+Open data
-Basic information
Entry | Database: PDB / ID: 8qyv | ||||||||||||
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Title | SWR1-hexasome complex | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / Chromatin remodelling complex / hexasome | ||||||||||||
Function / homology | Function and homology information ATP-dependent H2AZ histone chaperone activity / 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 ...ATP-dependent H2AZ histone chaperone activity / 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 / ATP-dependent chromatin remodeler activity / box C/D snoRNP assembly / 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 / rRNA transcription / Estrogen-dependent gene expression / intracellular copper ion homeostasis / nucleosome binding / Ub-specific processing proteases / CENP-A containing nucleosome / nucleosomal DNA binding / aerobic respiration / DNA helicase activity / transcription initiation-coupled chromatin remodeling / nuclear periphery / helicase activity / heterochromatin formation / structural constituent of chromatin / rRNA processing / nucleosome / nucleosome assembly / chromatin organization / histone binding / 5'-3' DNA helicase activity / DNA helicase / molecular adaptor activity / protein stabilization / chromatin remodeling / protein heterodimerization activity / DNA repair / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / structural molecule activity / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Jalal, A.S.B. / Wigley, D.B. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Mol Cell / Year: 2024 Title: Stabilization of the hexasome intermediate during histone exchange by yeast SWR1 complex. Authors: Adam S B Jalal / Paul Girvan / Eugene Y D Chua / Lexin Liu / Shijie Wang / Elizabeth A McCormack / Michael T Skehan / Carol L Knight / David S Rueda / Dale B Wigley / Abstract: The yeast SWR1 complex catalyzes the exchange of histone H2A/H2B dimers in nucleosomes with Htz1/H2B dimers. We use cryoelectron microscopy to determine the structure of an enzyme-bound hexasome ...The yeast SWR1 complex catalyzes the exchange of histone H2A/H2B dimers in nucleosomes with Htz1/H2B dimers. We use cryoelectron microscopy to determine the structure of an enzyme-bound hexasome intermediate in the reaction pathway of histone exchange, in which an H2A/H2B dimer has been extracted from a nucleosome prior to the insertion of a dimer comprising Htz1/H2B. The structure reveals a key role for the Swc5 subunit in stabilizing the unwrapping of DNA from the histone core of the hexasome. By engineering a crosslink between an Htz1/H2B dimer and its chaperone protein Chz1, we show that this blocks histone exchange by SWR1 but allows the incoming chaperone-dimer complex to insert into the hexasome. We use this reagent to trap an SWR1/hexasome complex with an incoming Htz1/H2B dimer that shows how the reaction progresses to the next step. Taken together the structures reveal insights into the mechanism of histone exchange by SWR1 complex. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qyv.cif.gz | 983 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qyv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8qyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qyv_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8qyv_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 8qyv_validation.xml.gz | 145.8 KB | Display | |
Data in CIF | 8qyv_validation.cif.gz | 223.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/8qyv ftp://data.pdbj.org/pub/pdb/validation_reports/qy/8qyv | HTTPS FTP |
-Related structure data
Related structure data | 18764MC 8qz0C 9fbwC 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 , 7 types, 9 molecules ABCDEGMPR
#1: Protein | Mass: 15374.983 Da / Num. of mol.: 2 / Mutation: Q120M, K121P, K125Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: HHT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61830 #2: Protein | Mass: 11395.390 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: HHF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02309 #3: Protein | | Mass: 14013.177 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: HTA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04911 #4: Protein | | Mass: 14280.362 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: HTB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02293 #7: Protein | | Mass: 174792.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SWR1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q05471 #8: Protein | | Mass: 34395.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SWC5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P38326 #9: Protein | | Mass: 50100.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: ARP6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12509 |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 36192.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 36641.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Vacuolar protein sorting-associated protein ... , 2 types, 2 molecules SZ
#10: Protein | Mass: 32073.479 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: VPS71 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q03433 |
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#13: Protein | Mass: 90709.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: VPS72, SWC2, YDR485C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q03388 |
-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 S288C (yeast) / Gene: RVB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q03940 #12: Protein | Mass: 51673.488 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RVB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12464 |
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-Non-polymers , 4 types, 20 molecules
#14: Chemical | ChemComp-ADP / #15: Chemical | #16: Chemical | ChemComp-MG / #17: Chemical | |
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-Details
Has ligand of interest | Y |
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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: SWR1-hexasome complex / Type: COMPLEX / Entity ID: #1-#13 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 300 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30312 / Symmetry type: POINT | ||||||||||||||||||||||||
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