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- PDB-9ync: Motor domains of phi-like human dynein-1 bound to dynactin-p150gl... -

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Entry
Database: PDB / ID: 9ync
TitleMotor domains of phi-like human dynein-1 bound to dynactin-p150glued and LIS1
Components
  • (Cytoplasmic dynein 1 ...) x 2
  • Dynactin subunit 1
  • Platelet-activating factor acetylhydrolase IB subunit beta
KeywordsMOTOR PROTEIN / Dynein-1 / phi-like conformation
Function / homology
Function and homology information


microtubule cytoskeleton organization involved in establishment of planar polarity / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / sterol sensor activity / cerebral cortex neuron differentiation / corpus callosum morphogenesis / centriolar subdistal appendage / establishment of centrosome localization / centriole-centriole cohesion / platelet activating factor metabolic process ...microtubule cytoskeleton organization involved in establishment of planar polarity / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / sterol sensor activity / cerebral cortex neuron differentiation / corpus callosum morphogenesis / centriolar subdistal appendage / establishment of centrosome localization / centriole-centriole cohesion / platelet activating factor metabolic process / positive regulation of neuromuscular junction development / acrosome assembly / platelet activating factor catabolic process / 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 / layer formation in cerebral cortex / central region of growth cone / Recruitment of mitotic centrosome proteins and complexes / microtubule anchoring at centrosome / auditory receptor cell development / microtubule sliding / lysosome to ER cholesterol transport / dynein light chain binding / transport along microtubule / ventral spinal cord development / dynein heavy chain binding / neuroblast proliferation / microtubule organizing center organization / positive regulation of embryonic development / retromer complex / brain morphogenesis / dynein complex / astral microtubule / microtubule plus-end / mitotic nuclear membrane disassembly / cortical microtubule organization / reelin-mediated signaling pathway / positive regulation of microtubule nucleation / positive regulation of dendritic spine morphogenesis / positive regulation of intracellular transport / positive regulation of spindle assembly / germ cell development / regulation of metaphase plate congression / stem cell division / neuromuscular process controlling balance / non-motile cilium assembly / stereocilium / establishment of spindle localization / microtubule plus-end binding / motor behavior / positive regulation of mitotic cell cycle spindle assembly checkpoint / motile cilium / vesicle transport along microtubule / neuron cellular homeostasis / retrograde transport, endosome to Golgi / retrograde axonal transport / COPI-independent Golgi-to-ER retrograde traffic / neuromuscular process / minus-end-directed microtubule motor activity / P-body assembly / microtubule associated complex / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / dynein light intermediate chain binding / cytoplasmic dynein complex / MHC class II antigen presentation / nuclear migration / Recruitment of NuMA to mitotic centrosomes / microtubule motor activity / kinesin complex / COPI-mediated anterograde transport / microtubule-based movement / male germ cell nucleus / intercellular bridge / establishment of mitotic spindle orientation / dynein intermediate chain binding / cell leading edge / transmission of nerve impulse / neuromuscular junction development / dynein complex binding / cochlea development / dynactin binding / positive regulation of axon extension / adult locomotory behavior / microtubule-based process / COPI-mediated anterograde transport / cytoplasmic microtubule / positive regulation of mitotic cell cycle / phospholipase binding / cytoplasmic microtubule organization / cholesterol homeostasis / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / neuron projection maintenance / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Recruitment of mitotic centrosome proteins and complexes / centriole
Similarity search - Function
: / : / PAC1 LisH domain / : / Domain of unknown function (DUF8221) / Dynein associated protein / Dynein associated protein / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein regulator LIS1 ...: / : / PAC1 LisH domain / : / Domain of unknown function (DUF8221) / Dynein associated protein / Dynein associated protein / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein regulator LIS1 / LIS1, N-terminal / : / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Lissencephaly type-1-like homology motif / 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 / LIS1 homology (LisH) motif profile. / LIS1 homology motif / : / 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 / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / 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 1 / Platelet-activating factor acetylhydrolase IB subunit beta / Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein 1 heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.93 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: Cytoplasmic dynein 1 heavy chain 1
B: Cytoplasmic dynein 1 heavy chain 1
C: Platelet-activating factor acetylhydrolase IB subunit beta
D: Platelet-activating factor acetylhydrolase IB subunit beta
E: Platelet-activating factor acetylhydrolase IB subunit beta
F: Platelet-activating factor acetylhydrolase IB subunit beta
G: Cytoplasmic dynein 1 intermediate chain 2
H: Cytoplasmic dynein 1 intermediate chain 2
I: Dynactin subunit 1
J: Dynactin subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,683,80522
Polymers1,680,13010
Non-polymers3,67512
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Cytoplasmic dynein 1 ... , 2 types, 4 molecules ABGH

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


Mass: 533083.250 Da / Num. of mol.: 2
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
#3: 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.: 2
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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Protein , 2 types, 6 molecules CDEFIJ

#2: Protein
Platelet-activating factor acetylhydrolase IB subunit beta / Lissencephaly-1 protein / LIS-1 / PAF acetylhydrolase 45 kDa subunit / PAF-AH 45 kDa subunit / PAF- ...Lissencephaly-1 protein / LIS-1 / PAF acetylhydrolase 45 kDa subunit / PAF-AH 45 kDa subunit / PAF-AH alpha / PAFAH alpha


Mass: 46709.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAFAH1B1, LIS1, MDCR, MDS, PAFAHA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43034
#4: 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

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Non-polymers , 3 types, 12 molecules

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


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / 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: Motor domains of phi-like human dynein-1 bound to dynactin-p150glued and LIS1
Type: COMPLEX / Entity ID: #1-#4 / 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: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90591 / Symmetry type: POINT
RefinementHighest resolution: 3.93 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00258060
ELECTRON MICROSCOPYf_angle_d0.55478804
ELECTRON MICROSCOPYf_dihedral_angle_d4.6977873
ELECTRON MICROSCOPYf_chiral_restr0.048926
ELECTRON MICROSCOPYf_plane_restr0.00410118

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