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- PDB-9dgt: structure of dynactin, dynein tail with one BICDR from dynein-dyn... -

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Basic information

Entry
Database: PDB / ID: 9dgt
Titlestructure of dynactin, dynein tail with one BICDR from dynein-dynactin-BICDR on microtubules
Components
  • (Cytoplasmic dynein 1 ...) x 2
  • (Dynactin subunit ...) x 6
  • (F-actin-capping protein subunit ...) x 2
  • Actin, cytoplasmic 1
  • Actin-related protein 10
  • Alpha-centractin
  • BICD family-like cargo adapter 1
  • Dynein light intermediate chain
KeywordsMOTOR PROTEIN / dynein / dynactin / microtubule
Function / homology
Function and homology information


Golgi to secretory granule transport / : / Factors involved in megakaryocyte development and platelet production / retrograde axonal transport of mitochondrion / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs ...Golgi to secretory granule transport / : / Factors involved in megakaryocyte development and platelet production / retrograde axonal transport of mitochondrion / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / Formation of the canonical BAF (cBAF) complex / Formation of the polybromo-BAF (pBAF) complex / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / UCH proteinases / Gap junction degradation / Formation of annular gap junctions / RHOF GTPase cycle / Clathrin-mediated endocytosis / Regulation of CDH1 Function / Formation of the dystrophin-glycoprotein complex (DGC) / dynactin complex / centriolar subdistal appendage / positive regulation of neuromuscular junction development / centriole-centriole cohesion / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of mitotic centrosome proteins and complexes / microtubule anchoring at centrosome / nuclear membrane disassembly / F-actin capping protein complex / WASH complex / ventral spinal cord development / cytoskeleton-dependent cytokinesis / retromer complex / microtubule plus-end / dynein complex / cellular response to cytochalasin B / positive regulation of microtubule nucleation / regulation of transepithelial transport / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / melanosome transport / protein localization to adherens junction / barbed-end actin filament capping / dense body / Tat protein binding / Neutrophil degranulation / coronary vasculature development / postsynaptic actin cytoskeleton / non-motile cilium assembly / regulation of cell morphogenesis / vesicle transport along microtubule / adherens junction assembly / retrograde transport, endosome to Golgi / apical protein localization / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / minus-end-directed microtubule motor activity / Recruitment of NuMA to mitotic centrosomes / microtubule associated complex / centrosome localization / tight junction / cytoplasmic dynein complex / dynein light intermediate chain binding / COPI-mediated anterograde transport / ventricular septum development / aorta development / microtubule-based movement / nuclear migration / apical junction complex / neuromuscular process / regulation of norepinephrine uptake / transporter regulator activity / establishment of mitotic spindle orientation / neuromuscular junction development / NuA4 histone acetyltransferase complex / dynein intermediate chain binding / motor behavior / establishment or maintenance of cell polarity / cell leading edge / cortical cytoskeleton / cleavage furrow / dynein complex binding / microtubule organizing center / nitric-oxide synthase binding / dynactin binding / brush border / regulation of synaptic vesicle endocytosis / kinesin binding / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / intercellular bridge / stress fiber
Similarity search - Function
: / Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / Dynamitin / : / Dynamitin / Dynactin subunit 6 / Dynein associated protein ...: / Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / Dynamitin / : / Dynamitin / Dynactin subunit 6 / Dynein associated protein / Dynein associated protein / Dynein 1 light intermediate chain / Dynactin subunit 5 / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / : / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / : / Dynein heavy chain, ATPase lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Trimeric LpxA-like superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / Dynactin subunit 1 / Cytoplasmic dynein 1 heavy chain 1 / Dynactin subunit 4 / Cytoplasmic dynein 1 intermediate chain 2 / Dynactin subunit 2 / Dynein light intermediate chain / Actin related protein 1A ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / Dynactin subunit 1 / Cytoplasmic dynein 1 heavy chain 1 / Dynactin subunit 4 / Cytoplasmic dynein 1 intermediate chain 2 / Dynactin subunit 2 / Dynein light intermediate chain / Actin related protein 1A / BICD family-like cargo adapter 1 / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Dynactin subunit 6 / Dynactin subunit 3 / Actin-related protein 10 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsRao, Q. / Chai, P. / Zhang, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM142959 United States
CitationJournal: bioRxiv / Year: 2024
Title: Molecular basis for the assembly of the dynein transport machinery on microtubules.
Authors: Qinhui Rao / Pengxin Chai / Kai Zhang /
Abstract: Cytoplasmic dynein-1, a microtubule-based motor protein, requires dynactin and an adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The role of microtubules in DDA assembly has ...Cytoplasmic dynein-1, a microtubule-based motor protein, requires dynactin and an adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The role of microtubules in DDA assembly has been elusive. Here, we reveal detailed structural insights into microtubule-mediated DDA assembly using cryo-electron microscopy. We find that an adaptor-independent dynein-dynactin complex (DD) predominantly forms on microtubules in an intrinsic 2:1 stoichiometry, induced by spontaneous parallelization of dynein upon microtubule binding. Adaptors can squeeze in and exchange within the assembled microtubule-bound DD complex, which is enabled by relative rotations between dynein and dynactin, and further facilitated by dynein light intermediate chains that assist in an adaptor 'search' mechanism. Our findings elucidate the dynamic adaptability of the dynein transport machinery, and reveal a new mode for assembly of the motile complex.
History
DepositionSep 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-centractin
B: Alpha-centractin
C: Alpha-centractin
D: Alpha-centractin
E: Alpha-centractin
F: Alpha-centractin
G: Alpha-centractin
H: Actin, cytoplasmic 1
I: Alpha-centractin
J: Actin-related protein 10
K: F-actin-capping protein subunit alpha-1
L: F-actin-capping protein subunit beta
M: Dynactin subunit 2
N: Dynactin subunit 2
O: Dynactin subunit 3
P: Dynactin subunit 2
Q: Dynactin subunit 2
R: Dynactin subunit 3
U: Dynactin subunit 6
V: Dynactin subunit 5
W: Dynactin subunit 1
Y: Dynactin subunit 4
Z: Dynactin subunit 1
c: BICD family-like cargo adapter 1
d: BICD family-like cargo adapter 1
e: Cytoplasmic dynein 1 heavy chain 1
f: Cytoplasmic dynein 1 heavy chain 1
g: Cytoplasmic dynein 1 intermediate chain 2
h: Cytoplasmic dynein 1 intermediate chain 2
j: Dynein light intermediate chain
m: Cytoplasmic dynein 1 heavy chain 1
n: Cytoplasmic dynein 1 heavy chain 1
o: Cytoplasmic dynein 1 intermediate chain 2
p: Cytoplasmic dynein 1 intermediate chain 2
q: Dynein light intermediate chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,741,12148
Polymers3,736,57335
Non-polymers4,54813
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 14 molecules ABCDEFGIHJcdjq

#1: Protein
Alpha-centractin


Mass: 42670.688 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1PMN0
#2: Protein Actin, cytoplasmic 1


Mass: 41782.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QAQ1
#3: Protein Actin-related protein 10


Mass: 46250.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LHK5
#12: Protein BICD family-like cargo adapter 1 / Bicaudal D-related protein 1 / BICD-related protein 1 / BICDR-1 / Coiled-coil domain-containing protein 64A


Mass: 65377.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bicdl1, Bicdr1, Ccdc64 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0JNT9
#15: Protein Dynein light intermediate chain


Mass: 54227.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0X6Z5

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F-actin-capping protein subunit ... , 2 types, 2 molecules KL

#4: Protein F-actin-capping protein subunit alpha-1


Mass: 33059.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0PFK5
#5: Protein F-actin-capping protein subunit beta / CapZ beta


Mass: 30669.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0PFK7

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Dynactin subunit ... , 6 types, 11 molecules MNPQORUVWZY

#6: Protein
Dynactin subunit 2


Mass: 44704.414 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2QD80
#7: Protein Dynactin subunit 3


Mass: 21192.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SEC0
#8: Protein Dynactin subunit 6


Mass: 20703.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: D0G6S1
#9: Protein Dynactin subunit 5


Mass: 20150.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZK88
#10: Protein Dynactin subunit 1 / 150 kDa dynein-associated polypeptide / p150-glued


Mass: 142015.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287B8J2
#11: Protein Dynactin subunit 4 / Dyn4


Mass: 52920.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TB62

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Cytoplasmic dynein 1 ... , 2 types, 8 molecules efmnghop

#13: Protein
Cytoplasmic dynein 1 heavy chain 1


Mass: 532739.562 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480I0V8
#14: Protein
Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein intermediate chain 2 / Dynein intermediate chain 2 / cytosolic


Mass: 68567.219 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VH50

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Non-polymers , 3 types, 13 molecules

#16: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#17: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#18: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dynactin, dynein tail with one BICDR of dynein-dynactin-BICDR complex on microtubules
Type: COMPLEX / Entity ID: #1-#15 / Source: MULTIPLE SOURCES
Molecular weightValue: 5 MDa / Experimental value: NO
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 3000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10750 / Symmetry type: POINT

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