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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


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
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 ...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.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: To Be Published
Title: Nucleosome flipping drives kinetic proof reading and processivity of histone exchange by yeast SWR1 complex
Authors: Girvan, P. / Jalal, A.S.B. / McCormack, E.A. / Skehan, M.T. / Wigley, D.B. / Rueda, D.S.
History
DepositionSep 18, 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
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

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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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