+Open data
-Basic information
Entry | Database: PDB / ID: 7mju | ||||||
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Title | Crystal structure of human AF10 PZP bound to histone H3 tail | ||||||
Components | Histone H3.1,Protein AF-10 | ||||||
Keywords | PEPTIDE BINDING PROTEIN / Histone binding Leukemia | ||||||
Function / homology | Function and homology information nucleosome binding / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events ...nucleosome binding / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Klein, B.J. / Kutateladze, T.G. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: The role of the PZP domain of AF10 in acute leukemia driven by AF10 translocations. Authors: Klein, B.J. / Deshpande, A. / Cox, K.L. / Xuan, F. / Zandian, M. / Barbosa, K. / Khanal, S. / Tong, Q. / Zhang, Y. / Zhang, P. / Sinha, A. / Bohlander, S.K. / Shi, X. / Wen, H. / Poirier, M. ...Authors: Klein, B.J. / Deshpande, A. / Cox, K.L. / Xuan, F. / Zandian, M. / Barbosa, K. / Khanal, S. / Tong, Q. / Zhang, Y. / Zhang, P. / Sinha, A. / Bohlander, S.K. / Shi, X. / Wen, H. / Poirier, M.G. / Deshpande, A.J. / Kutateladze, T.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mju.cif.gz | 87.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mju.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 7mju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/7mju ftp://data.pdbj.org/pub/pdb/validation_reports/mj/7mju | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 22609.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J, MLLT10, AF10 Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P68431, UniProt: P55197 | ||||||
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#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | Sequence details | amino-terminal thirteen residues of Histone H3.1 followed by SGS linker, and then the Histone H3- ...amino-terminal thirteen residues of Histone H3.1 followed by SGS linker, and then the Histone H3-interacting region of AF-10 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.85 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.09 M Tris, 22.5% PEG 3350, and 10 mM spermine tetrahydrochloride PH range: 8.5-8.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.27819 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Aug 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.27819 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→41.09 Å / Num. obs: 12143 / % possible obs: 97.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 28.17 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.1→2.16 Å / Num. unique obs: 845 / CC1/2: 0.637 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→41.084 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.79 / Stereochemistry target values: MLHL
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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: 98.34 Å2 / Biso mean: 35.5477 Å2 / Biso min: 11.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→41.084 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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