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- PDB-6gen: Chromatin remodeller-nucleosome complex at 4.5 A resolution. -

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Basic information

Entry
Database: PDB / ID: 6gen
TitleChromatin remodeller-nucleosome complex at 4.5 A resolution.
Components
  • (DNA (173-MER)) x 2
  • (RuvB-like protein ...) x 2
  • (Vacuolar protein sorting-associated protein ...Vacuole) x 2
  • Actin-like protein ARP6
  • Helicase SWR1
  • Histone H2A.1
  • Histone H2B.1
  • Histone H3
  • Histone H4
KeywordsNUCLEAR PROTEIN / Chromatin / Remodeller / ATPase / Histone
Function / homology
Function and homology information


ATP-dependent H2AZ histone chaperone activity / sexual sporulation resulting in formation of a cellular spore / HDMs demethylate histones / HATs acetylate histones / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / R2TP complex / Swr1 complex / protein targeting to vacuole ...ATP-dependent H2AZ histone chaperone activity / sexual sporulation resulting in formation of a cellular spore / HDMs demethylate histones / HATs acetylate histones / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / R2TP complex / Swr1 complex / protein targeting to vacuole / SUMOylation of chromatin organization proteins / Ino80 complex / 5'-3' DNA helicase activity / replication fork protection complex / RMTs methylate histone arginines / box C/D snoRNP assembly / recombinational repair / postreplication repair / ATP-dependent chromatin remodeler activity / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / nucleosome binding / CENP-A containing nucleosome / DNA helicase activity / nuclear periphery / helicase activity / rRNA processing / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / DNA helicase / protein stabilization / molecular adaptor activity / chromatin remodeling / protein heterodimerization activity / DNA repair / chromatin / structural molecule activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Actin-related protein 6 / Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Zinc finger, HIT-type / 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 ...Actin-related protein 6 / Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Zinc finger, HIT-type / 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 / Histone, subunit A / Histone, subunit A / 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 / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / ATPase, nucleotide binding domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H2B.1 / Histone H4 / Histone H2A.1 / Histone H3 / Vacuolar protein sorting-associated protein 71 ...ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H2B.1 / Histone H4 / Histone H2A.1 / Histone H3 / 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 (brewer's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWillhoft, O. / Chua, E.Y.D. / Wilkinson, M. / Wigley, D.B.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Wellcome Trust095519/Z/11/Z United Kingdom
Wellcome Trust209327/Z/17/Z United Kingdom
Cancer Research UKC6913/A21608 United Kingdom
Medical Research Council (United Kingdom)MR/N009258/1 United Kingdom
Medical Research Council (United Kingdom)MR/R009023/1 United Kingdom
CitationJournal: Science / Year: 2018
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
DepositionApr 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Assembly

Deposited unit
Z: Vacuolar protein sorting-associated protein 72
A: Histone H3
B: Histone H3
C: Histone H4
D: Histone H4
E: Histone H2A.1
F: Histone H2A.1
G: Histone H2B.1
H: Histone H2B.1
I: DNA (173-MER)
J: DNA (173-MER)
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)795,58740
Polymers791,71220
Non-polymers3,87520
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

#1: Protein Vacuolar protein sorting-associated protein 72 / Vacuole


Mass: 11166.757 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Production host: Trichoplusia ni (cabbage looper)
#10: Protein Vacuolar protein sorting-associated protein 71 / Vacuole / SWR complex protein 6


Mass: 32073.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: VPS71, SWC6, YML041C, YM8054.02C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q03433

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Protein , 6 types, 10 molecules ABCDEFGHMR

#2: Protein Histone H3 /


Mass: 15405.032 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Production host: Escherichia coli (E. coli) / References: UniProt: P61830
#3: Protein Histone H4 /


Mass: 11395.390 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: Escherichia coli (E. coli) / References: UniProt: P02309
#4: Protein Histone H2A.1


Mass: 14013.177 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HTA1, H2A1, SPT11, YDR225W, YD9934.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P04911
#5: Protein Histone H2B.1 / Suppressor of Ty protein 12


Mass: 14280.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HTB1, H2B1, SPT12, YDR224C, YD9934.09C / Production host: Escherichia coli (E. coli) / References: UniProt: P02293
#8: Protein Helicase SWR1 / Swi2/Snf2-related 1


Mass: 174792.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SWR1, YDR334W, D9651.6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q05471, DNA helicase
#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 (strain ATCC 204508 / S288c) (yeast)
Gene: ARP6, YLR085C, L2393, L9449.13 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12509

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DNA chain , 2 types, 2 molecules IJ

#6: DNA chain DNA (173-MER)


Mass: 53124.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#7: DNA chain DNA (173-MER)


Mass: 53694.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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

#11: Protein RuvB-like protein 1 / RUVBL1 / TIP49-homology protein 1 / TIP49a homolog


Mass: 50516.941 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RVB1, TIH1, TIP49A, YDR190C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q03940, DNA helicase
#12: Protein RuvB-like protein 2 / RUVBL2 / TIP49-homology protein 2 / TIP49b homolog


Mass: 51673.488 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RVB2, TIH2, TIP49B, YPL235W, P1060 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12464, DNA helicase

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Non-polymers , 4 types, 20 molecules

#13: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / 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
#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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

Component
IDNameTypeEntity IDParent-IDSource
1SWR1-nucleosome complexCOMPLEX#1-#120MULTIPLE SOURCES
2HistonesHistoneCOMPLEX#2-#51RECOMBINANT
3DNACOMPLEX#6-#71RECOMBINANT
4remodellerCOMPLEX#1, #8-#121RECOMBINANT
Molecular weightValue: 1.3 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
23synthetic construct (others)32630
34Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Escherichia coli (E. coli)562
34Trichoplusia ni (cabbage looper)7111
Buffer solutionpH: 7
Buffer component
IDConc.NameBuffer-ID
125 mMHEPES1
250 mMSodium chloride1
31 mMTCEP1
40.005 %Tween-201
53 mMADPAdenosine diphosphate1
65 mMMagnesium chloride1
73 mMBeryllium chloride1
815 mMSodium fluoride1
SpecimenConc.: 0.03 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage 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

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
4Gctf1.06CTF correction
10cryoSPARC0.6.5initial Euler assignment
11RELION2.1.0final Euler assignment
12RELION2.1.0classification
13RELION2.1.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98529 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00345877
ELECTRON MICROSCOPYf_angle_d0.69863561
ELECTRON MICROSCOPYf_dihedral_angle_d19.58226732
ELECTRON MICROSCOPYf_chiral_restr0.0437442
ELECTRON MICROSCOPYf_plane_restr0.0056874

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