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- EMDB-17027: CryoEM Structure INO80core Hexasome complex ATPase-hexasome refin... -

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Basic information

Entry
Database: EMDB / ID: EMD-17027
TitleCryoEM Structure INO80core Hexasome complex ATPase-hexasome refinement state 2
Map datactINO80 hexasome complex focused cryoEM map ATPase hexasome sharpened map
Sample
  • Complex: INO80 core module in complex with hexasome
    • Complex: INO80
      • Protein or peptide: Chromatin-remodeling ATPase Ino80
    • Complex: Histones
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: DNA
      • DNA: DNA strand 1
      • DNA: DNA Strand 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: TETRAFLUOROALUMINATE ION
KeywordsATP-dependent chromatin remodeler / DNA BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / antibacterial humoral response / UCH proteinases / nucleosome / heterochromatin formation / E3 ubiquitin ligases ubiquitinate target proteins / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / cytosol
Similarity search - Function
: / 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 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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.1 / Histone H2A type 1-C
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus) / Homo sapiens (human) / Synthetic construct (others) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsZhang M / Jungblut A / Hoffmann T / Eustermann S
Funding support Germany, European Union, 4 items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND847543 Germany
European Research Council (ERC)833613European Union
German Research Foundation (DFG)CRC136 Germany
German Research Foundation (DFG)CRC1064 Germany
CitationJournal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: Features and development of Coot.
Authors: P Emsley / B Lohkamp / W G Scott / K Cowtan /
Abstract: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations ...Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.
History
DepositionApr 5, 2023-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17027.png

Downloads & links

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Map

FileDownload / File: emd_17027.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationctINO80 hexasome complex focused cryoEM map ATPase hexasome sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 295.92 Å		0.82 Å/pix.
x 360 pix.
= 295.92 Å		0.82 Å/pix.
x 360 pix.
= 295.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.8057776 - 1.5419748
Average (Standard dev.)0.0015957278 (±0.02628243)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: ctINO80 hexasome complex focused cryoEM map ATPase hexasome...

Fileemd_17027_additional_1.map
AnnotationctINO80 hexasome complex focused cryoEM map ATPase hexasome unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ctINO80 hexasome complex focused cryoEM map ATPase hexasome half map

Fileemd_17027_half_map_1.map
AnnotationctINO80 hexasome complex focused cryoEM map ATPase hexasome half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ctINO80 hexasome complex focused cryoEM map ATPase hexasome half map

Fileemd_17027_half_map_2.map
AnnotationctINO80 hexasome complex focused cryoEM map ATPase hexasome half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : INO80 core module in complex with hexasome

EntireName: INO80 core module in complex with hexasome
Components
  • Complex: INO80 core module in complex with hexasome
    • Complex: INO80
      • Protein or peptide: Chromatin-remodeling ATPase Ino80
    • Complex: Histones
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: DNA
      • DNA: DNA strand 1
      • DNA: DNA Strand 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: TETRAFLUOROALUMINATE ION

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Supramolecule #1: INO80 core module in complex with hexasome

SupramoleculeName: INO80 core module in complex with hexasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: 11-subunit ct INO80 contains two modules (core and Arp8 module) Each module was picked and analyzed separately The core module + hexasome has an overall weight of 0.861MDa The 11-subunit ct ...Details: 11-subunit ct INO80 contains two modules (core and Arp8 module) Each module was picked and analyzed separately The core module + hexasome has an overall weight of 0.861MDa The 11-subunit ct INO80 + hexasome has an overall weight of 1.1MDa Ino80, Ies2, Ies6, Ies4,Arp6, Rvb1, Rvb2, Arp8, Arp4, Actin, Taf14 Hexasome DNA, 2xH3, 2xH4, H2A, H2B
Molecular weightTheoretical: 861 KDa

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Supramolecule #2: INO80

SupramoleculeName: INO80 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Thermochaetoides thermophila (fungus)

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Supramolecule #3: Histones

SupramoleculeName: Histones / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Synthetic construct (others)

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Macromolecule #1: Chromatin-remodeling ATPase Ino80

MacromoleculeName: Chromatin-remodeling ATPase Ino80 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 130.887656 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: LELKFQSKGY NQIYDQIWRD LARKDVSKVF RLATDSYATK ASNLKKTAIL ASKEAKRWQL RTNKGTKDLQ ARAKRVMRDM MGFWKRNER EERDLRKAAE RLELENARKE EADREAARQR RKLNFLISQT ELYSHFISKK IKTHEVERST DHPDVATDEK D KIPEPTLN ...String:
LELKFQSKGY NQIYDQIWRD LARKDVSKVF RLATDSYATK ASNLKKTAIL ASKEAKRWQL RTNKGTKDLQ ARAKRVMRDM MGFWKRNER EERDLRKAAE RLELENARKE EADREAARQR RKLNFLISQT ELYSHFISKK IKTHEVERST DHPDVATDEK D KIPEPTLN INVPEPTGPI APKVTDFNSL DFDNEDESAL QAAAMANAQN AIAEAQKKAR EFNKDETKLD EDGEMNFQHP EL TEFEVAQ PKLLNCQLKE YQLKGLNWLV NLYEQGINGI LADEMGLGKT VQSISVMAYL AERYDIWGPF LVVAPASTLH NWQ QEVSKF VPDFKVLPYW GTAADRKVLR KFWDRKHTTY KKDSPFHVMI TSYQLVVSDV AYFQKMKWQY MILDEAQAIK SSQS SRWKC LLGFHCRNRL LLTGTPIQNN MQELWALLHF IMPSLFDSHD EFSEWFSKDI ESHAQSNTKL NEDQLKRLHM ILKPF MLRR VKKHVQKELG DKIEIDVFCE LSYRQRAMYQ SLRNQISIMD LIEKATVGDN EDSATLMNLV MQFRKVCNHP DLFERA DTS SPFFCGHFAE TGSFLREGTN VALGYSTRSL VEYRLPRLIW CDGGRLDKPG PGNLVAGFRS KYLNHMMNIW TPENIRS SL EGIENFTWLR FVDTSLQEAY RASHTDVFAR AVDLASKQNR LGHMQIVYDE PEDKKWTPVH ALFQICEREN PKAVAEIT T EGVLRDLMNI ARVKYRELGL CRLEKAARPR ASAPPIEVVC DSRSAVIERE NIMFHPAMRK ALFGPTPSEI KEASFGPRP VTLYPPRALL PAPDHDKQRF TNITVPSMAR FVTDSGKLAK LDELLRELKE GGHRVLLYFQ MTRMIDLMEE YLTYRNYKYC RLDGSTKLE DRRDTVADFQ TRPEIFIFLL STRAGGLGIN LTTADTVIFY DSDWNPTIDS QAMDRAHRLG QTKQVTVYRL I TRGTIEER IRKRALQKEE VQRVVITGTG SVDFSGRRPP ENRNRDIAMW LADDEQAEMI ERREKELIES GEYDKIMQQR RK GGKRKRG AANGDTVPSL EDMYHEGEGH FDDNKGSGAA TPVDADSLGR GGKRKKAGGS KKAKTTKQRL AIADGEIDID YKD DDDKGT DYKDDDDK

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Macromolecule #4: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.305969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEACEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.1

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Macromolecule #5: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #6: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.004329 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKA RAKAKSRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 1-C

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Macromolecule #7: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.806018 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

UniProtKB: Histone H2B type 1-C/E/F/G/I

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Macromolecule #2: DNA strand 1

MacromoleculeName: DNA strand 1 / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 69.527195 KDa
SequenceString: (DC)(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) ...String:
(DC)(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)(DC)(DT)(DC) (DC)(DC)(DA)(DC)(DT)(DC)(DT)(DA)(DG)(DA) (DG)(DG)(DA)(DT)(DC)(DC)(DC)(DC)(DG)(DG) (DG)(DT)(DA)(DC)(DC)(DG)

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Macromolecule #3: DNA Strand 2

MacromoleculeName: DNA Strand 2 / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 70.043562 KDa
SequenceString: (DC)(DG)(DG)(DT)(DA)(DC)(DC)(DC)(DG)(DG) (DG)(DG)(DA)(DT)(DC)(DC)(DT)(DC)(DT)(DA) (DG)(DA)(DG)(DT)(DG)(DG)(DG)(DA)(DG) (DC)(DT)(DC)(DG)(DG)(DA)(DA)(DC)(DA)(DC) (DT) (DA)(DT)(DC)(DC)(DG)(DA) ...String:
(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DC)(DG)(DG) (DG)(DG)(DA)(DT)(DC)(DC)(DT)(DC)(DT)(DA) (DG)(DA)(DG)(DT)(DG)(DG)(DG)(DA)(DG) (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)(DG)

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Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: TETRAFLUOROALUMINATE ION

MacromoleculeName: TETRAFLUOROALUMINATE ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: ALF
Molecular weightTheoretical: 102.975 Da
Chemical component information

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.88 mg/mL
BufferpH: 7.5
Details: 30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 15 sec. / Details: Oxygen 10% Argon 90%
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807).
Details11-subunit ctINO80 reconstituted with hexasome

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 15384 / Average electron dose: 50.36 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2137460
Details: Particles were initially picked by WARP to generate an initial model, which was subsequently used for the 3D template picking
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 98967
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Details: de novo 3D model was generated by using gradient-driven algorithm implemented in RELION 4.0
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6fml

source_name: PDB, initial_model_type: experimental model

3i62

source_name: PDB, initial_model_type: experimental model

8av6

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: OTHER
Output model

PDB-8oos:
CryoEM Structure INO80core Hexasome complex ATPase-hexasome refinement state 2

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  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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