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Open data
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Basic information
Entry | Database: PDB / ID: 6gej | ||||||||||||||||||
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Title | Chromatin remodeller-nucleosome complex at 3.6 A resolution. | ||||||||||||||||||
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Function / homology | ![]() sexual sporulation resulting in formation of a cellular spore / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / SIRT1 negatively regulates rRNA expression / Condensation of Prophase Chromosomes / 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 / Swr1 complex ...sexual sporulation resulting in formation of a cellular spore / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / SIRT1 negatively regulates rRNA expression / Condensation of Prophase Chromosomes / 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 / Swr1 complex / HDACs deacetylate histones / protein targeting to vacuole / Ino80 complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / replication fork protection complex / RMTs methylate histone arginines / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Willhoft, O. / Chua, E.Y.D. / Wilkinson, M. / Wigley, D.B. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 818.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4395MC ![]() 4396C ![]() 6genC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() Production host: ![]() ![]() |
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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.) ![]() ![]() ![]() Gene: VPS71, SWC6, YML041C, YM8054.02C / Production host: ![]() ![]() |
-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.) ![]() ![]() ![]() Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Production host: ![]() ![]() ![]() #3: Protein | ![]() Mass: 11395.390 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: ![]() ![]() ![]() #4: Protein | Mass: 14013.177 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: HTA1, H2A1, SPT11, YDR225W, YD9934.10 / Production host: ![]() ![]() ![]() #5: Protein | Mass: 14280.362 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: HTB1, H2B1, SPT12, YDR224C, YD9934.09C / Production host: ![]() ![]() ![]() #8: Protein | | Mass: 174792.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: SWR1, YDR334W, D9651.6 / Production host: ![]() ![]() ![]() #9: Protein | | Mass: 50100.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: ARP6, YLR085C, L2393, L9449.13 / Production host: ![]() ![]() |
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-DNA chain , 2 types, 2 molecules IJ
#6: DNA chain | Mass: 47274.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() ![]() |
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#7: DNA chain | Mass: 47803.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() ![]() |
-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.) ![]() ![]() ![]() Gene: RVB1, TIH1, TIP49A, YDR190C / Production host: ![]() ![]() ![]() #12: Protein | Mass: 51673.488 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: RVB2, TIH2, TIP49B, YPL235W, P1060 / Production host: ![]() ![]() ![]() |
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-Non-polymers , 4 types, 20 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/MG.gif)
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![](data/chem/img/BEF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
#13: Chemical | ChemComp-ADP / ![]() #14: Chemical | #15: Chemical | ChemComp-MG / #16: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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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![]() ![]() | ||||||||||||||||||||||||||||||||||||
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 |
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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![]() ![]() |
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 |
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Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||
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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