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Yorodumi- PDB-7zry: Structure of the 2a splicing variant of the full-length human LSD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zry | ||||||
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Title | Structure of the 2a splicing variant of the full-length human LSD1 bound to CoREST (delta305) | ||||||
Components |
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Keywords | FLAVOPROTEIN / demethylase / histone / splicing / epigenetics | ||||||
Function / homology | Function and homology information positive regulation of megakaryocyte differentiation / DNA repair complex / histone deacetylase complex / Regulation of PTEN gene transcription / transcription repressor complex / erythrocyte differentiation / HDACs deacetylate histones / transcription corepressor activity / Factors involved in megakaryocyte development and platelet production / chromatin organization ...positive regulation of megakaryocyte differentiation / DNA repair complex / histone deacetylase complex / Regulation of PTEN gene transcription / transcription repressor complex / erythrocyte differentiation / HDACs deacetylate histones / transcription corepressor activity / Factors involved in megakaryocyte development and platelet production / chromatin organization / Potential therapeutics for SARS / transcription regulator complex / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / enzyme binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Caroli, J. / Mattevi, A. | ||||||
Funding support | Saudi Arabia, 1items
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Citation | Journal: Iscience / Year: 2022 Title: Fine-tuned KDM1A alternative splicing regulates human cardiomyogenesis through an enzymatic-independent mechanism. Authors: Astro, V. / Ramirez-Calderon, G. / Pennucci, R. / Caroli, J. / Saera-Vila, A. / Cardona-Londono, K. / Forastieri, C. / Fiacco, E. / Maksoud, F. / Alowaysi, M. / Sogne, E. / Falqui, A. / ...Authors: Astro, V. / Ramirez-Calderon, G. / Pennucci, R. / Caroli, J. / Saera-Vila, A. / Cardona-Londono, K. / Forastieri, C. / Fiacco, E. / Maksoud, F. / Alowaysi, M. / Sogne, E. / Falqui, A. / Gonzalez, F. / Montserrat, N. / Battaglioli, E. / Mattevi, A. / Adamo, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zry.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zry.ent.gz | 134.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zry_validation.pdf.gz | 804.9 KB | Display | wwPDB validaton report |
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Full document | 7zry_full_validation.pdf.gz | 824.2 KB | Display | |
Data in XML | 7zry_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 7zry_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/7zry ftp://data.pdbj.org/pub/pdb/validation_reports/zr/7zry | HTTPS FTP |
-Related structure data
Related structure data | 2v1dS S: Starting model for refinement |
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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: 94820.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1 / Production host: Escherichia coli BL21 (bacteria) References: [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase |
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#2: Protein | Mass: 20244.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RCOR1, KIAA0071, RCOR / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9UKL0 |
#3: Chemical | ChemComp-FAD / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 1.0-1.3 M Na/K Tartrate, 0.1 M ADA pH 6.5 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999998 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999998 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→49.12 Å / Num. obs: 69570 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.7→2.76 Å / Redundancy: 7.2 % / Rmerge(I) obs: 3.105 / Mean I/σ(I) obs: 0.68 / Num. unique obs: 701 / CC1/2: 0.307 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V1D Resolution: 2.7→49.12 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / 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: 157.27 Å2 / Biso mean: 98.4218 Å2 / Biso min: 53.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→49.12 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27
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