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

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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 ...) 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 / HDMs demethylate histones / sexual sporulation resulting in formation of a cellular spore / HATs acetylate histones / cupric reductase (NADH) activity / TTT Hsp90 cochaperone complex / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / R2TP complex / CENP-A containing nucleosome ...ATP-dependent H2AZ histone chaperone activity / HDMs demethylate histones / sexual sporulation resulting in formation of a cellular spore / HATs acetylate histones / cupric reductase (NADH) activity / TTT Hsp90 cochaperone complex / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / R2TP complex / CENP-A containing nucleosome / protein targeting to vacuole / Swr1 complex / SUMOylation of chromatin organization proteins / RMTs methylate histone arginines / Ino80 complex / rRNA transcription / DNA damage tolerance / box C/D snoRNP assembly / recombinational repair / kinetochore assembly / positive regulation of transcription by RNA polymerase I / NuA4 histone acetyltransferase complex / intracellular copper ion homeostasis / nucleolar large rRNA transcription by RNA polymerase I / 3'-5' DNA helicase activity / mitotic metaphase chromosome alignment / nucleosome binding / nuclear periphery / aerobic respiration / DNA helicase activity / transcription initiation-coupled chromatin remodeling / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nucleosomal DNA binding / kinetochore / rRNA processing / structural constituent of chromatin / nucleosome / nucleosome assembly / heterochromatin formation / histone binding / 5'-3' DNA helicase activity / chromatin organization / DNA helicase / molecular adaptor activity / protein stabilization / chromatin remodeling / protein heterodimerization activity / DNA repair / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / structural molecule activity / ATP hydrolysis activity / DNA binding / DNA-templated transcription / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RuvBL1 DNA/RNA binding domain / Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Zinc finger, HIT-type / : / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain ...RuvBL1 DNA/RNA binding domain / Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Zinc finger, HIT-type / : / 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 / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / Helicase, Ruva Protein; domain 3 - #60 / Histone, subunit A / Histone, subunit A / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase, Ruva Protein; domain 3 / Actin / Actin family / Actin / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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. / ATPase, nucleotide binding domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 / Alpha-Beta Complex / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
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 / Chromatin remodeling protein 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
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Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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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
Water00
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


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 / 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


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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Details

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

Component
IDNameTypeEntity IDParent-IDSource
1SWR1-nucleosome complexCOMPLEX#1-#120MULTIPLE SOURCES
2HistonesCOMPLEX#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 mMADP1
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 FIELD
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
8PHENIXmodel refinement
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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