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- PDB-8jko: T95R mutant IRF4 DNA-binding domain bound to an DNA containing GA... -

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Basic information

Entry
Database: PDB / ID: 8jko
TitleT95R mutant IRF4 DNA-binding domain bound to an DNA containing GATA motif
Components
  • GATA-Forward
  • GATA-Reverse
  • Interferon regulatory factor 4
KeywordsTRANSCRIPTION / IRF4 / transcription factor / protein-DNA complex
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of transcription by RNA polymerase II / 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsWang, G. / Feng, X. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030305 China
CitationJournal: Structure / Year: 2023
Title: Molecular basis for the functional roles of the multimorphic T95R mutation of IRF4 causing human autosomal dominant combined immunodeficiency.
Authors: Wang, G. / Feng, X. / Ding, J.
History
DepositionJun 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GATA-Forward
B: GATA-Reverse
C: Interferon regulatory factor 4
D: Interferon regulatory factor 4
E: GATA-Forward
F: GATA-Reverse
G: Interferon regulatory factor 4
H: Interferon regulatory factor 4


Theoretical massNumber of molelcules
Total (without water)77,8858
Polymers77,8858
Non-polymers00
Water00
1
A: GATA-Forward
B: GATA-Reverse
C: Interferon regulatory factor 4
D: Interferon regulatory factor 4


Theoretical massNumber of molelcules
Total (without water)38,9434
Polymers38,9434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-38 kcal/mol
Surface area17320 Å2
MethodPISA
2
E: GATA-Forward
F: GATA-Reverse
G: Interferon regulatory factor 4
H: Interferon regulatory factor 4


Theoretical massNumber of molelcules
Total (without water)38,9434
Polymers38,9434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-40 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.766, 116.766, 153.008
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: DNA chain GATA-Forward


Mass: 5791.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain GATA-Reverse


Mass: 5857.779 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein
Interferon regulatory factor 4 / Interferon regulatory factor 4 / isoform CRA_e


Mass: 13646.490 Da / Num. of mol.: 4 / Fragment: DNA-binding domain / Mutation: T95R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF4, hCG_20902 / Production host: Escherichia coli (E. coli) / References: UniProt: F2Z3D5

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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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MgCl2, 0.1 M sodium citrate (pH 5.0) and 15% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9752 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9752 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 26068 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.933 / CC star: 0.982 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.041 / Rrim(I) all: 0.182 / Χ2: 0.757 / Net I/σ(I): 2.9 / Num. measured all: 522535
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2.95-320.42.05312880.5780.8560.4642.1050.43
3-3.06201.43512990.820.9490.3291.4730.436
3.06-3.1119.10.96612680.9030.9740.2260.9930.481
3.11-3.1820.60.65912800.9750.9940.1480.6760.528
3.18-3.2520.90.52712850.9830.9960.1180.540.563
3.25-3.3220.80.52712870.9740.9930.1180.540.553
3.32-3.4120.50.4512550.980.9950.1010.4620.584
3.41-3.520.60.37813070.9810.9950.0850.3870.609
3.5-3.620.10.33612790.9820.9960.0760.3440.647
3.6-3.7219.20.28412990.9830.9960.0660.2920.698
3.72-3.8520.70.24812870.9860.9970.0560.2540.716
3.85-420.30.21113010.9930.9980.0480.2170.742
4-4.1919.40.18313000.9910.9980.0430.1880.845
4.19-4.4120.90.16612960.9940.9980.0370.170.842
4.41-4.6820.70.15413190.9940.9990.0340.1570.859
4.68-5.0420.10.13512980.9950.9990.0310.1380.903
5.04-5.5519.40.12913160.9950.9990.030.1320.897
5.55-6.3519.30.12113320.9940.9990.0280.1240.917
6.35-820.20.11113510.9950.9990.0250.1141.061
8-5017.90.10514210.9980.9990.0260.1081.849

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8JKL

8jkl


Resolution: 2.95→48.01 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 1268 5.01 %
Rwork0.2307 --
obs0.2318 25308 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3581 1560 0 0 5141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045426
X-RAY DIFFRACTIONf_angle_d1.2087645
X-RAY DIFFRACTIONf_dihedral_angle_d25.0252165
X-RAY DIFFRACTIONf_chiral_restr0.082788
X-RAY DIFFRACTIONf_plane_restr0.015716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.060.40451390.36122471X-RAY DIFFRACTION91
3.06-3.20.3251240.27692547X-RAY DIFFRACTION94
3.2-3.370.28491400.26762594X-RAY DIFFRACTION96
3.37-3.580.29771400.27742650X-RAY DIFFRACTION98
3.58-3.860.28351440.24732697X-RAY DIFFRACTION98
3.86-4.250.26041400.23262709X-RAY DIFFRACTION99
4.25-4.860.24841440.22432732X-RAY DIFFRACTION99
4.86-6.120.27151490.22532761X-RAY DIFFRACTION99
6.12-48.010.17871480.18522879X-RAY DIFFRACTION99

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