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Yorodumi- PDB-7x8f: Crystal structure of ENL T4 mutant YEATS domain in complex with h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7x8f | |||||||||||||||
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Title | Crystal structure of ENL T4 mutant YEATS domain in complex with histone H3 acetylation at K27 | |||||||||||||||
Components |
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Keywords | TRANSCRIPTION / YEATS domain / Complex / histone | |||||||||||||||
Function / homology | Function and homology information RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / lysine-acetylated histone binding / fibrillar center / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | |||||||||||||||
Authors | Li, Y. / Peng, B. / Li, H. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Mol.Cell / Year: 2022 Title: Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer. Authors: Song, L. / Yao, X. / Li, H. / Peng, B. / Boka, A.P. / Liu, Y. / Chen, G. / Liu, Z. / Mathias, K.M. / Xia, L. / Li, Q. / Mir, M. / Li, Y. / Li, H. / Wan, L. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x8f.cif.gz | 80.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x8f.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 7x8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/7x8f ftp://data.pdbj.org/pub/pdb/validation_reports/x8/7x8f | HTTPS FTP |
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-Related structure data
Related structure data | 7e74C 7x88C 7x8bC 7x8gC 5j9sS S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18915.779 Da / Num. of mol.: 2 / Mutation: insertions Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT1, ENL, LTG19, YEATS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03111 #2: Protein/peptide | Mass: 487.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 45.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 20 % (w/v) PEG 4000, 0.1 M sodium citrate pH 5.6, 20 % (v/v) 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Feb 6, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.44→40 Å / Num. obs: 13211 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.063 / Rrim(I) all: 0.163 / Χ2: 0.69 / Net I/σ(I): 3.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J9S Resolution: 2.44→38.4 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.39 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.58 Å2 / Biso mean: 52.6988 Å2 / Biso min: 26.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.44→38.4 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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