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- PDB-8qkv: SWR1-nucleosome complex in configuration 2 -

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Basic information

Entry
Database: PDB / ID: 8qkv
TitleSWR1-nucleosome complex in configuration 2
Components
  • (DNA (194-MER)) x 2
  • (RuvB-like protein ...) x 2
  • (Vacuolar protein sorting-associated protein ...) x 2
  • Actin-like protein ARP6
  • Helicase SWR1
  • Histone H2A.2
  • Histone H2B.1
  • Histone H3
  • Histone H4
KeywordsDNA BINDING PROTEIN / Chromatin remodelling complex / nucleosome / protein-DNA complex
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 / R2TP complex / Assembly of the ORC complex at the origin of replication ...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 / box C/D snoRNP assembly / Oxidative Stress Induced Senescence / replication fork protection complex / RMTs methylate histone arginines / postreplication repair / SUMOylation of chromatin organization proteins / recombinational repair / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / intracellular copper ion homeostasis / Ub-specific processing proteases / DNA helicase activity / CENP-A containing nucleosome / nucleosome binding / nuclear periphery / aerobic respiration / heterochromatin formation / nucleosome assembly / rRNA processing / structural constituent of chromatin / nucleosome / chromatin organization / 5'-3' DNA helicase activity / DNA helicase / molecular adaptor activity / histone binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / protein stabilization / chromatin remodeling / protein heterodimerization activity / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / 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
Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal / 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 ...Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal / 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 / 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 / HSA 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 H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / 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.2 / Histone H3 / Vacuolar protein sorting-associated protein 72 ...ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H2B.1 / Histone H4 / Histone H2A.2 / 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: 4.7 Å
AuthorsJalal, A.S.B. / Wigley, D.B.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust095519/Z/11/Z and 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: 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
DepositionSep 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 18, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Histone H3
C: Histone H4
D: Histone H4
F: Histone H2A.2
G: Histone H2B.1
H: Histone H2B.1
I: DNA (194-MER)
J: DNA (194-MER)
Z: Vacuolar protein sorting-associated protein 72
E: Histone H2A.2
A: Histone H3
M: Helicase SWR1
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)825,47240
Polymers821,59720
Non-polymers3,87520
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 10 molecules BACDFEGHMR

#1: Protein Histone H3


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 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.2


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 Histone H2B.1


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 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
#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 (194-MER)


Mass: 59686.957 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (194-MER)


Mass: 60110.285 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 ZS

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


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
#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

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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

#13: 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
#14: 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
#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#16: 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
Has protein modificationN

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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-nucleosome complex / Type: COMPLEX / Entity ID: #1-#12 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33595 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00347358
ELECTRON MICROSCOPYf_angle_d0.62865714
ELECTRON MICROSCOPYf_dihedral_angle_d25.0489192
ELECTRON MICROSCOPYf_chiral_restr0.0417657
ELECTRON MICROSCOPYf_plane_restr0.0046997

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