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- PDB-5mhk: ICP4 DNA-binding domain in complex with 19mer DNA duplex from its... -

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Basic information

Entry
Database: PDB / ID: 5mhk
TitleICP4 DNA-binding domain in complex with 19mer DNA duplex from its own promoter
Components
  • (DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)- ...) x 2
  • ICP4 DNA BINDING DOMAIN
  • RS1
KeywordsTRANSCRIPTION / Transcription factor / Herpes virus / Intercalation
Function / homology
Function and homology information


DNA-templated viral transcription / viral tegument / response to type I interferon / host cell cytoplasm / positive regulation of DNA-templated transcription / host cell nucleus / DNA binding
Similarity search - Function
Herpesvirus ICP4-like protein, C-terminal / Herpesvirus ICP4-like protein, N-terminal / Herpesvirus ICP4-like protein N-terminal region / Herpesvirus ICP4-like protein C-terminal region / :
Similarity search - Domain/homology
DNA / DNA (> 10) / Major viral transcription factor ICP4 / RS1
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
HUMAN HERPESVIRUS 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsTunnicliffe, R.B. / Lockhart-Cairns, M.P. / Levy, C. / Mould, P. / Jowitt, T.A. / Sito, H. / Baldock, C. / Sandri-Goldin, R.M. / Golovanov, A.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of HealthAI107803 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The herpes viral transcription factor ICP4 forms a novel DNA recognition complex.
Authors: Tunnicliffe, R.B. / Lockhart-Cairns, M.P. / Levy, C. / Mould, A.P. / Jowitt, T.A. / Sito, H. / Baldock, C. / Sandri-Goldin, R.M. / Golovanov, A.P.
History
DepositionNov 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 10, 2019Group: Data collection / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_seq_map_depositor_info
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3')
H: DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3')
E: DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3')
F: DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3')
A: RS1
C: RS1
D: RS1
B: RS1
J: ICP4 DNA BINDING DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,02718
Polymers121,2959
Non-polymers7329
Water4,252236
1
G: DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3')
H: DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3')
C: RS1
D: RS1
J: ICP4 DNA BINDING DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,19310
Polymers60,8455
Non-polymers3485
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3')
F: DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3')
A: RS1
B: RS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8358
Polymers60,4504
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10840 Å2
ΔGint-118 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.510, 100.730, 201.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)- ... , 2 types, 4 molecules GEHF

#1: DNA chain DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3')


Mass: 5877.783 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: SYNTHETIC DNA, SEQUENCES MATCHES A REGION FROM THE ICP4 PROMOTER (IE3)
Source: (synth.) HUMAN HERPESVIRUS 1 (Herpes simplex virus type 1)
#2: DNA chain DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3')


Mass: 5775.739 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: SYNTHETIC DNA, SEQUENCES MATCHES A REGION FROM THE ICP4 PROMOTER (IE3)
Source: (synth.) HUMAN HERPESVIRUS 1 (Herpes simplex virus type 1)

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Protein / Protein/peptide , 2 types, 5 molecules ACDBJ

#3: Protein
RS1


Mass: 24398.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: DNA BINDING DOMAIN OF ICP4, RESIDUES 258-487
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Plasmid: PET-21A / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): T7 EXPRESS LYSY / References: UniProt: Q09I77, UniProt: P08392*PLUS
#4: Protein/peptide ICP4 DNA BINDING DOMAIN


Mass: 394.422 Da / Num. of mol.: 1
Fragment: LIkely N-terminus of chain D, but chain connectivity is ambiguous
Source method: isolated from a genetically manipulated source
Details: DNA BINDING DOMAIN OF ICP4, RESIDUES 258-487
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Plasmid: PET-21A / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): T7 EXPRESS LYSY / References: UniProt: Q09I77, UniProt: P08392*PLUS

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Non-polymers , 4 types, 245 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Ammonium sulfate, 0.1 Bis/Tris pH 5.5 & 25% w/v PEG3350 [SG1 B8 Molecular Dimensions]. Cryoprotected with 20% PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.28→71.3 Å / Num. obs: 58110 / % possible obs: 99.92 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.1613 / Net I/σ(I): 8.69
Reflection shellResolution: 2.28→2.362 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.333 / Mean I/σ(I) obs: 1.39 / CC1/2: 0.574 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.28→71.3 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.31
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 2849 4.9 %Random selection
Rwork0.2115 ---
obs0.2131 58104 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.28→71.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5847 1388 37 236 7508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037600
X-RAY DIFFRACTIONf_angle_d0.55910629
X-RAY DIFFRACTIONf_dihedral_angle_d16.4464200
X-RAY DIFFRACTIONf_chiral_restr0.0371101
X-RAY DIFFRACTIONf_plane_restr0.0041172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.31930.33771410.29862697X-RAY DIFFRACTION100
2.3193-2.36150.31161260.28432765X-RAY DIFFRACTION100
2.3615-2.40690.3341460.26722713X-RAY DIFFRACTION100
2.4069-2.45610.31991520.26432724X-RAY DIFFRACTION100
2.4561-2.50950.30361540.26322693X-RAY DIFFRACTION100
2.5095-2.56790.31681560.25552747X-RAY DIFFRACTION100
2.5679-2.63210.27211280.2552712X-RAY DIFFRACTION100
2.6321-2.70330.30831250.24752739X-RAY DIFFRACTION100
2.7033-2.78280.30941280.24082763X-RAY DIFFRACTION100
2.7828-2.87260.261510.21972704X-RAY DIFFRACTION100
2.8726-2.97530.26431470.22722757X-RAY DIFFRACTION100
2.9753-3.09440.27371160.23072788X-RAY DIFFRACTION100
3.0944-3.23530.28241360.22542765X-RAY DIFFRACTION100
3.2353-3.40580.24681520.21862740X-RAY DIFFRACTION100
3.4058-3.61920.23841420.1882779X-RAY DIFFRACTION100
3.6192-3.89860.20451390.18552784X-RAY DIFFRACTION100
3.8986-4.29090.19311510.17842766X-RAY DIFFRACTION100
4.2909-4.91170.19191540.18372808X-RAY DIFFRACTION100
4.9117-6.18770.24721480.21162852X-RAY DIFFRACTION100
6.1877-71.33760.22461570.19752959X-RAY DIFFRACTION99

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