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- PDB-4hlx: The crystal structure of the DNA binding domain of vIRF-1 from th... -

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Basic information

Entry
Database: PDB / ID: 4hlx
TitleThe crystal structure of the DNA binding domain of vIRF-1 from the oncogenic KSHV
ComponentsK9
KeywordsDNA BINDING PROTEIN / helix-turn-helix
Function / homology
Function and homology information


immune system process / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding
Similarity search - Function
Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / 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 / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / 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
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.379 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 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: K9
D: K9


Theoretical massNumber of molelcules
Total (without water)61,2384
Polymers61,2384
Non-polymers00
Water2,108117
1
A: K9


Theoretical massNumber of molelcules
Total (without water)15,3091
Polymers15,3091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: K9


Theoretical massNumber of molelcules
Total (without water)15,3091
Polymers15,3091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: K9


Theoretical massNumber of molelcules
Total (without water)15,3091
Polymers15,3091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: K9


Theoretical massNumber of molelcules
Total (without water)15,3091
Polymers15,3091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.770, 128.843, 228.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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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.: 4 / 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES pH 7, 27% Jeffamine-ED 2001, 10 mM ATP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.96722 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2011
RadiationMonochromator: Rh Coated Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96722 Å / Relative weight: 1
ReflectionResolution: 2.379→23.292 Å / Num. all: 18285 / Num. obs: 18285 / % possible obs: 92.5 % / Redundancy: 6.6 %
Reflection shellHighest resolution: 2.38 Å / Redundancy: 6.6 % / Num. unique all: 18285 / % possible all: 92.58

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.379→23.292 Å / SU ML: 0.36 / σ(F): 1.42 / Phase error: 32.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2862 886 5.12 %Random
Rwork0.2507 ---
obs0.2525 17306 87.63 %-
all-18285 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.379→23.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 0 117 3305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023286
X-RAY DIFFRACTIONf_angle_d0.5674416
X-RAY DIFFRACTIONf_dihedral_angle_d10.5351230
X-RAY DIFFRACTIONf_chiral_restr0.036453
X-RAY DIFFRACTIONf_plane_restr0.002579
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.379-2.52790.36721550.2834295695
2.5279-2.72280.3781140.3094208668
2.7228-2.99630.29111670.2818303298
2.9963-3.42860.3471590.2586288896
3.4286-4.31520.23841300.2272225277
4.3152-23.29290.24171610.2251320699

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