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Yorodumi- EMDB-17012: CryoEM Structure INO80core Hexasome complex Arp5 Ies6 refinement ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17012 | |||||||||||||||
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Title | CryoEM Structure INO80core Hexasome complex Arp5 Ies6 refinement state1 | |||||||||||||||
Map data | ctINO80-hexasome complex Arp5 Ies6 focused refinement sharpened map | |||||||||||||||
Sample |
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Keywords | ATP-dependent chromatin remodeler / DNA BINDING PROTEIN | |||||||||||||||
Function / homology | Function and homology information DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / attachment of spindle microtubules to kinetochore / Ino80 complex / attachment of mitotic spindle microtubules to kinetochore / mitotic spindle / kinetochore / chromatin remodeling / regulation of DNA-templated transcription / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Thermochaetoides thermophila (fungus) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||
Authors | Zhang M / Jungblut A / Hoffmann T / Eustermann S | |||||||||||||||
Funding support | Germany, European Union, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17012.map.gz | 8.8 MB | EMDB map data format | |
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Header (meta data) | emd-17012-v30.xml emd-17012.xml | 25.9 KB 25.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17012_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_17012.png | 71.2 KB | ||
Filedesc metadata | emd-17012.cif.gz | 7.7 KB | ||
Others | emd_17012_additional_1.map.gz emd_17012_half_map_1.map.gz emd_17012_half_map_2.map.gz | 140.3 MB 140.8 MB 140.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17012 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17012 | HTTPS FTP |
-Validation report
Summary document | emd_17012_validation.pdf.gz | 750.4 KB | Display | EMDB validaton report |
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Full document | emd_17012_full_validation.pdf.gz | 750 KB | Display | |
Data in XML | emd_17012_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | emd_17012_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17012 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17012 | HTTPS FTP |
-Related structure data
Related structure data | 8oofMC 8oo7C 8oo9C 8ooaC 8oocC 8ookC 8oopC 8oorC 8oosC 8ootC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17012.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | ctINO80-hexasome complex Arp5 Ies6 focused refinement sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: ctINO80-hexasome complex Arp5 Ies6 focused refinement unsharpened map
File | emd_17012_additional_1.map | ||||||||||||
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Annotation | ctINO80-hexasome complex Arp5 Ies6 focused refinement unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: ctINO80-hexasome complex Arp5 Ies6 focused refinement half map 1
File | emd_17012_half_map_1.map | ||||||||||||
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Annotation | ctINO80-hexasome complex Arp5 Ies6 focused refinement half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: ctINO80-hexasome complex Arp5 Ies6 focused refinement half map 2
File | emd_17012_half_map_2.map | ||||||||||||
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Annotation | ctINO80-hexasome complex Arp5 Ies6 focused refinement half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : INO80 core module in complex with hexasome
Entire | Name: INO80 core module in complex with hexasome |
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Components |
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-Supramolecule #1: INO80 core module in complex with hexasome
Supramolecule | Name: INO80 core module in complex with hexasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 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 |
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Source (natural) | Organism: Thermochaetoides thermophila (fungus) |
Molecular weight | Theoretical: 861 KDa |
-Macromolecule #1: Chromatin-remodeling complex subunit IES6
Macromolecule | Name: Chromatin-remodeling complex subunit IES6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermochaetoides thermophila (fungus) |
Molecular weight | Theoretical: 23.127523 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MSNPDAQSAQ AAHQALVEQL DLHSIHKTFR NPNWRPNQRR NKTIKAILGE SQRKEASSTS AVATPRADDN GGGSGADTPA NNDNNDGLS TSGTSTPANG NGSGAGTPAS NGQPNLAQAS RSLQKLVLEK SLASAQAPDK KAANGFASSA PTATYTNIES A PSLAPMKH ...String: MSNPDAQSAQ AAHQALVEQL DLHSIHKTFR NPNWRPNQRR NKTIKAILGE SQRKEASSTS AVATPRADDN GGGSGADTPA NNDNNDGLS TSGTSTPANG NGSGAGTPAS NGQPNLAQAS RSLQKLVLEK SLASAQAPDK KAANGFASSA PTATYTNIES A PSLAPMKH YCDVTGLPAP YLDPKTRLRY HNKEIFAMIR NLPQGMGEQF LEARGAHTVL K UniProtKB: Vps72/YL1 C-terminal domain-containing protein |
-Macromolecule #2: Actin-related protein 5
Macromolecule | Name: Actin-related protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermochaetoides thermophila (fungus) |
Molecular weight | Theoretical: 87.773086 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MAPSAVAEPP PIPQRDEPWK RLPPPTVYPV KEARFEKYIP PQLDGRERAL AQPPGQVAIV IDNGSHSVRA GWNFEDKPRL AIPPIMSKY RDRKMGKTFS FAGSDCYADT TARSHIRNAF EAGTGIVSNW DVMEHVLDYV FVKLGMNECD GAIDMPIVMT E AVANLPYS ...String: MAPSAVAEPP PIPQRDEPWK RLPPPTVYPV KEARFEKYIP PQLDGRERAL AQPPGQVAIV IDNGSHSVRA GWNFEDKPRL AIPPIMSKY RDRKMGKTFS FAGSDCYADT TARSHIRNAF EAGTGIVSNW DVMEHVLDYV FVKLGMNECD GAIDMPIVMT E AVANLPYS RKSMSEIIFE CYGAPSLVYG IDSLFSFRHN QGQTGLVVSS SYSATHVIPV YNRKALLSQA IRLNWGGWHM AE YMLKLLK LKYYTGFPGK LNSSQTEHMV RDFCYVSLDY DRELAGYLDW TGLEDRERIV QYPYTEEVVV QKTEEELARI AER KKESGR RLQEQAAKMR LERLMKKEQE LEYYKDIQRR MQGESKKEIK RLLDEAELKD EAALERVIRD LERSIKRARQ KDLG EPEEE EVPDFSLLDV PDDQLDEAGL RQKRQQRLLK SNWEARQRAK AEKEAEKARL AEEARLDEER RKNDLEGWLE EKRQL RLAK LNQLKERERL KADLGNRKSL ASQIRMKNIA NLASDNPTGS GSRKRRRGGA GADQDDDFGA DDADWGVYRS VAIGAN KGD DSDDEEGEED LEAAIRSLEN DLLRYDKTFS YDMTLDAQRD WSKSLLHAFR YGPRPFDPSS QAETHRVHLN VERIRVP EV LFQPAAIAGV DQAGLVEIAG DILCQRLPSL PGIQDAPDAF LRDVFLTGGN TLFQNFDERL RQGLMALLPV GAPLRVRR A QDAILDAWRG AAGWACTEEA KAAWITREEY LEKGGEYIKE HDLGNAFA UniProtKB: Uncharacterized protein |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.88 mg/mL |
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Buffer | pH: 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 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 15 sec. / Details: 10% oxygene 90% argon |
Vitrification | Cryogen 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). |
Details | 11-subunit ctINO80 reconstituted with hexasome |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 15384 / Average electron dose: 50.36 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |