P.
History
DepositionOct 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 7, 2016Group: Derived calculations / Source and taxonomy
Revision 1.3Sep 14, 2016Group: Derived calculations
Revision 1.4Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: K9
B: K9
C: 5'-D(*GP*CP*GP*TP*CP*GP*AP*GP*AP*CP*GP*C)-3'
D: 5'-D(*GP*CP*GP*TP*CP*GP*AP*GP*AP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)37,9964
Polymers37,9964
Non-polymers00
Water4,179232
1
A: K9

C: 5'-D(*GP*CP*GP*TP*CP*GP*AP*GP*AP*CP*GP*C)-3'
D: 5'-D(*GP*CP*GP*TP*CP*GP*AP*GP*AP*CP*GP*C)-3'

B: K9
C: 5'-D(*GP*CP*GP*TP*CP*GP*AP*GP*AP*CP*GP*C)-3'
D: 5'-D(*GP*CP*GP*TP*CP*GP*AP*GP*AP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)45,3736
Polymers45,3736
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_645x+1,y-1,z1
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.536, 38.577, 48.562
Angle α, β, γ (deg.)91.32, 88.48, 63.13
Int Tables number1
Space group name H-MP1

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Components

#1: Protein K9 / Latent viral interferon regulatory factor / Lytic viral interferon regulatory factor / ORF K9 / VIRF-1 protein


Mass: 15309.481 Da / Num. of mol.: 2 / Fragment: DNA binding domain, UNP RESIDUES 88-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF K9, vIRF, vIRF-1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-Rosetta / References: UniProt: Q77Q82, UniProt: F5HF68*PLUS
#2: DNA chain 5'-D(*GP*CP*GP*TP*CP*GP*AP*GP*AP*CP*GP*C)-3'


Mass: 3688.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.69 Å3/Da / Density % sol: 27.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1M phosphate citrate pH 4.2, 40% PEG 300, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.96722 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 29, 2010
RadiationMonochromator: Rh Coated Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96722 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.598
11K, H, -L20.402
ReflectionResolution: 1.48→50 Å / Num. all: 41661 / Num. obs: 41661 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.106
Reflection shellHighest resolution: 1.48 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 41661 / Rsym value: 0.507 / % possible all: 92.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.48→19.53 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.216 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22788 1941 4.9 %RANDOM
Rwork0.1964 ---
obs0.19792 37481 94.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.589 Å2
Baniso -1Baniso -2Baniso -3
1-7.03 Å27.63 Å2-4 Å2
2---5.23 Å2-0.42 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 1.48→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 490 0 232 2456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0172368
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.7393292
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.955220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.75420.62596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22415329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1181533
X-RAY DIFFRACTIONr_chiral_restr0.0830.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211681
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.476→1.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 127 -
Rwork0.282 2514 -
obs--85.5 %

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