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- PDB-1pdq: Polycomb chromodomain complexed with the histone H3 tail containi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pdq | ||||||
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Title | Polycomb chromodomain complexed with the histone H3 tail containing trimethyllysine 27. | ||||||
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![]() | STRUCTURAL PROTEIN / methyllysine / chromodomain / histone H3 / polycomb / lysine methylation / trimethyllysine / cation-pi / chromo | ||||||
Function / homology | ![]() negative regulation of response to gamma radiation / specification of segmental identity, abdomen / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / syncytial blastoderm mitotic cell cycle / polytene chromosome band / Oxidative Stress Induced Senescence ...negative regulation of response to gamma radiation / specification of segmental identity, abdomen / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / syncytial blastoderm mitotic cell cycle / polytene chromosome band / Oxidative Stress Induced Senescence / ventral cord development / PRC1 complex / polytene chromosome / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / anterior/posterior axis specification / neuron remodeling / nucleus organization / spermatid development / subtelomeric heterochromatin formation / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / heterochromatin formation / nucleosomal DNA binding / Inhibition of DNA recombination at telomere / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / embryo implantation / Assembly of the ORC complex at the origin of replication / DNA methylation / neurogenesis / 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) / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / wound healing / 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 / multicellular organism growth / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / osteoblast differentiation / structural constituent of chromatin / male gonad development / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cell population proliferation / sequence-specific DNA binding / chromosome, telomeric region / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fischle, W. / Wang, Y. / Jacobs, S.A. / Kim, Y. / Allis, C.D. / Khorasanizadeh, S. | ||||||
![]() | ![]() Title: Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains Authors: Fischle, W. / Wang, Y. / Jacobs, S.A. / Kim, Y. / Allis, C.D. / Khorasanizadeh, 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 | ![]() | 31.4 KB | Display | ![]() |
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PDB format | ![]() | 19.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.2 KB | Display | ![]() |
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Full document | ![]() | 440 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 10.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1knaS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 8853.055 Da / Num. of mol.: 1 / Fragment: residues 15-77 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1929.290 Da / Num. of mol.: 1 / Fragment: residues 15-32 / Mutation: K27(M3L) / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: P06351, UniProt: P84243*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.83 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl, 0.2 M Lithium sulfate, 30 % PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 or 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2003 |
Radiation | Monochromator: double crystal SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. all: 9494 / Num. obs: 9494 / % possible obs: 93.7 % / Observed criterion σ(F): 2.95 / Observed criterion σ(I): 2.95 / Redundancy: 4.1 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.03 / Rsym value: 0.033 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 1.76→1.82 Å / Redundancy: 2.95 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 2.95 / Num. unique all: 1190 / Rsym value: 0.212 / % possible all: 74.2 |
Reflection | *PLUS Lowest resolution: 50 Å / Rmerge(I) obs: 0.033 |
Reflection shell | *PLUS % possible obs: 74.2 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.212 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 1KNA Resolution: 1.76→27.59 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 82.0875 Å2 / ksol: 0.405418 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.76→27.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.87 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.2523 / Rfactor Rwork: 0.2233 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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