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- PDB-8hcl: zebrafish IRF-10 DBD complex with DNA -

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Basic information

Entry
Database: PDB / ID: 8hcl
Titlezebrafish IRF-10 DBD complex with DNA
Components
  • DNA (5'-D(P*AP*CP*TP*TP*TP*CP*AP*CP*TP*TP*CP*A)-3')
  • DNA (5'-D(P*TP*GP*AP*AP*GP*TP*GP*AP*AP*AP*GP*T)-3')
  • Interferon regulatory factor 10
KeywordsDNA BINDING PROTEIN/DNA / zebrafish / IRF / DBD / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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 / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleus
Similarity search - Function
Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / 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 ...Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / 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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Interferon regulatory factor 10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWang, Z.X. / Zhang, Y.A. / Ouyang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725026; 82225028; 82172287 China
CitationJournal: J Immunol. / Year: 2024
Title: Crystal Structures of DNA-bound Fish IRF10 and IRF11 Reveal the Determinants of IFN Regulation.
Authors: Wang, Z.X. / Liu, B. / Xie, H. / Liu, X. / Li, X. / Shi, F. / Ouyang, S. / Zhang, Y.A.
History
DepositionNov 1, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(P*TP*GP*AP*AP*GP*TP*GP*AP*AP*AP*GP*T)-3')
D: DNA (5'-D(P*AP*CP*TP*TP*TP*CP*AP*CP*TP*TP*CP*A)-3')
E: DNA (5'-D(P*AP*CP*TP*TP*TP*CP*AP*CP*TP*TP*CP*A)-3')
F: DNA (5'-D(P*TP*GP*AP*AP*GP*TP*GP*AP*AP*AP*GP*T)-3')
A: Interferon regulatory factor 10
B: Interferon regulatory factor 10


Theoretical massNumber of molelcules
Total (without water)40,7016
Polymers40,7016
Non-polymers00
Water3,333185
1
C: DNA (5'-D(P*TP*GP*AP*AP*GP*TP*GP*AP*AP*AP*GP*T)-3')
D: DNA (5'-D(P*AP*CP*TP*TP*TP*CP*AP*CP*TP*TP*CP*A)-3')
A: Interferon regulatory factor 10


Theoretical massNumber of molelcules
Total (without water)20,3513
Polymers20,3513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-26 kcal/mol
Surface area9710 Å2
MethodPISA
2
E: DNA (5'-D(P*AP*CP*TP*TP*TP*CP*AP*CP*TP*TP*CP*A)-3')
F: DNA (5'-D(P*TP*GP*AP*AP*GP*TP*GP*AP*AP*AP*GP*T)-3')
B: Interferon regulatory factor 10


Theoretical massNumber of molelcules
Total (without water)20,3513
Polymers20,3513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-22 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.010, 86.470, 57.150
Angle α, β, γ (deg.)90.000, 103.966, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: DNA chain DNA (5'-D(P*TP*GP*AP*AP*GP*TP*GP*AP*AP*AP*GP*T)-3')


Mass: 3750.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*CP*TP*TP*TP*CP*AP*CP*TP*TP*CP*A)-3')


Mass: 3572.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Interferon regulatory factor 10


Mass: 13027.696 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: irf10, SO:0001217 / Production host: Escherichia coli (E. coli) / References: UniProt: A8E5I1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate trihydrate pH 4.5, 25% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 298.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.99→55.46 Å / Num. obs: 25670 / % possible obs: 98.83 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.84 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.6
Reflection shellResolution: 1.99→8.9 Å / Redundancy: 2.3 % / Num. unique obs: 1894 / CC1/2: 0.74 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX1.19.2_4158phasing
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IRF

2irf


Resolution: 1.99→38.83 Å / SU ML: 0.2869 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.3332
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.259 3550 7.77 %
Rwork0.2225 42139 -
obs0.2254 25631 89.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.61 Å2
Refinement stepCycle: LAST / Resolution: 1.99→38.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 984 0 185 2925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01082900
X-RAY DIFFRACTIONf_angle_d1.50854105
X-RAY DIFFRACTIONf_chiral_restr0.0733427
X-RAY DIFFRACTIONf_plane_restr0.0123356
X-RAY DIFFRACTIONf_dihedral_angle_d27.3567700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.020.33821420.32651611X-RAY DIFFRACTION87.26
2.02-2.050.37691370.31691672X-RAY DIFFRACTION88.5
2.05-2.080.36161490.30361676X-RAY DIFFRACTION88.64
2.08-2.110.38251440.2881740X-RAY DIFFRACTION88.62
2.11-2.140.35011270.29031594X-RAY DIFFRACTION88.67
2.14-2.180.32791470.28471671X-RAY DIFFRACTION89.25
2.18-2.220.33461390.27551708X-RAY DIFFRACTION88.37
2.22-2.260.33331430.26821618X-RAY DIFFRACTION88.27
2.26-2.310.31371400.27681650X-RAY DIFFRACTION88.05
2.31-2.360.32231410.27081713X-RAY DIFFRACTION88.92
2.36-2.410.31771420.26591635X-RAY DIFFRACTION89.39
2.41-2.470.35181470.26571730X-RAY DIFFRACTION90.5
2.47-2.540.27461260.25481629X-RAY DIFFRACTION87.23
2.54-2.620.28291420.25041646X-RAY DIFFRACTION88.6
2.62-2.70.31491480.25581676X-RAY DIFFRACTION88.41
2.7-2.80.31181440.26371701X-RAY DIFFRACTION89.69
2.8-2.910.3131410.25011660X-RAY DIFFRACTION89.92
2.91-3.040.30071430.25571742X-RAY DIFFRACTION91.28
3.04-3.20.31671420.24461706X-RAY DIFFRACTION90.9
3.2-3.40.27371440.21361675X-RAY DIFFRACTION88.91
3.4-3.660.21941350.19631719X-RAY DIFFRACTION90.84
3.67-4.030.2171480.17591773X-RAY DIFFRACTION94.03
4.03-4.620.21391420.16671735X-RAY DIFFRACTION93.11
4.62-5.810.18061450.19241777X-RAY DIFFRACTION93.39
5.81-38.830.18971520.18851682X-RAY DIFFRACTION90.08

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