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- PDB-9dgv: structure of dynactin, dynein tail with TRAK2 from dynein-dynacti... -

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Basic information

Entry
Database: PDB / ID: 9dgv
Titlestructure of dynactin, dynein tail with TRAK2 from dynein-dynactin-TRAK2 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
  • Trafficking protein, kinesin binding 2
KeywordsMOTOR PROTEIN / dynein / TRAK2 / dynactin / microtubule
Function / homology
Function and homology information


RHOT1 GTPase cycle / RHOT2 GTPase cycle / dendritic transport of mitochondrion / mitochondrion distribution / : / 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 ...RHOT1 GTPase cycle / RHOT2 GTPase cycle / dendritic transport of mitochondrion / mitochondrion distribution / : / 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 / UCH proteinases / Gap junction degradation / Formation of annular gap junctions / RHOF GTPase cycle / Clathrin-mediated endocytosis / 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 / F-actin capping protein complex / WASH complex / Recruitment of mitotic centrosome proteins and complexes / microtubule anchoring at centrosome / negative regulation of axonogenesis / ventral spinal cord development / retromer complex / cytoskeleton-dependent cytokinesis / microtubule plus-end / cellular response to cytochalasin B / nuclear membrane disassembly / positive regulation of microtubule nucleation / regulation of transepithelial transport / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / GABA receptor binding / protein localization to adherens junction / barbed-end actin filament capping / melanosome transport / protein O-linked glycosylation / dense body / Tat protein binding / postsynaptic actin cytoskeleton / coronary vasculature development / Neutrophil degranulation / non-motile cilium assembly / vesicle transport along microtubule / regulation of cell morphogenesis / dynein complex / 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 / Recruitment of NuMA to mitotic centrosomes / tight junction / microtubule associated complex / minus-end-directed microtubule motor activity / COPI-mediated anterograde transport / dynein light intermediate chain binding / cytoplasmic dynein complex / aorta development / ventricular septum development / microtubule-based movement / neuromuscular process / nuclear migration / apical junction complex / endosome to lysosome transport / dendrite morphogenesis / myosin binding / regulation of norepinephrine uptake / neuromuscular junction development / nitric-oxide synthase binding / transporter regulator activity / cortical cytoskeleton / TPR domain binding / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / cell leading edge / motor behavior / dynein intermediate chain binding / dynein complex binding / microtubule organizing center / cleavage furrow / brush border / establishment of mitotic spindle orientation / kinesin binding / regulation of synaptic vesicle endocytosis / axonal growth cone
Similarity search - Function
HAP1, N-terminal / Trafficking kinesin-binding protein, C-terminal / : / HAP1 N-terminal conserved region / Kinesin associated protein / Kinesin associated protein / HAP1 N-terminal conserved region / Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 ...HAP1, N-terminal / Trafficking kinesin-binding protein, C-terminal / : / HAP1 N-terminal conserved region / Kinesin associated protein / Kinesin associated protein / HAP1 N-terminal conserved region / Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / Dynamitin / : / Dynamitin / Dynactin subunit 6 / Dynein associated protein / Dynein associated protein / Dynactin subunit 5 / 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 / Actin related protein 1A / F-actin-capping protein subunit alpha-1 ...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 / Actin related protein 1A / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Dynactin subunit 6 / Dynactin subunit 3 / Actin-related protein 10 / Trafficking protein, kinesin binding 2 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.8 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
a: Trafficking protein, kinesin binding 2
b: Trafficking protein, kinesin binding 2
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,704,75046
Polymers3,700,20233
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 , 4 types, 12 molecules ABCDEFGIHJab

#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 / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: Q6QAQ1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#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 Trafficking protein, kinesin binding 2


Mass: 101418.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trak2, Als2cr3 / Production host: Homo sapiens (human) / References: UniProt: Q6P9N8

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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 / Disks large homolog 1 isoform X1


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

#15: 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
#16: 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
#17: 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 TRAK2 of dynein-dynactin-TRAK2 complex on microtubules
Type: COMPLEX / Entity ID: #1-#14 / 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: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52920 / Symmetry type: POINT

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