+
Open data
-
Basic information
Entry | Database: PDB / ID: 8jkl | ||||||
---|---|---|---|---|---|---|---|
Title | IRF4 DNA-binding domain bound to an DNA containing GATA motif | ||||||
![]() |
| ||||||
![]() | TRANSCRIPTION / IRF4 / transcription factor / protein-DNA complex | ||||||
Function / homology | ![]() immune system process / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, G. / Feng, X. / Ding, J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 143 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 106.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 491.2 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jknC ![]() 8jkoC ![]() 8jkqC ![]() 8jksC ![]() 7jm4S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||
2 | ![]()
| ||||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 5791.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #2: DNA chain | Mass: 5857.779 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Protein | Mass: 13590.400 Da / Num. of mol.: 4 / Fragment: DNA-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69 % |
---|---|
Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9752 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.94→38.48 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|