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

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Basic information

Entry
Database: PDB / ID: 8jks
TitleT95R mutant IRF4 DNA-binding domain bound to an DNA containing GAGA motif
Components
  • GAGA-Forward
  • GAGA-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: 3.3 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: GAGA-Forward
B: GAGA-Reverse
C: Interferon regulatory factor 4
D: Interferon regulatory factor 4
E: GAGA-Forward
F: GAGA-Reverse
G: 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: GAGA-Forward
B: GAGA-Reverse
C: Interferon regulatory factor 4
D: 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 area5500 Å2
ΔGint-44 kcal/mol
Surface area17600 Å2
MethodPISA
2
E: GAGA-Forward
F: GAGA-Reverse
G: 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 area5580 Å2
ΔGint-48 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.610, 68.010, 246.600
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 GAGA-Forward


Mass: 5816.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain GAGA-Reverse


Mass: 5833.754 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: 2.83 Å3/Da / Density % sol: 56.57 %
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: 3.3→41.03 Å / Num. obs: 13978 / % possible obs: 99.7 % / Redundancy: 12.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.072 / Rrim(I) all: 0.262 / Χ2: 1.01 / Net I/σ(I): 10.1 / Num. measured all: 180176
Reflection shellResolution: 3.3→3.39 Å / % possible obs: 99.1 % / Redundancy: 13.6 % / Rmerge(I) obs: 1.382 / Num. measured all: 13384 / Num. unique obs: 981 / CC1/2: 0.993 / Rpim(I) all: 0.388 / Rrim(I) all: 1.437 / Χ2: 0.94 / Net I/σ(I) obs: 2.8

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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: 3.3→40.02 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2869 693 5.02 %
Rwork0.235 --
obs0.2376 13818 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→40.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 1560 0 0 5218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035508
X-RAY DIFFRACTIONf_angle_d0.9877764
X-RAY DIFFRACTIONf_dihedral_angle_d26.3021231
X-RAY DIFFRACTIONf_chiral_restr0.072799
X-RAY DIFFRACTIONf_plane_restr0.006735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.550.35251450.32282471X-RAY DIFFRACTION96
3.55-3.910.35591420.26252580X-RAY DIFFRACTION99
3.91-4.480.26961120.2412645X-RAY DIFFRACTION100
4.48-5.640.24741430.24622662X-RAY DIFFRACTION100
5.64-40.020.27511510.19952767X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 25.3457 Å / Origin y: 14.8786 Å / Origin z: -29.0331 Å
111213212223313233
T0.6911 Å20.0364 Å2-0.0366 Å2-0.7356 Å2-0.1043 Å2--0.6512 Å2
L0.9073 °20.4009 °2-0.0949 °2-0.8491 °2-0.2599 °2---0.1486 °2
S0.1112 Å °0.2065 Å °-0.0678 Å °0.2608 Å °-0.0937 Å °-0.0579 Å °-0.1221 Å °0.0105 Å °-0 Å °
Refinement TLS groupSelection details: all

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