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Yorodumi- PDB-4x23: CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE P... -
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-Basic information
Entry | Database: PDB / ID: 4x23 | |||||||||
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Title | CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE | |||||||||
Components |
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Keywords | structural protein/dna / NUCLEOSOME CORE PARTICLE / WIDOM 601 DNA FRAGMMENT / HISTONE FOLD / CENP-C COMPLEX / SEGREGATION / CHROMOSOME CENTROMERE / KINETOCHORE ASSEMBLY / CONSTITUTIVE CENTROMERE-ASSOCIATED NETWORK (CCAN) PROTEINS / STRUCTURAL PROTEIN-DNA COMPLEX | |||||||||
Function / homology | Function and homology information pericentric heterochromatin => GO:0005721 / condensed chromosome, centromeric region => GO:0000779 / kinetochore => GO:0000776 / HDMs demethylate histones / Interleukin-7 signaling / PKMTs methylate histone lysines / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex ...pericentric heterochromatin => GO:0005721 / condensed chromosome, centromeric region => GO:0000779 / kinetochore => GO:0000776 / HDMs demethylate histones / Interleukin-7 signaling / PKMTs methylate histone lysines / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / Metalloprotease DUBs / Factors involved in megakaryocyte development and platelet production / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RNA Polymerase I Promoter Escape / polytene chromosome band / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / larval somatic muscle development / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / UCH proteinases / spindle attachment to meiosis I kinetochore / polytene chromosome / centromeric DNA binding / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / nuclear chromosome / pericentric heterochromatin / nucleosomal DNA binding / chromosome segregation / heterochromatin formation / kinetochore / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / mitotic cell cycle / chromosome / nucleic acid binding / protein heterodimerization activity / protein-containing complex binding / chromatin / DNA binding / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Drosophila melanogaster (fruit fly) Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Jiang, J.S. | |||||||||
Citation | Journal: Science / Year: 2013 Title: A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C. Authors: Kato, H. / Jiang, J.S. / Zhou, B.R. / Rozendaal, M. / Feng, H. / Ghirlando, R. / Xiao, T.S. / Straight, A.F. / Bai, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x23.cif.gz | 618.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x23.ent.gz | 482.9 KB | Display | PDB format |
PDBx/mmJSON format | 4x23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/4x23 ftp://data.pdbj.org/pub/pdb/validation_reports/x2/4x23 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-DNA chain , 2 types, 4 molecules ISJT
#1: DNA chain | Mass: 45138.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 147 BP WIDOM 601 DNA FRAGMENT (+ STRAND) / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: DNA chain | Mass: 45610.043 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 147 BP WIDOM 601 DNA FRAGMENT (- STRAND) / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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-Protein , 4 types, 16 molecules AEKOBFLPCGMQDHNR
#3: Protein | Mass: 11365.296 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 41-133 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His3 / Production host: Escherichia coli (E. coli) / References: UniProt: P02299 #4: Protein | Mass: 8910.394 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 25-103 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His4 / Production host: Escherichia coli (E. coli) / References: UniProt: P84040 #5: Protein | Mass: 11093.877 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 16-117 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His2A / Production host: Escherichia coli (E. coli) / References: UniProt: P84051 #6: Protein | Mass: 10019.455 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 33-122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His2B / Production host: Escherichia coli (E. coli) / References: UniProt: P02283 |
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-Protein/peptide , 1 types, 4 molecules VUXW
#7: Protein/peptide | Mass: 3222.686 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 710-734 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q66LH7 |
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-Details
Sequence details | THE DISCREPANCY AT THE C-TERM OF H3 SEQUENCES (CHAINS A,E,K,O) IS A RESULT OF CHIMERIC CENP-A, I.E. ...THE DISCREPANC |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.25 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% MPD, 40MM SODIUM CACODYLATE, 24MM SPERMINE TETRA-HCL, 80MM SODIUM CHLORIDE, 20MM MAGNESIUM CHLORIDE; RESERVIOR 35% MPD. PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K PH range: 7.4 - 7.6 |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3.5→50 Å / Num. obs: 48623 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 122.9 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 11 | ||||||||||||||||||
Reflection shell | Resolution: 3.5→3.56 Å / Redundancy: 3 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1.5 / % possible all: 78.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PYO, 3MVD Resolution: 3.5→49.543 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.82 / Stereochemistry target values: ML / Details: CNS 1.3 WAS USED FOR LOW RESOLUTION REFINEMENT
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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 mean: 157.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→49.543 Å
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Refine LS restraints |
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LS refinement shell |
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