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Yorodumi- EMDB-4170: C terminal region of the dynein heavy chains in the dynein tail/d... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4170 | |||||||||
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Title | C terminal region of the dynein heavy chains in the dynein tail/dynactin/BICDR1 complex | |||||||||
Map data | Map of C terminal of dynein tail domains, bound to BICDR and dynactin | |||||||||
Sample |
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Keywords | Cryo-EM / Complex / MOTOR PROTEIN | |||||||||
Function / homology | Function and homology information positive regulation of intracellular transport / regulation of metaphase plate congression / establishment of spindle localization / positive regulation of spindle assembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / retrograde axonal transport / cytoplasmic dynein complex / dynein light intermediate chain binding ...positive regulation of intracellular transport / regulation of metaphase plate congression / establishment of spindle localization / positive regulation of spindle assembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / retrograde axonal transport / cytoplasmic dynein complex / dynein light intermediate chain binding / P-body assembly / nuclear migration / dynein intermediate chain binding / cytoplasmic microtubule / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / stress granule assembly / Mitotic Prometaphase / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / EML4 and NUDC in mitotic spindle formation / Recruitment of mitotic centrosome proteins and complexes / axon cytoplasm / Recruitment of NuMA to mitotic centrosomes / regulation of mitotic spindle organization / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / HCMV Early Events / Aggrephagy / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / positive regulation of cold-induced thermogenesis / cell cortex / microtubule / cell division / centrosome / Neutrophil degranulation / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Urnavicius L / Lau CK | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nature / Year: 2018 Title: Cryo-EM shows how dynactin recruits two dyneins for faster movement. Authors: Linas Urnavicius / Clinton K Lau / Mohamed M Elshenawy / Edgar Morales-Rios / Carina Motz / Ahmet Yildiz / Andrew P Carter / Abstract: Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. ...Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. Here we use electron microscopy and single-molecule studies to show that adaptors can recruit a second dynein to dynactin. Whereas BICD2 is biased towards recruiting a single dynein, the adaptors BICDR1 and HOOK3 predominantly recruit two dyneins. We find that the shift towards a double dynein complex increases both the force and speed of the microtubule motor. Our 3.5 Å resolution cryo-electron microscopy reconstruction of a dynein tail-dynactin-BICDR1 complex reveals how dynactin can act as a scaffold to coordinate two dyneins side-by-side. Our work provides a structural basis for understanding how diverse adaptors recruit different numbers of dyneins and regulate the motile properties of the dynein-dynactin transport machine. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4170.map.gz | 287.5 MB | EMDB map data format | |
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Header (meta data) | emd-4170-v30.xml emd-4170.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | emd_4170.png | 135.5 KB | ||
Filedesc metadata | emd-4170.cif.gz | 6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4170 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4170 | HTTPS FTP |
-Validation report
Summary document | emd_4170_validation.pdf.gz | 189.9 KB | Display | EMDB validaton report |
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Full document | emd_4170_full_validation.pdf.gz | 189.5 KB | Display | |
Data in XML | emd_4170_validation.xml.gz | 502 B | Display | |
Data in CIF | emd_4170_validation.cif.gz | 371 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4170 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4170 | HTTPS FTP |
-Related structure data
Related structure data | 6f1vMC 4168C 4169C 4171C 4172C 4177C 5owoC 6f1tC 6f1uC 6f1yC 6f1zC 6f38C 6f3aC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4170.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of C terminal of dynein tail domains, bound to BICDR and dynactin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Two dynein tail domains bound to dynactin and BICDR1
Entire | Name: Two dynein tail domains bound to dynactin and BICDR1 |
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Components |
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-Supramolecule #1: Two dynein tail domains bound to dynactin and BICDR1
Supramolecule | Name: Two dynein tail domains bound to dynactin and BICDR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Cytoplasmic dynein 1 heavy chain 1
Macromolecule | Name: Cytoplasmic dynein 1 heavy chain 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 136.786094 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSEPGGGGGE DGSAGLEVSA VQNVADVSVL QKHLRKLVPL LLEDGGEAPA ALEAALEEKS ALEQMRKFLS DPQVHTVLVE RSTLKEDVG DEGEEEKEFI SYNINIDIHY GVKSNSLAFI KRTPVIDADK PVSSQLRVLT LSEDSPYETL HSFISNAVAP F FKSYIRES ...String: MSEPGGGGGE DGSAGLEVSA VQNVADVSVL QKHLRKLVPL LLEDGGEAPA ALEAALEEKS ALEQMRKFLS DPQVHTVLVE RSTLKEDVG DEGEEEKEFI SYNINIDIHY GVKSNSLAFI KRTPVIDADK PVSSQLRVLT LSEDSPYETL HSFISNAVAP F FKSYIRES GKADRDGDKM APSVEKKIAE LEMGLLHLQQ NIEIPEISLP IHPMITNVAK QCYERGEKPK VTDFGDKVED PT FLNQLQS GVNRWIREIQ KVTKLDRDPA SGTALQEISF WLNLERALYR IQEKRESPEV LLTLDILKHG KRFHATVSFD TDT GLKQAL ETVNDYNPLM KDFPLNDLLS ATELDKIRQA LVAIFTHLRK IRNTKYPIQR ALRLVEAISR DLSSQLLKVL GTRK LMHVA YEEFEKVMVA CFEVFQTWDD EYEKLQVLLR DIVKRKREEN LKMVWRINPA HRKLQARLDQ MRKFRRQHEQ LRAVI VRVL RPQVTAVAQQ NQGEVPEPQD MKVAEVLFDA ADANAIEEVN LAYENVKEVD GLDVSKEGTE AWEAAMKRYD ERIDRV ETR ITARLRDQLG TAKNANEMFR IFSRFNALFV RPHIRGAIRE YQTQLIQRVK DDIESLHDKF KVQYPQSQAC KMSHVRD LP PVSGSIIWAK QIDRQLTAYM KRVEDVLGKG WENHVEGQKL KQDGDSFRMK LNTQEIFDDW ARKVQQRNLG VSGRIFTI E STRVRGRTGN VLKLKVNFLP EIITLSKEVR NLKWLGFRVP LAIVNKAHQA NQLYPFAISL IESVRTYERT CEKVEERNT ISLLVAGLKK EVQALIAEGI ALVWESYKLD PYVQRLAETV FNFQEKVDDL LIIEEKIDLE VRSLETCMYD HKTFSEILNR VQKAVDDLN LHSYSNLPIW VNKLDMEIER ILGVRLQAGL RAWTQVLLGQ AEDKAEVDMD TDAPQVSHKP GGEPKIKNVV H ELRITNQV IYLNPPIEEC RYKLYQEMFA WKMVVLSLPR IQSQRYQVGV HYELTEEEKF YRNALTRMPD GPVALEESYS AV MGIVSEV EQYVKVWLQY QCLWDMQAEN IYNRLGEDLN KWQALLVQIR KARGTFDNAE TKKEFGPVVI DYGKVQSKVN LKY DSWHKE VLSKFGQMLG SNMTEFHSQI SKSRQELEQH SVDTASTSDA VTFITYVQSL KRKIKQFEKQ UniProtKB: Cytoplasmic dynein 1 heavy chain 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: Details: Initial model low pass filtered to 50 A |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 86030 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION Details: Particle signal subtraction used to remove regions outside of the C terminus of the dynein tails before final 3D classification and refinement |
-Atomic model buiding 1
Refinement | Space: REAL / Target criteria: Cross-correlation coefficient |
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Output model | PDB-6f1v: |