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- PDB-6gej: Chromatin remodeller-nucleosome complex at 3.6 A resolution. -

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Basic information

Entry
Database: PDB / ID: 6gej
TitleChromatin remodeller-nucleosome complex at 3.6 A resolution.
Components
  • (DNA (154-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 / homologyTIP49 AAA-lid domain / RuvB-like helicase 1 / C-terminus of histone H2A / Centromere kinetochore component CENP-T histone fold / HSA / TIP49 P-loop domain / Helicase conserved C-terminal domain / SNF2 family N-terminal domain / Core histone H2A/H2B/H3/H4 / Actin ...TIP49 AAA-lid domain / RuvB-like helicase 1 / C-terminus of histone H2A / Centromere kinetochore component CENP-T histone fold / HSA / TIP49 P-loop domain / Helicase conserved C-terminal domain / SNF2 family N-terminal domain / Core histone H2A/H2B/H3/H4 / Actin / RuvB-like helicase 2 / CENP-T/Histone H4, histone fold / Histone H4 signature. / Histone H2A conserved site / Histone H2A, C-terminal domain / Actin-related protein 6 / P-loop containing nucleoside triphosphate hydrolase / RuvB-like / Histone H4, conserved site / Helicase/SANT-associated domain / Helicase superfamily 1/2, ATP-binding domain / Histone-fold / Zinc finger, HIT-type / Histone H2A signature. / Histone H3 signature 1. / Actin family / HATs acetylate histones / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Metalloprotease DUBs / Ub-specific processing proteases / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / SUMOylation of chromatin organization proteins / SIRT1 negatively regulates rRNA expression / RMTs methylate histone arginines / HDMs demethylate histones / Histone H2B signature. / PKMTs methylate histone lysines / HDACs deacetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Condensation of Prophase Chromosomes / HSA domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Zinc finger HIT-type profile. / Histone H3 signature 2. / Histone H2A/H2B/H3 / TIP49, P-loop domain / AAA+ ATPase domain / Histone H2B / Histone H3/CENP-A / SNF2-related, N-terminal domain / Histone H2A / Helicase, C-terminal / Histone H4 / regulation of histone deacetylation / CENP-A containing nucleosome / transfer RNA gene-mediated silencing / sexual sporulation resulting in formation of a cellular spore / R2TP complex / ATP-dependent 5'-3' DNA helicase activity / Swr1 complex / histone H3-K79 methylation / histone exchange / ATP-dependent 3'-5' DNA helicase activity / Ino80 complex / replication fork protection complex / rRNA transcription / nucleosome binding / chromatin assembly or disassembly / box C/D snoRNP assembly / NuA4 histone acetyltransferase complex / postreplication repair / histone acetylation / nuclear periphery / nucleosomal DNA binding / nuclear nucleosome / DNA helicase / global genome nucleotide-excision repair / helicase activity / rRNA processing / nucleosome assembly / histone deacetylase binding / chromatin remodeling / histone binding / regulation of transcription by RNA polymerase II / DNA repair / structural molecule activity / protein heterodimerization activity / negative regulation of transcription by RNA polymerase II / regulation of transcription, DNA-templated / transcription, DNA-templated / DNA binding / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsWillhoft, O. / Chua, E.Y.D. / Wilkinson, M. / Wigley, D.B.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 26, 2018 / Release: Oct 17, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 17, 2018Structure modelrepositoryInitial release
1.1Oct 24, 2018Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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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 (154-MER)
J: DNA (154-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)783,84540
Polyers779,97120
Non-polymers3,87520
Water0
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)139750
ΔGint (kcal/M)-955
Surface area (Å2)254510
MethodPISA

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Components

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

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


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


Mass: 32073.479 Da / Num. of mol.: 1
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/peptide , 6 types, 10 molecules ABCDEFGHMR

#2: Protein/peptide Histone H3 /


Mass: 15405.032 Da / Num. of mol.: 2
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/peptide Histone H4 /


Mass: 11395.390 Da / Num. of mol.: 2
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/peptide Histone H2A.1


Mass: 14013.177 Da / Num. of mol.: 2
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/peptide Histone H2B.1 / Suppressor of Ty protein 12


Mass: 14280.362 Da / Num. of mol.: 2
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/peptide Helicase SWR1 / Swi2/Snf2-related 1


Mass: 174792.969 Da / Num. of mol.: 1
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/peptide Actin-like protein ARP6


Mass: 50100.582 Da / Num. of mol.: 1
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 (154-MER)


Mass: 47274.102 Da / Num. of mol.: 1 / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#7: DNA chain DNA (154-MER)


Mass: 47803.430 Da / Num. of mol.: 1 / 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/peptide RuvB-like protein 1 / RUVBL1 / TIP49-homology protein 1 / TIP49a homolog


Mass: 50516.941 Da / Num. of mol.: 3
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/peptide RuvB-like protein 2 / RUVBL2 / TIP49-homology protein 2 / TIP49b homolog


Mass: 51673.488 Da / Num. of mol.: 3
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 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#14: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Formula: BeF3
#15: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn / Zinc

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1SWR1-nucleosome complexCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 120MULTIPLE SOURCES
2HistoneCOMPLEX2, 3, 4, 51RECOMBINANT
3DNACOMPLEX6, 71RECOMBINANT
4remodellerCOMPLEX1, 8, 9, 10, 11, 121RECOMBINANT
Molecular weightValue: 1.3 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
2332630synthetic construct (others)
34559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
12562Escherichia coli (E. coli)
23562Escherichia coli (E. coli)
347111Trichoplusia ni (cabbage looper)
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 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.2 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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: 1.71794871794872 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Number of grids imaged: 1 / Number of real images: 5517

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / 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
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 98529 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00245001
ELECTRON MICROSCOPYf_angle_d0.52762211
ELECTRON MICROSCOPYf_dihedral_angle_d18.31826349
ELECTRON MICROSCOPYf_chiral_restr0.0377293
ELECTRON MICROSCOPYf_plane_restr0.0036834

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