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Yorodumi- PDB-7cj0: Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cj0 | ||||||||||||
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Title | Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD | ||||||||||||
Components |
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Keywords | CHAPERONE / Histone chaperone | ||||||||||||
Function / homology | Function and homology information Switching of origins to a post-replicative state / Unwinding of DNA / negative regulation of chromosome condensation / Barr body / nuclear origin of replication recognition complex / regulation of centromere complex assembly / muscle cell differentiation / CMG complex / pericentric heterochromatin formation / inner kinetochore ...Switching of origins to a post-replicative state / Unwinding of DNA / negative regulation of chromosome condensation / Barr body / nuclear origin of replication recognition complex / regulation of centromere complex assembly / muscle cell differentiation / CMG complex / pericentric heterochromatin formation / inner kinetochore / MCM complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / positive regulation of ATP-dependent activity / protein folding chaperone complex / oocyte maturation / single-stranded DNA helicase activity / regulation of DNA-templated DNA replication initiation / 3'-5' DNA helicase activity / cochlea development / nucleus organization / DNA unwinding involved in DNA replication / DNA replication origin binding / spermatid development / Activation of the pre-replicative complex / single fertilization / DNA replication initiation / subtelomeric heterochromatin formation / negative regulation of megakaryocyte differentiation / nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / cellular response to interleukin-4 / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Activation of ATR in response to replication stress / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / 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 / Inhibition of DNA recombination at telomere / heat shock protein binding / Meiotic synapsis / telomere organization / embryo implantation / 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 / Assembly of the pre-replicative complex / HDACs deacetylate histones / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Orc1 removal from chromatin / osteoblast differentiation / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / male gonad development / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / single-stranded DNA binding / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Processing of DNA double-strand break ends / histone binding / protein-folding chaperone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / DNA helicase / Estrogen-dependent gene expression / cell population proliferation Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||||||||
Authors | Bao, H. / Huang, H. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Mol.Cell / Year: 2021 Title: DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network. Authors: Hammond, C.M. / Bao, H. / Hendriks, I.A. / Carraro, M. / Garcia-Nieto, A. / Liu, Y. / Reveron-Gomez, N. / Spanos, C. / Chen, L. / Rappsilber, J. / Nielsen, M.L. / Patel, D.J. / Huang, H. / Groth, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cj0.cif.gz | 249.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cj0.ent.gz | 201.9 KB | Display | PDB format |
PDBx/mmJSON format | 7cj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/7cj0 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/7cj0 | HTTPS FTP |
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-Related structure data
Related structure data | 7cizC 5bnvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 4 types, 8 molecules EBFCGHDA
#1: Protein | Mass: 9026.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P84243 #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62805 #3: Protein | Mass: 7860.354 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49736, DNA helicase #4: Protein | Mass: 9455.661 Da / Num. of mol.: 2 / Mutation: C243S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJC9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8WXX5 |
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-Non-polymers , 2 types, 70 molecules
#5: Chemical | ChemComp-GOL / |
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#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 2.67 Å3/Da / Density % sol: 58.48 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.17 M Sodium acetate, 0.1 M Tris, pH8.5, 25% (v/v) PEG 4000, 20% (v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å | ||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2017 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin | Operator: -h,-k,l / Fraction: 0.13 | ||||||||||||||||||
Reflection | Resolution: 2.24→41.084 Å / Num. obs: 41413 / % possible obs: 99.9 % / Redundancy: 17.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 17.7 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BNV Resolution: 2.5→41.08 Å / Cross valid method: THROUGHOUT / σ(F): 32.39 / Phase error: 34.6 / Stereochemistry target values: TWIN_LSQ_F
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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: 162.75 Å2 / Biso mean: 81.1957 Å2 / Biso min: 29.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→41.08 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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