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- PDB-8qyv: SWR1-hexasome complex -

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Basic information

Entry
Database: PDB / ID: 8qyv
TitleSWR1-hexasome complex
Components
  • (DNA (118-MER)) x 2
  • (RuvB-like protein ...) x 2
  • (Vacuolar protein sorting-associated protein ...) x 2
  • Actin-like protein ARP6
  • Helicase SWR1
  • Histone H2A.1
  • Histone H2B.1
  • Histone H3
  • Histone H4
  • SWR1-complex protein 5
KeywordsDNA 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
BCNT-C domain / SWR1-complex protein 5/Craniofacial development protein 1/2 / Bucentaur or craniofacial development / Bucentaur C-terminal (BCNT-C) domain profile. / Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal / Vps72/YL1 family / YL1 nuclear protein / Zinc finger, HIT-type ...BCNT-C domain / SWR1-complex protein 5/Craniofacial development protein 1/2 / Bucentaur or craniofacial development / Bucentaur C-terminal (BCNT-C) domain profile. / Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal / Vps72/YL1 family / YL1 nuclear protein / Zinc finger, HIT-type / : / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / domain in helicases and associated with SANT domains / HSA domain / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Actin / Actin family / Actin / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / ATPase, nucleotide binding domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H2B.1 / Histone H4 / Histone H2A.1 / SWR1-complex protein 5 / Histone H3 ...ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H2B.1 / Histone H4 / Histone H2A.1 / SWR1-complex protein 5 / Histone H3 / Vacuolar protein sorting-associated protein 72 / Vacuolar protein sorting-associated protein 71 / RuvB-like protein 1 / Helicase SWR1 / RuvB-like protein 2 / Actin-like protein ARP6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsJalal, A.S.B. / Wigley, D.B.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust095519/Z/11/Z & 209327/Z/17/Z United Kingdom
Cancer Research UKC6913/A21608 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N009258/1 & MR/R009023/1 United Kingdom
CitationJournal: 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
DepositionOct 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3
B: Histone H3
C: Histone H4
D: Histone H4
E: Histone H2A.1
G: Histone H2B.1
I: DNA (118-MER)
J: DNA (118-MER)
M: Helicase SWR1
P: SWR1-complex protein 5
R: Actin-like protein ARP6
S: Vacuolar protein sorting-associated protein 71
T: RuvB-like protein 1
U: RuvB-like protein 2
V: RuvB-like protein 1
W: RuvB-like protein 2
X: RuvB-like protein 1
Y: RuvB-like protein 2
Z: Vacuolar protein sorting-associated protein 72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)847,18639
Polymers843,31119
Non-polymers3,87520
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 7 types, 9 molecules ABCDEGMPR

#1: Protein Histone H3


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 Histone H4


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 Histone H2A.1


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 Histone H2B.1


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 Helicase SWR1


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 SWR1-complex protein 5


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 Actin-like protein ARP6


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 DNA (118-MER)


Mass: 36192.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (118-MER)


Mass: 36641.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Vacuolar protein sorting-associated protein ... , 2 types, 2 molecules SZ

#10: Protein Vacuolar protein sorting-associated protein 71


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
#13: Protein Vacuolar protein sorting-associated protein 72 / SWR complex protein 2


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

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RuvB-like protein ... , 2 types, 6 molecules TVXUWY

#11: Protein RuvB-like protein 1


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 RuvB-like protein 2


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 / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#15: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SWR1-hexasome complex / Type: COMPLEX / Entity ID: #1-#13 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30312 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00343116
ELECTRON MICROSCOPYf_angle_d0.63459346
ELECTRON MICROSCOPYf_dihedral_angle_d20.3187599
ELECTRON MICROSCOPYf_chiral_restr0.0416950
ELECTRON MICROSCOPYf_plane_restr0.0046736

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