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Yorodumi- PDB-7xyf: Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to S... -
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-Basic information
Entry | Database: PDB / ID: 7xyf | |||||||||
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Title | Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA binding / remodeler / nucleosome / Fft3-nucleosome complex | |||||||||
Function / homology | Function and homology information attachment of telomeric heterochromatin to nuclear envelope / ATP-dependent H3-H4 histone complex chaperone activity / HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins ...attachment of telomeric heterochromatin to nuclear envelope / ATP-dependent H3-H4 histone complex chaperone activity / HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RCAF complex / Factors involved in megakaryocyte development and platelet production / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Regulation of endogenous retroelements by KRAB-ZFP proteins / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / larval somatic muscle development / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / UCH proteinases / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / polytene chromosome / histone chaperone activity / DNA repair-dependent chromatin remodeling / transcription elongation-coupled chromatin remodeling / nuclear chromosome / replication fork processing / ATP-dependent activity, acting on DNA / heterochromatin / nucleosomal DNA binding / helicase activity / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / chromosome / DNA helicase / nucleic acid binding / damaged DNA binding / chromatin remodeling / protein heterodimerization activity / chromatin binding / protein-containing complex binding / chromatin / ATP hydrolysis activity / DNA binding / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) Schizosaccharomyces pombe 972h- (yeast) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Nan, Z. / Tao, J. / Yangao, H. | |||||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome (Class I Fft3-nucleosome complex) Authors: Nan, Z. / Tao, J. / Yangao, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xyf.cif.gz | 405.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xyf.ent.gz | 311 KB | Display | PDB format |
PDBx/mmJSON format | 7xyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xyf_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7xyf_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7xyf_validation.xml.gz | 52.3 KB | Display | |
Data in CIF | 7xyf_validation.cif.gz | 81.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/7xyf ftp://data.pdbj.org/pub/pdb/validation_reports/xy/7xyf | HTTPS FTP |
-Related structure data
Related structure data | 33520MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 9 molecules CGDHKAEBF
#1: Protein | Mass: 11552.494 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A: ...Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A:CG33829, CG33829, His2A:CG33832, CG33832, His2A:CG33835, CG33835, His2A:CG33838, CG33838, His2A:CG33841, CG33841, His2A:CG33844, CG33844, His2A:CG33847, CG33847, His2A:CG33850, CG33850, His2A:CG33862, CG33862, His2A:CG33865, CG33865 Production host: Escherichia coli (E. coli) / References: UniProt: P84051 #2: Protein | Mass: 10721.382 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, ...Gene: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, CG33880, His2B:CG33882, CG33882, His2B:CG33884, CG33884, His2B:CG33886, CG33886, His2B:CG33888, CG33888, His2B:CG33890, CG33890, His2B:CG33892, CG33892, His2B:CG33894, CG33894, His2B:CG33896, CG33896, His2B:CG33898, CG33898, His2B:CG33900, CG33900, His2B:CG33902, CG33902, His2B:CG33904, CG33904, His2B:CG33906, CG33906, His2B:CG33908, CG33908, His2B:CG33910, CG33910 Production host: Escherichia coli (E. coli) / References: UniProt: P02283 #5: Protein | | Mass: 78351.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast) Strain: 972 / ATCC 24843 / Gene: fft3, snf2SR, SPAC25A8.01c / Production host: Escherichia coli (E. coli) / References: UniProt: O42861, DNA helicase #6: Protein | Mass: 11488.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: His3, His3:CG31613, CG31613, His3:CG33803, CG33803, His3:CG33806, CG33806, His3:CG33809, CG33809, His3:CG33812, CG33812, His3:CG33815, CG33815, His3:CG33818, CG33818, His3:CG33821, CG33821, ...Gene: His3, His3:CG31613, CG31613, His3:CG33803, CG33803, His3:CG33806, CG33806, His3:CG33809, CG33809, His3:CG33812, CG33812, His3:CG33815, CG33815, His3:CG33818, CG33818, His3:CG33821, CG33821, His3:CG33824, CG33824, His3:CG33827, CG33827, His3:CG33830, CG33830, His3:CG33833, CG33833, His3:CG33836, CG33836, His3:CG33839, CG33839, His3:CG33842, CG33842, His3:CG33845, CG33845, His3:CG33848, CG33848, His3:CG33851, CG33851, His3:CG33854, CG33854, His3:CG33857, CG33857, His3:CG33860, CG33860, His3:CG33863, CG33863, His3:CG33866, CG33866 Production host: Escherichia coli (E. coli) / References: UniProt: P02299 #7: Protein | Mass: 9861.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: His4, H4, His4r, H4r, CG3379, His4:CG31611, CG31611, His4:CG33869, CG33869, His4:CG33871, CG33871, His4:CG33873, CG33873, His4:CG33875, CG33875, His4:CG33877, CG33877, His4:CG33879, CG33879, ...Gene: His4, H4, His4r, H4r, CG3379, His4:CG31611, CG31611, His4:CG33869, CG33869, His4:CG33871, CG33871, His4:CG33873, CG33873, His4:CG33875, CG33875, His4:CG33877, CG33877, His4:CG33879, CG33879, His4:CG33881, CG33881, His4:CG33883, CG33883, His4:CG33885, CG33885, His4:CG33887, CG33887, His4:CG33889, CG33889, His4:CG33891, CG33891, His4:CG33893, CG33893, His4:CG33895, CG33895, His4:CG33897, CG33897, His4:CG33899, CG33899, His4:CG33901, CG33901, His4:CG33903, CG33903, His4:CG33905, CG33905, His4:CG33907, CG33907, His4:CG33909, CG33909 Production host: Escherichia coli (E. coli) / References: UniProt: P84040 |
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-DNA chain , 2 types, 2 molecules JI
#3: DNA chain | Mass: 45274.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 44856.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of Fft3-nucleosome complex with Fft3 bound to SHL+2 of the nucleosome (Class I Fft3-nucleosome complex) Type: COMPLEX / Entity ID: #6-#7, #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Schizosaccharomyces pombe 972h- (yeast) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178242 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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