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- PDB-6fml: CryoEM Structure INO80core Nucleosome complex -

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Entry
Database: PDB / ID: 6fml
TitleCryoEM Structure INO80core Nucleosome complex
Components
  • (Nucleosomal DNA Strand ...) x 2
  • (RuvB-like helicase) x 2
  • Actin related protein 5
  • Histone H2A type 1
  • Histone H2B type 1-C/E/F/G/I
  • Histone H3.2
  • Histone H4
  • Ies6
  • Ino80
  • les2
KeywordsDNA BINDING PROTEIN / INO80 / Nucleosome / ATP dependent Chromatin Remodeller
Function / homologyTIP49 AAA-lid domain / UCH proteinases / Histone H3 signature 1. / Histone H2B signature. / Histone H3 signature 2. / HDACs deacetylate histones / HATs acetylate histones / RMTs methylate histone arginines / Ub-specific processing proteases / Histone H2A signature. ...TIP49 AAA-lid domain / UCH proteinases / Histone H3 signature 1. / Histone H2B signature. / Histone H3 signature 2. / HDACs deacetylate histones / HATs acetylate histones / RMTs methylate histone arginines / Ub-specific processing proteases / Histone H2A signature. / Metalloprotease DUBs / Meiotic synapsis / Interleukin-7 signaling / Packaging Of Telomere Ends / Pre-NOTCH Transcription and Translation / Formation of the beta-catenin:TCF transactivating complex / Histone H4 signature. / C-terminus of histone H2A / Condensation of Prophase Chromosomes / RuvB-like helicase 1 / P-loop containing nucleoside triphosphate hydrolase / Actin-related protein 5 / INO80 complex, subunit Ies6 / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / RuvB-like helicase 2 / Centromere kinetochore component CENP-T histone fold / Actin / Core histone H2A/H2B/H3/H4 / PAPA-1-like conserved region / TIP49 P-loop domain / YL1 nuclear protein C-terminal domain / DASH complex subunit Dad4 / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / Histone H4, conserved site / RNA Polymerase I Chain Elongation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / Deposition of new CENPA-containing nucleosomes at the centromere / G2/M DNA damage checkpoint / RNA Polymerase I Promoter Opening / E3 ubiquitin ligases ubiquitinate target proteins / Ub-specific processing proteases / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Estrogen-dependent gene expression / Meiotic recombination / Amyloid fiber formation / Factors involved in megakaryocyte development and platelet production / Metalloprotease DUBs / UCH proteinases / Senescence-Associated Secretory Phenotype (SASP) / Chromatin modifying enzymes / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / PKMTs methylate histone lysines / HDMs demethylate histones / HATs acetylate histones / RMTs methylate histone arginines / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / NoRC negatively regulates rRNA expression / SUMOylation of chromatin organization proteins / B-WICH complex positively regulates rRNA expression / DNA methylation / Transcriptional regulation by small RNAs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RuvB-like / INO80 complex, subunit Ies2 / DASH complex subunit Dad4 / Actin family / Vps72/YL1, C-terminal / Histone H2B / Histone H4 / Histone H2A / AAA+ ATPase domain / Histone H3/CENP-A / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / Histone-fold / TIP49, P-loop domain / INO80 complex subunit B-like conserved region / DASH complex / attachment of spindle microtubules to kinetochore / R2TP complex / Swr1 complex / nuclear telomeric heterochromatin / histone exchange / ATP-dependent 5'-3' DNA helicase activity / Ino80 complex / ATP-dependent 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / box C/D snoRNP assembly / negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome assembly / DNA replication-independent nucleosome assembly
Function and homology information
Specimen sourceChaetomium thermophilum (fungus)
Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.34 Å resolution
AuthorsEustermann, S. / Schall, K. / Kostrewa, D. / Strauss, M. / Hopfner, K.
CitationJournal: Nature / Year: 2018
Title: Structural basis for ATP-dependent chromatin remodelling by the INO80 complex.
Authors: Sebastian Eustermann / Kevin Schall / Dirk Kostrewa / Kristina Lakomek / Mike Strauss / Manuela Moldt / Karl-Peter Hopfner
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 31, 2018 / Release: Apr 25, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 25, 2018Structure modelrepositoryInitial release
1.1May 2, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
A: RuvB-like helicase
B: RuvB-like helicase
C: RuvB-like helicase
D: RuvB-like helicase
E: RuvB-like helicase
F: RuvB-like helicase
G: Ino80
H: les2
I: Ies6
J: Actin related protein 5
K: Nucleosomal DNA Strand 1
L: Nucleosomal DNA Strand 2
M: Histone H3.2
N: Histone H4
O: Histone H2A type 1
P: Histone H2B type 1-C/E/F/G/I
Q: Histone H3.2
R: Histone H4
S: Histone H2A type 1
T: Histone H2B type 1-C/E/F/G/I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)915,37827
Polyers912,30820
Non-polymers3,0707
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)149430
ΔGint (kcal/M)-836
Surface area (Å2)228890
MethodPISA

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Components

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Protein/peptide , 10 types, 18 molecules ABCDEFGHIJMQNROSPT

#1: Protein/peptide RuvB-like helicase


Mass: 50451.848 Da / Num. of mol.: 3
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0006820 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0RYI5, DNA helicase
#2: Protein/peptide RuvB-like helicase


Mass: 53212.746 Da / Num. of mol.: 3
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0006170 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0RYC2, DNA helicase
#3: Protein/peptide Ino80


Mass: 210443.344 Da / Num. of mol.: 1
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Production host: Trichoplusia ni (cabbage looper)
#4: Protein/peptide les2


Mass: 52018.512 Da / Num. of mol.: 1
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus), (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0004910 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0RY01
#5: Protein/peptide Ies6


Mass: 23127.523 Da / Num. of mol.: 1
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0032670 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0S590
#6: Protein/peptide Actin related protein 5


Mass: 85996.453 Da / Num. of mol.: 1
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus), (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0032660 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0S589
#9: Protein/peptide Histone H3.2 / Histone H3/m / Histone H3/o


Mass: 15289.904 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: HIST2H3A, HIST2H3C, H3F2, H3FM, HIST2H3D / Production host: Escherichia coli (E. coli) / References: UniProt: Q71DI3
#10: Protein/peptide Histone H4 /


Mass: 11263.231 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#11: Protein/peptide Histone H2A type 1


Mass: 13990.342 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0S9, UniProt: P0C0S8*PLUS
#12: Protein/peptide Histone H2B type 1-C/E/F/G/I / Histone H2B.1 A / Histone H2B.a / H2B/a / Histone H2B.g / H2B/g / Histone H2B.h / H2B/h / Histone H2B.k / H2B/k / Histone H2B.l / H2B/l


Mass: 13806.018 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H2BC, H2BFL, HIST1H2BE, H2BFH, HIST1H2BF, H2BFG, HIST1H2BG, H2BFA, HIST1H2BI, H2BFK
Production host: Escherichia coli (E. coli) / References: UniProt: P62807

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Nucleosomal DNA Strand ... , 2 types, 2 molecules KL

#7: DNA chain Nucleosomal DNA Strand 1


Mass: 60652.645 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)
#8: DNA chain Nucleosomal DNA Strand 2


Mass: 60376.426 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 7 molecules

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


Mass: 427.201 Da / Num. of mol.: 6 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#14: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM

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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
1INO80core Nucleosome ComplexCOMPLEX1,2,3,4,5,6,7,8,9,10,11,120MULTIPLE SOURCES
2INO80coreCOMPLEX1,2,3,4,5,61RECOMBINANT
3Histone octamerCOMPLEX9,10,11,121RECOMBINANT
4Synthetic deoxyribonucleic acidCOMPLEX7,81RECOMBINANT
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
22759272Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
339606Homo sapiens (human)
4432630synthetic construct (others)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
227111Trichoplusia ni (cabbage looper)
33562Escherichia coli (E. coli)
4432630synthetic construct (others)
Buffer solutionDetails: 20 mM HEPES pH 8, 60 mM KCl, 0.5% glycerol, 0.25 mM CaCl2, 20 uM ZnCl2, 0.25 mM DTT, 0.05% Octyl-beta-glucoside
pH: 8
SpecimenConc.: 1 mg/ml
Details: Monodisperse sample: INO80core complex reconstituted with nucleosomal substrate was purified by gelfiltration. Addition of nucleotides or crosslinking was not required.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 281 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3500 nm / Calibrated defocus min: 1300 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 59.6 e/Å2
Details: Images were collected in movie mode with 4 frames per second and 10s total aquisition
Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 3992
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2.1.1bparticle selection
2SerialEM3.6image acquisition
4CTFFIND4CTF correction
7Coot0.8.9model fitting
9cryoSPARCinitial Euler assignment
10RELION2.1.1bfinal Euler assignment
12RELION2.1.1b3D reconstruction
13PHENIX1.12model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 251692
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 33937 / Symmetry type: POINT

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