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- PDB-6hts: Cryo-EM structure of the human INO80 complex bound to nucleosome -

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Entry
Database: PDB / ID: 6hts
TitleCryo-EM structure of the human INO80 complex bound to nucleosome
Components
  • (DNA (150-MER)) x 2
  • Actin-related protein 5
  • Chromatin-remodeling ATPase INO80
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
  • INO80 complex subunit B
  • RuvB-like 1
  • RuvB-like 2
KeywordsDNA BINDING PROTEIN / Chromatin / Remodeller / Nucleosome / DNA Binding / Histones / DNA repair / ATPase / Helicase / Sliding / Complex
Function / homologyTIP49 AAA-lid domain / Helicase conserved C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / RuvB-like helicase 1 / RuvB-like helicase 2 / SNF2-like, N-terminal domain superfamily / Actin / Core histone H2A/H2B/H3/H4 / SNF2 family N-terminal domain ...TIP49 AAA-lid domain / Helicase conserved C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / RuvB-like helicase 1 / RuvB-like helicase 2 / SNF2-like, N-terminal domain superfamily / Actin / Core histone H2A/H2B/H3/H4 / SNF2 family N-terminal domain / HIT zinc finger / DNA helicase Ino80 / PAPA-1-like conserved region / TIP49 P-loop domain / DNA-binding domain / Centromere kinetochore component CENP-T histone fold / C-terminus of histone H2A / Histone H2A signature. / Histone H4 signature. / Histone H3 signature 1. / Histone H2B signature. / Histone H2A, C-terminal domain / INO80 complex, subunit Ies2 / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / TATA box binding protein associated factor (TAF) / Histone H3/CENP-A / SNF2-related, N-terminal domain / Histone H2B / Helicase, C-terminal / Histone H4 / Histone H2A / AAA+ ATPase domain / Actin family / Actin, conserved site / INO80 complex subunit B-like conserved region / Actin-related protein 5 / Histone H2A/H2B/H3 / Zinc finger, HIT-type / Histone-fold / TIP49, P-loop domain / Helicase superfamily 1/2, ATP-binding domain / Histone H4, conserved site / DBINO domain / RuvB-like / P-loop containing nucleoside triphosphate hydrolase / Actins signature 2. / Histone H3 signature 2. / Superfamilies 1 and 2 helicase C-terminal domain profile. / DNA Damage Recognition in GG-NER / Transcriptional regulation by small RNAs / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / 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 / DBINO domain profile. / DNA methylation / SUMOylation of chromatin organization proteins / Senescence-Associated Secretory Phenotype (SASP) / Meiotic synapsis / Interleukin-7 signaling / Packaging Of Telomere Ends / Telomere Extension By Telomerase / Pre-NOTCH Transcription and Translation / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Condensation of Prophase Chromosomes / NoRC negatively regulates rRNA expression / Oxidative Stress Induced Senescence / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / PKMTs methylate histone lysines / HDMs demethylate histones / HATs acetylate histones / RMTs methylate histone arginines / Chromatin modifying enzymes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / negative regulation of estrogen receptor binding / positive regulation of nuclear cell cycle DNA replication / transcriptional activation by promoter-enhancer looping / histone H2A acetylation / positive regulation of telomerase RNA localization to Cajal body / regulation of G1/S transition of mitotic cell cycle / establishment of protein localization to chromatin
Function and homology information
Specimen sourceHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.8 Å resolution
AuthorsAyala, R. / Willhoft, O. / Aramayo, R.J. / Wilkinson, M. / McCormack, E.A. / Ocloo, L. / Wigley, D.B. / Zhang, X.
CitationJournal: Nature / Year: 2018
Title: Structure and regulation of the human INO80-nucleosome complex.
Authors: Rafael Ayala / Oliver Willhoft / Ricardo J Aramayo / Martin Wilkinson / Elizabeth A McCormack / Lorraine Ocloo / Dale B Wigley / Xiaodong Zhang
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 4, 2018 / Release: Nov 7, 2018

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: RuvB-like 1
B: RuvB-like 2
C: RuvB-like 1
D: RuvB-like 2
E: RuvB-like 1
F: RuvB-like 2
G: Chromatin-remodeling ATPase INO80
H: Actin-related protein 5
I: Histone H3.1
J: Histone H4
K: Histone H2A type 1-B/E
L: Histone H2B type 1-J
M: Histone H3.1
N: Histone H4
O: Histone H2A type 1-B/E
P: Histone H2B type 1-J
R: INO80 complex subunit B
X: DNA (150-MER)
Y: DNA (150-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)811,32326
Polyers808,69519
Non-polymers2,6297
Water0
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration, SEC-MALS
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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Protein/peptide , 9 types, 17 molecules ACEBDFGHIMJNKOLPR

#1: Protein/peptide RuvB-like 1 / / 49 kDa TATA box-binding protein-interacting protein / 49 kDa TBP-interacting protein / 54 kDa erythrocyte cytosolic protein / ECP-54 / INO80 complex subunit H / Nuclear matrix protein 238 / NMP 238 / Pontin 52 / TIP49a / TIP60-associated protein 54-alpha / TAP54-alpha


Mass: 50296.914 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL1, INO80H, NMP238, TIP49, TIP49ARuvB-like 1 / Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): Sf9 / References: UniProt: Q9Y265, DNA helicase
#2: Protein/peptide RuvB-like 2 / 48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa erythrocyte cytosolic protein / ECP-51 / INO80 complex subunit J / Repressing pontin 52 / Reptin 52 / TIP49b / TIP60-associated protein 54-beta / TAP54-beta


Mass: 51222.465 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL2, INO80J, TIP48, TIP49B, CGI-46 / Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): Sf9 / References: UniProt: Q9Y230, DNA helicase
#3: Protein/peptide Chromatin-remodeling ATPase INO80 / hINO80 / DNA helicase-related INO80 complex homolog 1 / DNA helicase-related protein INO80 / INO80 complex subunit A


Mass: 146390.703 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: INO80, INO80A, INOC1, KIAA1259 / Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): Sf9 / References: UniProt: Q9ULG1, EC: 3.6.4.-
#4: Protein/peptide Actin-related protein 5 / hARP5 / Sarcoma antigen NY-SAR-16


Mass: 68372.336 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: ACTR5, ARP5 / Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): Sf9 / References: UniProt: Q9H9F9
#5: Protein/peptide Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15437.167 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#6: Protein/peptide Histone H4 /


Mass: 11394.426 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
#7: Protein/peptide Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14165.551 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#8: Protein/peptide Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 13935.239 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899
#9: Protein/peptide INO80 complex subunit B / High mobility group AT-hook 1-like 4 / IES2 homolog / hIes2 / PAP-1-associated protein 1 / PAPA-1 / Zinc finger HIT domain-containing protein 4


Mass: 38704.172 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: INO80B, HMGA1L4, PAPA1, ZNHIT4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9C086

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DNA chain , 2 types, 2 molecules XY

#10: DNA chain DNA (150-MER)


Mass: 70604.938 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)
#11: DNA chain DNA (150-MER)


Mass: 70199.641 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 7 molecules

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


Mass: 427.201 Da / Num. of mol.: 6 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#13: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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
1Complex of core human INO80 with nucleosomeCOMPLEX1,2,3,4,5,6,7,8,9,10,110MULTIPLE SOURCES
2nucleosomeCOMPLEX1,2,3,4,51RECOMBINANT
4human INO80COMPLEX9,10,111RECOMBINANT
3Histone subunitsCOMPLEX6,7,81RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129606Homo sapiens (human)
239606Homo sapiens (human)
319606Homo sapiens (human)
4432630synthetic construct (others)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
1432630synthetic construct (others)
227108Spodoptera frugiperda (fall armyworm)
33562Escherichia coli (E. coli)
Buffer solutionpH: 8
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
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 / Cs: 2.7 mm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameCategory
4GctfCTF correction
10cryoSPARCinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 58145 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00439901
ELECTRON MICROSCOPYf_angle_d0.53355316
ELECTRON MICROSCOPYf_dihedral_angle_d17.02223216
ELECTRON MICROSCOPYf_chiral_restr0.0376487
ELECTRON MICROSCOPYf_plane_restr0.0036100

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