+Open data
-Basic information
Entry | Database: PDB / ID: 8k4l | ||||||
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Title | Crystal structure of NRF1 homodimer in complex with DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Nuclear respiratory factor 1 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm ...Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Liu, K. / Li, W.F. / Min, J.R. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2024 Title: Molecular mechanism of specific DNA sequence recognition by NRF1. Authors: Liu, K. / Li, W. / Xiao, Y. / Lei, M. / Zhang, M. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k4l.cif.gz | 217.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k4l.ent.gz | 168.8 KB | Display | PDB format |
PDBx/mmJSON format | 8k4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/8k4l ftp://data.pdbj.org/pub/pdb/validation_reports/k4/8k4l | HTTPS FTP |
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-Related structure data
Related structure data | 8k3dC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25866.557 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NRF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q16656 #2: DNA chain | Mass: 4280.792 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 2% (v/v) Tacsimate (pH 6.0), 0.1 M Bis-Tris (pH 6.5),20% (w/v) Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 2, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→42.53 Å / Num. obs: 32991 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 0.978 / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.1→2.16 Å / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2615 / CC1/2: 0.955 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.43 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→38.43 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -15.8827 Å / Origin y: 2.4757 Å / Origin z: -16.2569 Å
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Refinement TLS group | Selection details: all |