+Open data
-Basic information
Entry | Database: PDB / ID: 6gen | ||||||||||||||||||
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Title | Chromatin remodeller-nucleosome complex at 4.5 A resolution. | ||||||||||||||||||
Components |
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Keywords | NUCLEAR PROTEIN / Chromatin / Remodeller / ATPase / Histone | ||||||||||||||||||
Function / homology | Function and homology information sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / R2TP complex ...sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / R2TP complex / HDACs deacetylate histones / protein targeting to vacuole / Swr1 complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Ino80 complex / replication fork protection complex / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / postreplication repair / recombinational repair / SUMOylation of chromatin organization proteins / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / 3'-5' DNA helicase activity / positive regulation of transcription by RNA polymerase I / NuA4 histone acetyltransferase complex / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / CENP-A containing nucleosome / intracellular copper ion homeostasis / nucleosome binding / Ub-specific processing proteases / nucleosomal DNA binding / DNA helicase activity / nuclear periphery / helicase activity / heterochromatin formation / aerobic respiration / structural constituent of chromatin / rRNA processing / nucleosome / nucleosome assembly / chromatin organization / histone binding / 5'-3' DNA helicase activity / DNA helicase / molecular adaptor activity / chromatin remodeling / protein stabilization / protein heterodimerization activity / DNA repair / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / structural molecule activity / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||||||||
Authors | Willhoft, O. / Chua, E.Y.D. / Wilkinson, M. / Wigley, D.B. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: Science / Year: 2018 Title: Structure and dynamics of the yeast SWR1-nucleosome complex. Authors: Oliver Willhoft / Mohamed Ghoneim / Chia-Liang Lin / Eugene Y D Chua / Martin Wilkinson / Yuriy Chaban / Rafael Ayala / Elizabeth A McCormack / Lorraine Ocloo / David S Rueda / Dale B Wigley / Abstract: The yeast SWR1 complex exchanges histone H2A in nucleosomes with Htz1 (H2A.Z in humans). The cryo-electron microscopy structure of the SWR1 complex bound to a nucleosome at 3.6-angstrom resolution ...The yeast SWR1 complex exchanges histone H2A in nucleosomes with Htz1 (H2A.Z in humans). The cryo-electron microscopy structure of the SWR1 complex bound to a nucleosome at 3.6-angstrom resolution reveals details of the intricate interactions between components of the SWR1 complex and its nucleosome substrate. Interactions between the Swr1 motor domains and the DNA wrap at superhelical location 2 distort the DNA, causing a bulge with concomitant translocation of the DNA by one base pair, coupled to conformational changes of the histone core. Furthermore, partial unwrapping of the DNA from the histone core takes place upon binding of nucleosomes to SWR1 complex. The unwrapping, as monitored by single-molecule data, is stabilized and has its dynamics altered by adenosine triphosphate binding but does not require hydrolysis. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6gen.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6gen.ent.gz | 813.6 KB | Display | PDB format |
PDBx/mmJSON format | 6gen.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gen_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6gen_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6gen_validation.xml.gz | 124.1 KB | Display | |
Data in CIF | 6gen_validation.cif.gz | 192.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/6gen ftp://data.pdbj.org/pub/pdb/validation_reports/ge/6gen | HTTPS FTP |
-Related structure data
Related structure data | 4396MC 4395C 6gejC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Vacuolar protein sorting-associated protein ... , 2 types, 2 molecules ZS
#1: Protein | Mass: 11166.757 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Production host: Trichoplusia ni (cabbage looper) |
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#10: Protein | Mass: 32073.479 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: VPS71, SWC6, YML041C, YM8054.02C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q03433 |
-Protein , 6 types, 10 molecules ABCDEFGHMR
#2: Protein | Mass: 15405.032 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Production host: Escherichia coli (E. coli) / References: UniProt: P61830 #3: Protein | Mass: 11395.390 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: Escherichia coli (E. coli) / References: UniProt: P02309 #4: Protein | Mass: 14013.177 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: HTA1, H2A1, SPT11, YDR225W, YD9934.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P04911 #5: Protein | Mass: 14280.362 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: HTB1, H2B1, SPT12, YDR224C, YD9934.09C / Production host: Escherichia coli (E. coli) / References: UniProt: P02293 #8: Protein | | Mass: 174792.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: SWR1, YDR334W, D9651.6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q05471, DNA helicase #9: Protein | | Mass: 50100.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: ARP6, YLR085C, L2393, L9449.13 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12509 |
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-DNA chain , 2 types, 2 molecules IJ
#6: DNA chain | Mass: 53124.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#7: DNA chain | Mass: 53694.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
-RuvB-like protein ... , 2 types, 6 molecules TVXUWY
#11: Protein | Mass: 50516.941 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: RVB1, TIH1, TIP49A, YDR190C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q03940, DNA helicase #12: Protein | Mass: 51673.488 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: RVB2, TIH2, TIP49B, YPL235W, P1060 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12464, DNA helicase |
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-Non-polymers , 4 types, 20 molecules
#13: Chemical | ChemComp-ADP / #14: Chemical | #15: Chemical | ChemComp-MG / #16: Chemical | |
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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
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Molecular weight | Value: 1.3 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7 | ||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.03 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.2 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 1 sec. / Electron dose: 1.7179487179487 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5517 |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98529 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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