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Open data
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Basic information
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Title | Dynactin pointed end bound to JIP3 | ||||||||||||
![]() | 3D map after focussed 3D refinement of pointed end | ||||||||||||
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![]() | Dynein / AAA-Atpase / p150 / LIS1 / MOTOR PROTEIN | ||||||||||||
Function / homology | ![]() retrograde axonal transport of mitochondrion / dynactin complex / anterograde axonal protein transport / MAP-kinase scaffold activity / Neutrophil degranulation / JUN kinase binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / axon regeneration ...retrograde axonal transport of mitochondrion / dynactin complex / anterograde axonal protein transport / MAP-kinase scaffold activity / Neutrophil degranulation / JUN kinase binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / axon regeneration / dynein complex binding / axon development / kinesin binding / regulation of JNK cascade / stress fiber / vesicle-mediated transport / axon cytoplasm / sarcomere / mitotic spindle organization / positive regulation of JNK cascade / kinetochore / signaling receptor complex adaptor activity / cell cortex / cell body / growth cone / cytoplasmic vesicle / protein stabilization / axon / Golgi membrane / centrosome / dendrite / negative regulation of apoptotic process / perinuclear region of cytoplasm / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
![]() | Singh K / Lau CK / Manigrasso G / Gassmann R / Carter AP | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanism of dynein-dynactin complex assembly by LIS1. Authors: Kashish Singh / Clinton K Lau / Giulia Manigrasso / José B Gama / Reto Gassmann / Andrew P Carter / ![]() ![]() Abstract: Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil ...Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil adaptor. However, how dynein and dynactin recognize diverse adaptors, how they interact with each other during complex formation, and the role of critical regulators such as lissencephaly-1 (LIS1) protein (LIS1) remain unclear. In this study, we determined the cryo-electron microscopy structure of dynein-dynactin on microtubules with LIS1 and the lysosomal adaptor JIP3. This structure reveals the molecular basis of interactions occurring during dynein activation. We show how JIP3 activates dynein despite its atypical architecture. Unexpectedly, LIS1 binds dynactin's p150 subunit, tethering it along the length of dynein. Our data suggest that LIS1 and p150 constrain dynein-dynactin to ensure efficient complex formation. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 335.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 28.2 KB 28.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.3 KB | Display | ![]() |
Images | ![]() | 69.6 KB | ||
Masks | ![]() | 371.3 MB | ![]() | |
Filedesc metadata | ![]() | 7.4 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() | 296.4 MB 336.3 MB 298.3 MB 298.3 MB 298.2 MB 298.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 994.2 KB | Display | ![]() |
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Full document | ![]() | 993.7 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pr4MC ![]() 8pqvC ![]() 8pqwC ![]() 8pqyC ![]() 8pqzC ![]() 8pr0C ![]() 8pr1C ![]() 8pr2C ![]() 8pr3C ![]() 8pr5C ![]() 8ptkC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | 3D map after focussed 3D refinement of pointed end | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: #1
File | emd_17834_additional_1.map | ||||||||||||
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Density Histograms |
-Additional map: 3D map prior to focussed 3D refinement of pointed end
File | emd_17834_additional_2.map | ||||||||||||
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Annotation | 3D map prior to focussed 3D refinement of pointed end | ||||||||||||
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Density Histograms |
-Additional map: half map 1 of 3D map prior to focussed 3D refinement of pointed end
File | emd_17834_additional_3.map | ||||||||||||
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Annotation | half map 1 of 3D map prior to focussed 3D refinement of pointed end | ||||||||||||
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Density Histograms |
-Additional map: half map 2 of 3D map prior to focussed 3D refinement of pointed end
File | emd_17834_additional_4.map | ||||||||||||
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Annotation | half map 2 of 3D map prior to focussed 3D refinement of pointed end | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17834_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17834_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Dynactin pointed end bound to JIP3
Entire | Name: Dynactin pointed end bound to JIP3 |
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Components |
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-Supramolecule #1: Dynactin pointed end bound to JIP3
Supramolecule | Name: Dynactin pointed end bound to JIP3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Arp11
Macromolecule | Name: Arp11 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 46.250785 KDa |
Sequence | String: MPLYEGLGSG GEKTAVVIDL GEAFTKCGFA GETGPRCIIP SVIKKAGMPK PIKVVQYNIN TEELYSYLKE FIHILYFRHL LVNPRDRRV VVIESVLCPS HFRETLTRVL FKYFEVPSVL LAPSHLMALL TLGINSAMVL DCGYRESLVL PIYEGIPVLN C WGALPLGG ...String: MPLYEGLGSG GEKTAVVIDL GEAFTKCGFA GETGPRCIIP SVIKKAGMPK PIKVVQYNIN TEELYSYLKE FIHILYFRHL LVNPRDRRV VVIESVLCPS HFRETLTRVL FKYFEVPSVL LAPSHLMALL TLGINSAMVL DCGYRESLVL PIYEGIPVLN C WGALPLGG KALHKELETQ LLEQCTVDTG AAKEQSLPSV MGSIPEGVLE DIKVRTCFVS DLTRGLKIQA AKFNIDGNTE RP SPPPNVD YPLDGEKILH VLGSIRDSVV EILFEQDNEE KSVATLILDS LMQCPIDTRK QLAENLVIIG GTSMLPGFLH RLL AEIRYL VEKPKYKKTL GTKTFRIHTP PAKANCVAWL GGAIFGALQD ILGSRSVSKE YYNQTGRIPD WCSLNNPPLE MVFD VGKSQ PPLMKRAFST EK UniProtKB: Actin-related protein 10 |
-Macromolecule #2: Dynactin 6
Macromolecule | Name: Dynactin 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20.70391 KDa |
Sequence | String: MAEKTQKSVK IAPGAVVCVE SEIRGDVTIG PRTVIHPKAR IIAEAGPIVI GEGNLIEEQA LIINAHPDNI TPDAEDSEPK PMIIGTNNV FEVGCYSQAM KMGDNNVIES KAYVGRNVIL TSGCIIGACC NLNTFEVIPE NTVIYGADCL RRVQTERPQP Q TLQLDFLM KILPNYHHLK KTMKGSSTPV KN UniProtKB: Dynactin subunit 6 |
-Macromolecule #3: Dynactin subunit 5
Macromolecule | Name: Dynactin subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20.150533 KDa |
Sequence | String: MELGELLYNK SEYIETASGN KVSRQSVLCG SQNIVLNGKT IVMNDCIIRG DLANVRVGRH CVVKSRSVIR PPFKKFSKGV AFFPLHIGD HVFIEEDCVV NAAQIGSYVH VGKNCVIGRR CVLKDCCKIL DNTVLPPETV VPPFTVFSGC PGLFSGELPE C TQELMIDV TKSYYQKFLP LTQV UniProtKB: Dynactin subunit 5 |
-Macromolecule #4: Dynactin subunit 4
Macromolecule | Name: Dynactin subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 52.920434 KDa |
Sequence | String: MASLLQSERV LYLVQGEKKV RAPLSQLYFC RYCSELRSLE CVSHEVDSHY CPSCLENMPS AEAKLKKNRC ANCFDCPGCM HTLSTRATS ISTQLPDDPA KTAVKKAYYL ACGFCRWTSR DVGMADKSVA SGGWQEPDHP HTQRMNKLIE YYQQLAQKEK V ERDRKKLA ...String: MASLLQSERV LYLVQGEKKV RAPLSQLYFC RYCSELRSLE CVSHEVDSHY CPSCLENMPS AEAKLKKNRC ANCFDCPGCM HTLSTRATS ISTQLPDDPA KTAVKKAYYL ACGFCRWTSR DVGMADKSVA SGGWQEPDHP HTQRMNKLIE YYQQLAQKEK V ERDRKKLA RRRNYMPLAF SQHTIHVVDK YGLGTRLQRP RAGTTITALA GLSLKEGEDQ KEIKIEPAQA VDEVEPLPED YY TRPVNLT EVTTLQQRLL QPDFQPICAS QLYPRHKHLL IKRSLRCRQC EHNLSKPEFN PTSIKFKIQL VAVNYIPEVR IMS IPNLRY MKESQVLLTL TNPVENLTHV TLLECEEGDP DDTNSTAKVS VPPTELVLAG KDAAAEYDEL AEPQDFPDDP DVVA FRKAN KVGVFIKVTP QREEGDVTVC FKLKHDFKNL AAPIRPVEEA DPGAEVSWLT QHVELSLGPL LP UniProtKB: Dynactin subunit 4 |
-Macromolecule #5: C-Jun-amino-terminal kinase-interacting protein 3
Macromolecule | Name: C-Jun-amino-terminal kinase-interacting protein 3 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 65.975398 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SNIEFLKMME IQMDEGGGVV VYQDDYCSGS VMSERVSGLA GSIYREFERL IHCYDEEVVK ELMPLVVNVL ENLDSVLSEN QEHEVELEL LREDNEQLLT QYEREKALRR QAEEKFIEFE DALEQEKKEL QIQVEHYEFQ TRQLELKAKN YADQISRLEE R ESEMKKEY ...String: SNIEFLKMME IQMDEGGGVV VYQDDYCSGS VMSERVSGLA GSIYREFERL IHCYDEEVVK ELMPLVVNVL ENLDSVLSEN QEHEVELEL LREDNEQLLT QYEREKALRR QAEEKFIEFE DALEQEKKEL QIQVEHYEFQ TRQLELKAKN YADQISRLEE R ESEMKKEY NALHQRHTEM IQTYVEHIER SKMQQVGGNS QTESSLPGRR KERPTSLNVF PLADGTVRAQ IGGKLVPAGD HW HLSDLGQ LQSSSSYQCP QDEMSESGQS SAAATPSTTG TKSNTPTSSV PSAAVTPLNE SLQPLGDYGV GSKNSKRARE KRD SRNMEV QVTQEMRNVS IGMGSSDEWS DVQDIIDSTP ELDMCPETRL DRTGSSPTQG IVNKAFGINT DSLYHELSTA GSEV IGDVD EGADLLGEFS VRDDFFGMGK EVGNLLLENS QLLETKNALN VVKNDLIAKV DQLSGEQEVL RGELEAAKQA KVKLE NRIK ELEEELKRVK SEAIIARREP KEEAEDVSSY LCTESDKIPM AQRRRFTRVE MARVLMERNQ YKERLMELQE AVRWTE MIR ASREGSGSGR WSHPQFEK UniProtKB: C-Jun-amino-terminal kinase-interacting protein 3 |
-Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |