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Yorodumi- EMDB-4171: Dynein light intermediate chain region of the dynein tail/dynacti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4171 | |||||||||
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Title | Dynein light intermediate chain region of the dynein tail/dynactin/BICDR1 complex | |||||||||
Map data | Map of C terminal half of dynein tail in complex with dynactin and BICDR1, focussed on light intermediate chain. | |||||||||
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 / dynein heavy chain binding / 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 / dynein light intermediate chain binding ...positive regulation of intracellular transport / regulation of metaphase plate congression / dynein heavy chain binding / 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 / dynein light intermediate chain binding / cytoplasmic dynein complex / P-body assembly / nuclear migration / centrosome localization / dynein intermediate chain binding / microtubule-based movement / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / cytoplasmic microtubule organization / stress granule assembly / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of mitotic spindle organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / axon cytoplasm / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / AURKA Activation by TPX2 / mitotic spindle organization / cellular response to nerve growth factor stimulus / filopodium / RHO GTPases Activate Formins / HCMV Early Events / kinetochore / microtubule cytoskeleton organization / Aggrephagy / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / late endosome / 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 / identical protein 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_4171.map.gz | 287.1 MB | EMDB map data format | |
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Header (meta data) | emd-4171-v30.xml emd-4171.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_4171.png | 111.6 KB | ||
Filedesc metadata | emd-4171.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4171 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4171 | HTTPS FTP |
-Validation report
Summary document | emd_4171_validation.pdf.gz | 216.2 KB | Display | EMDB validaton report |
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Full document | emd_4171_full_validation.pdf.gz | 215.4 KB | Display | |
Data in XML | emd_4171_validation.xml.gz | 8.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4171 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4171 | HTTPS FTP |
-Related structure data
Related structure data | 6f1yMC 4168C 4169C 4170C 4172C 4177C 5owoC 6f1tC 6f1uC 6f1vC 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_4171.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 half of dynein tail in complex with dynactin and BICDR1, focussed on light intermediate chain. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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,Dynein heavy chain
Macromolecule | Name: Cytoplasmic dynein 1 heavy chain 1,Dynein heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 33.117113 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: SLIESVRTYE RTCEKVEERN TISLLVAGLK KEVQALIAEG IALVWESYKL DPYVQRLAET VFNFQEKVDD LLIIEEKIDL EVRSLETCM YDHKTFSEIL NRVQKAVDDL NLHSYSNLPI WVNKLDMEIE RILGVRLQAG LRAWTQVLL(UNK) (UNK) (UNK)(UNK)(UNK) ...String: SLIESVRTYE RTCEKVEERN TISLLVAGLK KEVQALIAEG IALVWESYKL DPYVQRLAET VFNFQEKVDD LLIIEEKIDL EVRSLETCM YDHKTFSEIL NRVQKAVDDL NLHSYSNLPI WVNKLDMEIE RILGVRLQAG LRAWTQVLL(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)LEESY SAVMGIVSEV EQYVKV (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) UniProtKB: Cytoplasmic dynein 1 heavy chain 1 |
-Macromolecule #2: Cytoplasmic dynein 1 light intermediate chain 2
Macromolecule | Name: Cytoplasmic dynein 1 light intermediate chain 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 38.502941 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: SSILSEVSTR ARSKLPSGKN ILVFGEDGSG KTTLMTKLQG AEHGKKGRGL EYLYLSVHDE DRDDHTRCNV WILDGDLYHK GLLKFAVSA ESLPETLVIF VADMSRPWTV MESLQKWASV LREHIDKMKI PPEKMRELER KFVKDFQDYM EPEEGCQGSP Q RRGPLTSG ...String: SSILSEVSTR ARSKLPSGKN ILVFGEDGSG KTTLMTKLQG AEHGKKGRGL EYLYLSVHDE DRDDHTRCNV WILDGDLYHK GLLKFAVSA ESLPETLVIF VADMSRPWTV MESLQKWASV LREHIDKMKI PPEKMRELER KFVKDFQDYM EPEEGCQGSP Q RRGPLTSG SDEENVALPL GDNVLTHNLG IPVLVVCTKC DAVSVLEKEH DYRDEHLDFI QSHLRRFCLQ YGAALIYTSV KE EKNLDLL YKYIVHKTYG FHFTTPALVV EKDAVFIPAG WDNEKKIAIL HENFTTVKPE DAYEDFIVKP PVRKLVHDKE LAA EDEQVF LMKQQSLLAK Q UniProtKB: Cytoplasmic dynein 1 light intermediate chain 2 |
-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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient |
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Output model | PDB-6f1y: |