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Open data
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Basic information
Entry | Database: PDB / ID: 4yhp | |||||||||
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Title | Crystal structure of 309M3-B Fab in complex with H3K9me3 peptide | |||||||||
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![]() | IMMUNE SYSTEM / Antibody / Fab / Head-to-head dimerization / H3K9me3 | |||||||||
Function / homology | ![]() 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 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression ...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 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hattori, T. / Dementieva, I.S. / Montano, S.P. / Koide, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation. Authors: Hattori, T. / Lai, D. / Dementieva, I.S. / Montano, S.P. / Kurosawa, K. / Zheng, Y. / Akin, L.R. / Swist-Rosowska, K.M. / Grzybowski, A.T. / Koide, A. / Krajewski, K. / Strahl, B.D. / ...Authors: Hattori, T. / Lai, D. / Dementieva, I.S. / Montano, S.P. / Kurosawa, K. / Zheng, Y. / Akin, L.R. / Swist-Rosowska, K.M. / Grzybowski, A.T. / Koide, A. / Krajewski, K. / Strahl, B.D. / Kelleher, N.L. / Ruthenburg, A.J. / Koide, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 344.2 KB | Display | ![]() |
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PDB format | ![]() | 280.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484 KB | Display | ![]() |
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Full document | ![]() | 495.1 KB | Display | |
Data in XML | ![]() | 62.6 KB | Display | |
Data in CIF | ![]() | 88.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yhyC ![]() 4yhzC ![]() 1mhpS ![]() 2dd8S ![]() 2r8sS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 1704.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P68431*PLUS #2: Antibody | Mass: 24670.701 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | Mass: 23269.580 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.29 Å3/Da / Density % sol: 71.34 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 22% PEG 3350, 8% Tacsimate (pH8.0), 3% Xylitol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 112308 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2R8S, 2DD8, 1MHP Resolution: 2.53→31.38 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.55 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.53→31.38 Å
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Refine LS restraints |
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LS refinement shell |
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