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- EMDB-4277: CryoEM Structure INO80core Nucleosome complex -

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Entry
Database: EMDB / ID: 4277
TitleCryoEM Structure INO80core Nucleosome complex
Map data
SampleINO80core Nucleosome Complex:
INO80core / Histone octamer / Synthetic deoxyribonucleic acid / (RuvB-like helicase) x 2 / Ino80 / les2 / Ies6 / Actin related protein 5 / (nucleic-acidNucleic acid) x 2 / Histone H3.2 ...INO80core / Histone octamer / Synthetic deoxyribonucleic acid / (RuvB-like helicase) x 2 / Ino80 / les2 / Ies6 / Actin related protein 5 / (nucleic-acidNucleic acid) x 2 / Histone H3.2 / Histone H4 / Histone H2A type 1 / Histone H2B type 1-C/E/F/G/I / (ligand) x 2
Function / homologyINO80 complex, subunit Ies2 / Histone H2A/H2B/H3 / Histone H2A, C-terminal domain / INO80 complex, subunit Ies6 / Actin-related protein 5 / P-loop containing nucleoside triphosphate hydrolase / RuvB-like / Histone H4, conserved site / DASH complex subunit Dad4 / Vps72/YL1, C-terminal ...INO80 complex, subunit Ies2 / Histone H2A/H2B/H3 / Histone H2A, C-terminal domain / INO80 complex, subunit Ies6 / Actin-related protein 5 / P-loop containing nucleoside triphosphate hydrolase / RuvB-like / Histone H4, conserved site / DASH complex subunit Dad4 / Vps72/YL1, C-terminal / TIP49, P-loop domain / Histone-fold / INO80 complex subunit B-like conserved region / CENP-T/Histone H4, histone fold / TATA box binding protein associated factor (TAF) / Actin family / AAA+ ATPase domain / Histone H2A / Histone H4 / Histone H2B / Histone H3/CENP-A / Condensation of Prophase Chromosomes / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Histone H2A conserved site / RuvB-like helicase 1 / PRC2 methylates histones and DNA / Histone H3 signature 2. / Pre-NOTCH Transcription and Translation / Packaging Of Telomere Ends / Interleukin-7 signaling / Meiotic synapsis / Metalloprotease DUBs / Ub-specific processing proteases / UCH proteinases / RMTs methylate histone arginines / HATs acetylate histones / HDACs deacetylate histones / Histone H2B signature. / RuvB-like helicase 2 / Histone H3 signature 1. / Histone H4 signature. / Histone H2A signature. / C-terminus of histone H2A / Centromere kinetochore component CENP-T histone fold / DASH complex subunit Dad4 / YL1 nuclear protein C-terminal domain / TIP49 P-loop domain / PAPA-1-like conserved region / Core histone H2A/H2B/H3/H4 / Actin / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / PKMTs methylate histone lysines / Deposition of new CENPA-containing nucleosomes at the centromere / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / UCH proteinases / Ub-specific processing proteases / Metalloprotease DUBs / 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 / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Promoter Opening / RNA Polymerase I Chain Elongation / E3 ubiquitin ligases ubiquitinate target proteins / 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 / DNA methylation / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / SUMOylation of chromatin organization proteins / HDMs demethylate histones / NoRC negatively regulates rRNA expression / HATs acetylate histones / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / RMTs methylate histone arginines / Chromatin modifying enzymes / DASH complex / attachment of spindle microtubules to kinetochore / R2TP complex / Swr1 complex / histone exchange / ATP-dependent 5'-3' DNA helicase activity / nuclear telomeric heterochromatin / 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 / telomere capping
Function and homology information
SourceChaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Homo sapiens (human) / synthetic construct (others) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsingle 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 ReportPDB-ID: 6fml

SummaryFull reportAbout validation report
DateDeposition: Jan 31, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: Apr 25, 2018 / Last update: May 2, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6fml
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4277.map.gz (map file in CCP4 format, 157217 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
340 pix
1.06 Å/pix.
= 360.4 Å
340 pix
1.06 Å/pix.
= 360.4 Å
340 pix
1.06 Å/pix.
= 360.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.034 (by author), 0.034 (movie #1):
Minimum - Maximum-0.078898385 - 0.14019749
Average (Standard dev.)0.00019601843 (0.004939095)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions340340340
Origin0.00.00.0
Limit339.0339.0339.0
Spacing340340340
CellA=B=C: 360.4 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z360.400360.400360.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0790.1400.000

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Supplemental data

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Sample components

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Entire INO80core Nucleosome Complex

EntireName: INO80core Nucleosome Complex / Number of components: 18

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Component #1: protein, INO80core Nucleosome Complex

ProteinName: INO80core Nucleosome Complex / Recombinant expression: No
MassTheoretical: 1000 kDa

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Component #2: protein, INO80core

ProteinName: INO80core / Recombinant expression: No
SourceSpecies: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: protein, Histone octamer

ProteinName: Histone octamer / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Synthetic deoxyribonucleic acid

ProteinName: Synthetic deoxyribonucleic acid / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

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Component #5: protein, RuvB-like helicase

ProteinName: RuvB-like helicase / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 50.451848 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #6: protein, RuvB-like helicase

ProteinName: RuvB-like helicase / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 53.212746 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #7: protein, Ino80

ProteinName: Ino80 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 210.443344 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #8: protein, les2

ProteinName: les2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.018512 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #9: protein, Ies6

ProteinName: Ies6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.127523 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #10: protein, Actin related protein 5

ProteinName: Actin related protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 85.996453 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #11: nucleic-acid, Nucleosomal DNA Strand 1

Nucleic-acidName: Nucleosomal DNA Strand 1 / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DT)(DC)(DG)(DG)(DA)(DA)(DC)(DA)(DC) (DT)(DA)(DT)(DC)(DC)(DG)(DA)(DC)(DT)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG)(DC)(DA)(DA) (DG)(DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT) (DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT) (DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG) (DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DT)(DG)(DC)(DT)(DA) (DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DC)(DA)
MassTheoretical: 60.652645 kDa
SourceSpecies: synthetic construct (others)

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Component #12: nucleic-acid, Nucleosomal DNA Strand 2

Nucleic-acidName: Nucleosomal DNA Strand 2 / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT) (DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DC) (DA)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC) (DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG) (DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA) (DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC) (DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA) (DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DC)(DT)(DG)(DT)(DG)(DC)(DA)(DT) (DG)(DT)(DA)(DT)(DT)(DG)(DA)(DA)(DC)(DA) (DG)(DC)(DG)(DA)(DC)(DC)(DT)(DT)(DG)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DA)(DG)(DT) (DC)(DG)(DG)(DA)(DT)(DA)(DG)(DT)(DG)(DT) (DT)(DC)(DC)(DG)(DA)(DG)
MassTheoretical: 60.376426 kDa
SourceSpecies: synthetic construct (others)

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Component #13: protein, Histone H3.2

ProteinName: Histone H3.2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.289904 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #14: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.263231 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #15: protein, Histone H2A type 1

ProteinName: Histone H2A type 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.990342 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #16: protein, Histone H2B type 1-C/E/F/G/I

ProteinName: Histone H2B type 1-C/E/F/G/I / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.806018 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #17: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Component #18: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 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
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 281 K / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 59.6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: - 3500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3992
Details: Images were collected in movie mode with 4 frames per second and 10s total aquisition

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 33937
3D reconstructionSoftware: RELION / Resolution: 4.34 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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