+Open data
-Basic information
Entry | Database: PDB / ID: 8qkv | ||||||||||||
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Title | SWR1-nucleosome complex in configuration 2 | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / Chromatin remodelling complex / nucleosome / protein-DNA complex | ||||||||||||
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 / R2TP complex ...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 / R2TP complex / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / Swr1 complex / protein targeting to vacuole / Ino80 complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / replication fork protection complex / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / postreplication repair / box C/D snoRNP assembly / recombinational repair / SUMOylation of chromatin organization proteins / ATP-dependent chromatin remodeler activity / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / positive regulation of transcription by RNA polymerase I / 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 / DNA helicase activity / aerobic respiration / nuclear periphery / transcription initiation-coupled chromatin remodeling / 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 / identical protein 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: 4.7 Å | ||||||||||||
Authors | Jalal, A.S.B. / Wigley, D.B. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Nature / Year: 2024 Title: Nucleosome flipping drives kinetic proofreading and processivity by SWR1. Authors: Paul Girvan / Adam S B Jalal / Elizabeth A McCormack / Michael T Skehan / Carol L Knight / Dale B Wigley / David S Rueda / Abstract: The yeast SWR1 complex catalyses the exchange of histone H2A-H2B dimers in nucleosomes, with Htz1-H2B dimers. Here we used single-molecule analysis to demonstrate two-step double exchange of the two ...The yeast SWR1 complex catalyses the exchange of histone H2A-H2B dimers in nucleosomes, with Htz1-H2B dimers. Here we used single-molecule analysis to demonstrate two-step double exchange of the two H2A-H2B dimers in a canonical yeast nucleosome with Htz1-H2B dimers, and showed that double exchange can be processive without release of the nucleosome from the SWR1 complex. Further analysis showed that bound nucleosomes flip between two states, with each presenting a different face, and hence histone dimer, to SWR1. The bound dwell time is longer when an H2A-H2B dimer is presented for exchange than when presented with an Htz1-H2B dimer. A hexasome intermediate in the reaction is bound to the SWR1 complex in a single orientation with the 'empty' site presented for dimer insertion. Cryo-electron microscopy analysis revealed different populations of complexes showing nucleosomes caught 'flipping' between different conformations without release, each placing a different dimer into position for exchange, with the Swc2 subunit having a key role in this process. Together, the data reveal a processive mechanism for double dimer exchange that explains how SWR1 can 'proofread' the dimer identities within nucleosomes. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qkv.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8qkv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8qkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qkv_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8qkv_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8qkv_validation.xml.gz | 151.1 KB | Display | |
Data in CIF | 8qkv_validation.cif.gz | 235 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/8qkv ftp://data.pdbj.org/pub/pdb/validation_reports/qk/8qkv | HTTPS FTP |
-Related structure data
Related structure data | 18472MC 8qkuC 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 , 6 types, 10 molecules BACDFEGHMR
#1: Protein | Mass: 15405.032 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Production host: Trichoplusia ni (cabbage looper) / 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: 17064.666 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: HTA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04912 #4: Protein | Mass: 14280.362 Da / Num. of mol.: 2 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 #8: 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 #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: 59686.957 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 60110.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Vacuolar protein sorting-associated protein ... , 2 types, 2 molecules ZS
#7: Protein | Mass: 21970.316 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 |
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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 S288C (yeast) / Gene: VPS71 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q03433 |
-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
#13: Chemical | ChemComp-ADP / #14: Chemical | #15: Chemical | ChemComp-MG / #16: Chemical | |
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-Details
Has ligand of interest | Y |
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Has protein modification | N |
-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-nucleosome complex / Type: COMPLEX / Entity ID: #1-#12 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 7 |
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: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33595 / Symmetry type: POINT | ||||||||||||||||||||||||
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