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

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Basic information

Entry
Database: PDB / ID: 8jkq
TitleT95R mutant IRF4 DNA-binding domain bound to an DNA containing GACA motif
Components
  • GACA-Forward
  • GACA-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
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: 3.09 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,8878
Polymers77,8878
Non-polymers00
Water00
1
A: GACA-Forward
B: GACA-Reverse
D: Interferon regulatory factor 4
G: Interferon regulatory factor 4


Theoretical massNumber of molelcules
Total (without water)38,9444
Polymers38,9444
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-45 kcal/mol
Surface area17430 Å2
MethodPISA
2
C: GACA-Forward
E: GACA-Reverse
F: Interferon regulatory factor 4
H: Interferon regulatory factor 4


Theoretical massNumber of molelcules
Total (without water)38,9444
Polymers38,9444
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-49 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.630, 68.890, 247.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain GACA-Forward


Mass: 5776.780 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain GACA-Reverse


Mass: 5873.778 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate (pH 5.0) and 10% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9752 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9752 Å / Relative weight: 1
ReflectionResolution: 3.09→41.71 Å / Num. obs: 17407 / % possible obs: 99.2 % / Redundancy: 12.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.053 / Rrim(I) all: 0.19 / Χ2: 1.01 / Net I/σ(I): 10.8 / Num. measured all: 223083
Reflection shellResolution: 3.09→3.17 Å / % possible obs: 99.6 % / Redundancy: 13.3 % / Rmerge(I) obs: 1.27 / Num. measured all: 17005 / Num. unique obs: 1281 / CC1/2: 0.984 / Rpim(I) all: 0.36 / Rrim(I) all: 1.321 / Χ2: 0.88 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8JKL

8jkl


Resolution: 3.09→30.08 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2708 804 4.71 %
Rwork0.2445 --
obs0.2458 17071 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.09→30.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 1560 0 0 5104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035388
X-RAY DIFFRACTIONf_angle_d0.9637604
X-RAY DIFFRACTIONf_dihedral_angle_d26.3781209
X-RAY DIFFRACTIONf_chiral_restr0.071791
X-RAY DIFFRACTIONf_plane_restr0.005709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.280.42171060.39972583X-RAY DIFFRACTION94
3.28-3.540.34921260.32552595X-RAY DIFFRACTION95
3.54-3.890.32871280.28322678X-RAY DIFFRACTION98
3.89-4.450.28861530.24972723X-RAY DIFFRACTION99
4.45-5.60.26311330.24052780X-RAY DIFFRACTION99
5.61-30.080.22481580.19542908X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 25.7303 Å / Origin y: 15.4162 Å / Origin z: -29.2377 Å
111213212223313233
T1.0783 Å20.0752 Å2-0.0601 Å2-0.9169 Å2-0.1126 Å2--0.6916 Å2
L0.9948 °20.7047 °2-0.4147 °2-1.0942 °2-0.4126 °2--0.1283 °2
S0.1274 Å °0.2574 Å °-0.0537 Å °0.2776 Å °-0.0832 Å °0.0198 Å °-0.2647 Å °-0.1089 Å °-0.0414 Å °
Refinement TLS groupSelection details: all

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