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- PDB-9yng: Dynactin and dynein-1 tail region of dynein-dynactin complex on m... -

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Entry
Database: PDB / ID: 9yng
TitleDynactin and dynein-1 tail region of dynein-dynactin complex on microtubule in the presence of LIS1
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
KeywordsMOTOR PROTEIN / Dynein-1 / Dynactin
Function / homology
Function and homology information


: / 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 ...: / 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 / F-actin capping protein complex / nuclear membrane disassembly / WASH complex / dynein light chain binding / transport along microtubule / ventral spinal cord development / dynein heavy chain binding / cytoskeleton-dependent cytokinesis / retromer complex / dynein complex / microtubule plus-end / cellular response to cytochalasin B / positive regulation of microtubule nucleation / positive regulation of intracellular transport / regulation of transepithelial transport / regulation of metaphase plate congression / positive regulation of spindle assembly / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / melanosome transport / establishment of spindle localization / protein localization to adherens junction / barbed-end actin filament capping / dense body / Neutrophil degranulation / Tat protein binding / coronary vasculature development / postsynaptic actin cytoskeleton / non-motile cilium assembly / regulation of cell morphogenesis / retrograde transport, endosome to Golgi / adherens junction assembly / retrograde axonal transport / apical protein localization / COPI-independent Golgi-to-ER retrograde traffic / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / P-body assembly / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / minus-end-directed microtubule motor activity / MHC class II antigen presentation / microtubule associated complex / Recruitment of NuMA to mitotic centrosomes / dynein light intermediate chain binding / cytoplasmic dynein complex / tight junction / microtubule motor activity / COPI-mediated anterograde transport / ventricular septum development / aorta development / microtubule-based movement / nuclear migration / apical junction complex / neuromuscular process / establishment of mitotic spindle orientation / neuromuscular junction development / regulation of norepinephrine uptake / transporter regulator activity / dynein intermediate chain binding / NuA4 histone acetyltransferase complex / motor behavior / cell leading edge / establishment or maintenance of cell polarity / cortical cytoskeleton / cleavage furrow / microtubule organizing center / dynein complex binding / nitric-oxide synthase binding
Similarity search - Function
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 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 / Trp-Asp (WD) repeats circular profile. / 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 / Dynactin subunit 4 / Dynactin subunit 2 / Actin related protein 1A / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Dynactin subunit 6 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / Dynactin subunit 1 / Dynactin subunit 4 / 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 / Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein 1 heavy chain 1 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesSus scrofa (pig)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsYang, J. / Rao, 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: Nature / Year: 2026
Title: Roles of microtubules and LIS1 in dynein transport machinery assembly.
Authors: Qinhui Rao / Jun Yang / Pengxin Chai / Steven Markus / Kai Zhang /
Abstract: Cytoplasmic dynein-1, a microtubule (MT)-based motor protein, requires dynactin and a coiled-coil adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The roles of MTs and dynein ...Cytoplasmic dynein-1, a microtubule (MT)-based motor protein, requires dynactin and a coiled-coil adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The roles of MTs and dynein regulator lissencephaly-1 (LIS1) in DDA assembly have remained elusive. Here we use cryo-electron microscopy to determine the structural basis of MT- and LIS1-mediated DDA assembly. We show that an adaptor-independent dynein-dynactin complex spontaneously forms on MTs with an intrinsic 2:1 stoichiometry in a highly efficient manner, driven by parallel alignment of dynein tails upon MT binding. Adaptors can wedge into and exchange within the assembled MT-bound dynein-dynactin complex; these processes are enabled by relative rotations between dynein and dynactin and facilitated by the dynein light-intermediate chains that assist the adaptor 'search' mechanism. Although LIS1 is dispensable for efficient DD(A)-MT assembly, its presence expands the conformational landscape of DD(A) assemblies on MTs. Cryo-electron microscopy reveals that LIS1 bridges dynactin p150 and dynein in both the closed Phi-like and open prepowerstroke states, stabilizing low-MT-affinity intermediates that tether dynein molecules in proximity to MTs and prime them for subsequent DD(A) assembly through alternative pathways. These findings demonstrate the dynamic adaptability of the dynein transport machinery and the coordinated roles of MTs and LIS1 in DDA assembly.
History
DepositionOct 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
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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
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)3,515,20444
Polymers3,510,65631
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 , 3 types, 10 molecules ABCDEFGIHJ

#1: Protein
Alpha-centractin


Mass: 42670.688 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A8D1PMN0
#2: Protein Actin, cytoplasmic 1 / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ACTB / Production host: Spodoptera frugiperda (fall armyworm)
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 genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ACTR10, ARP11 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: I3LHK5

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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 genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CAPZA1, Capza, CP alpha1 / Production host: Spodoptera frugiperda (fall armyworm) / 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 genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CAPZB / Production host: Spodoptera frugiperda (fall armyworm) / 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 genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DCTN2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A5G2QD80
#7: Protein Dynactin subunit 3


Mass: 21192.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DCTN3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F1SEC0
#8: Protein Dynactin subunit 6


Mass: 20703.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DCTN6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D0G6S1
#9: Protein Dynactin subunit 5


Mass: 20150.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DCTN5 / Production host: Spodoptera frugiperda (fall armyworm) / 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 genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DCTN1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A287B8J2
#11: Protein Dynactin subunit 4 / Dyn4


Mass: 52920.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DCTN4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A4X1TB62

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

#12: Protein
Cytoplasmic dynein 1 heavy chain 1 / Cytoplasmic dynein heavy chain 1 / Dynein heavy chain / cytosolic


Mass: 533083.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14204
#13: Protein
Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein intermediate chain 2 / Dynein intermediate chain 2 / cytosolic / DH IC-2


Mass: 71546.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1I2, DNCI2, DNCIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13409

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Non-polymers , 3 types, 13 molecules

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


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


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


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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 and dynein tail region of dynein-dynactin complex on microtubule in the presence of LIS1
Type: COMPLEX / Entity ID: #1-#13 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.2
SpecimenConc.: 2 mg/ml / Embedding 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 magnification: 45000 X / Calibrated magnification: 45000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 2600 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
8PHENIXmodel refinement
13PHENIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91824 / Symmetry type: POINT
RefinementHighest resolution: 4.07 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00284823
ELECTRON MICROSCOPYf_angle_d0.507115433
ELECTRON MICROSCOPYf_dihedral_angle_d5.2312425
ELECTRON MICROSCOPYf_chiral_restr0.04113439
ELECTRON MICROSCOPYf_plane_restr0.00415163

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