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Yorodumi- PDB-3r45: Structure of a CENP-A-Histone H4 Heterodimer in complex with chap... -
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-Basic information
Entry | Database: PDB / ID: 3r45 | ||||||
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Title | Structure of a CENP-A-Histone H4 Heterodimer in complex with chaperone HJURP | ||||||
Components |
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Keywords | NUCLEAR PROTEIN / histone fold / Centromere / CENP-A / Histone Chaperone / HJURP | ||||||
Function / homology | Function and homology information regulation of DNA binding / kinetochore => GO:0000776 / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / chromosome, centromeric region / mitotic cytokinesis / regulation of protein-containing complex assembly ...regulation of DNA binding / kinetochore => GO:0000776 / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / chromosome, centromeric region / mitotic cytokinesis / regulation of protein-containing complex assembly / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / pericentric heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Mitotic Prometaphase / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Resolution of Sister Chromatid Cohesion / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / 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 / chromosome segregation / HDACs deacetylate histones / RHO GTPases Activate Formins / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / 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 / Separation of Sister Chromatids / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / cell cycle / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / nucleolus / protein-containing complex / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Hu, H. / Liu, Y. / Wang, M. / Fang, J. / Huang, H. / Yang, N. / Li, Y. / Wang, J. / Yao, X. / Shi, Y. ...Hu, H. / Liu, Y. / Wang, M. / Fang, J. / Huang, H. / Yang, N. / Li, Y. / Wang, J. / Yao, X. / Shi, Y. / Li, G. / Xu, R.M. | ||||||
Citation | Journal: Genes Dev. / Year: 2011 Title: Structure of a CENP-A-histone H4 heterodimer in complex with chaperone HJURP Authors: Hu, H. / Liu, Y. / Wang, M. / Fang, J. / Huang, H. / Yang, N. / Li, Y. / Wang, J. / Yao, X. / Shi, Y. / Li, G. / Xu, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r45.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r45.ent.gz | 85.3 KB | Display | PDB format |
PDBx/mmJSON format | 3r45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r45_validation.pdf.gz | 471 KB | Display | wwPDB validaton report |
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Full document | 3r45_full_validation.pdf.gz | 473.6 KB | Display | |
Data in XML | 3r45_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 3r45_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/3r45 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/3r45 | HTTPS FTP |
-Related structure data
Related structure data | 3nqjS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 17843.510 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPA / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / References: UniProt: P49450 |
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#2: Protein | Mass: 11394.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / References: UniProt: P62805 |
#3: Protein | Mass: 9636.992 Da / Num. of mol.: 1 / Fragment: residues 1-80 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HJURP / Plasmid: pET28a-smt3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NCD3 |
-Non-polymers , 3 types, 50 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.22 Å3/Da / Density % sol: 44.58 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9788 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 7, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 10958 / Num. obs: 10744 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 44.12 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1099 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NQJ Resolution: 2.6→43.386 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8488 / SU ML: 0.29 / σ(F): 0 / Phase error: 22.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.605 Å2 / ksol: 0.387 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.23 Å2 / Biso mean: 53.4206 Å2 / Biso min: 16.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→43.386 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Origin x: 22.4909 Å / Origin y: 3.3793 Å / Origin z: 24.0981 Å
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Refinement TLS group |
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