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- PDB-8jkl: IRF4 DNA-binding domain bound to an DNA containing GATA motif -

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Basic information

Entry
Database: PDB / ID: 8jkl
TitleIRF4 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


positive regulation of multicellular organismal process / RNA polymerase II cis-regulatory region sequence-specific DNA 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: 2.94 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
E: GATA-Forward
F: GATA-Reverse
G: Interferon regulatory factor 4
C: Interferon regulatory factor 4
D: Interferon regulatory factor 4
H: Interferon regulatory factor 4


Theoretical massNumber of molelcules
Total (without water)77,6618
Polymers77,6618
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)38,8304
Polymers38,8304
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-43 kcal/mol
Surface area17220 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)38,8304
Polymers38,8304
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-38 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.560, 117.560, 150.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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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: 13590.400 Da / Num. of mol.: 4 / Fragment: DNA-binding domain
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: 3.97 Å3/Da / Density % sol: 69 %
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 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9752 Å / Relative weight: 1
ReflectionResolution: 2.94→38.48 Å / Num. obs: 26113 / % possible obs: 99.9 % / Redundancy: 19.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.052 / Rrim(I) all: 0.234 / Χ2: 0.99 / Net I/σ(I): 14 / Num. measured all: 516859
Reflection shellResolution: 2.94→3.02 Å / % possible obs: 100 % / Redundancy: 19.2 % / Rmerge(I) obs: 1.923 / Num. measured all: 36412 / Num. unique obs: 1894 / CC1/2: 0.785 / Rpim(I) all: 0.449 / Rrim(I) all: 1.976 / Χ2: 0.92 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JM4

7jm4


Resolution: 2.94→38.48 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2762 1340 5.14 %
Rwork0.2411 --
obs0.2428 26049 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.94→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3610 1560 0 0 5170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035459
X-RAY DIFFRACTIONf_angle_d1.0497700
X-RAY DIFFRACTIONf_dihedral_angle_d25.5112170
X-RAY DIFFRACTIONf_chiral_restr0.074796
X-RAY DIFFRACTIONf_plane_restr0.007724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-3.050.48181280.3952414X-RAY DIFFRACTION100
3.05-3.170.27861620.30442422X-RAY DIFFRACTION100
3.17-3.310.28881460.27132394X-RAY DIFFRACTION99
3.31-3.490.33641230.27472445X-RAY DIFFRACTION100
3.49-3.70.29171200.26032466X-RAY DIFFRACTION100
3.7-3.990.28451280.24142479X-RAY DIFFRACTION100
3.99-4.390.25151340.23232449X-RAY DIFFRACTION100
4.39-5.020.23741390.21592484X-RAY DIFFRACTION100
5.02-6.320.25131330.22222525X-RAY DIFFRACTION100
6.33-38.480.25281270.19282631X-RAY DIFFRACTION100

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