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- PDB-9ynd: Motor domain of human dynein-1 in pre-power stroke bound to dynac... -

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Basic information

Entry
Database: PDB / ID: 9ynd
TitleMotor domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B and LIS1
Components
  • (Cytoplasmic dynein 1 ...) x 2
  • Dynactin subunit 1
  • Platelet-activating factor acetylhydrolase IB subunit beta
KeywordsMOTOR PROTEIN / Dynein-1 / Lis1 / p150glued
Function / homology
Function and homology information


cell cortex region / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / corpus callosum morphogenesis / centriolar subdistal appendage / maintenance of centrosome location / positive regulation of neuromuscular junction development / centriole-centriole cohesion ...cell cortex region / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / corpus callosum morphogenesis / centriolar subdistal appendage / maintenance of centrosome location / positive regulation of neuromuscular junction development / centriole-centriole cohesion / platelet activating factor metabolic process / transport along microtubule / radial glia-guided pyramidal neuron migration / acrosome assembly / central region of growth cone / microtubule anchoring at centrosome / cerebral cortex neuron differentiation / establishment of centrosome localization / microtubule sliding / dynein light chain binding / maintenance of synapse structure / ventral spinal cord development / dynein heavy chain binding / positive regulation of cytokine-mediated signaling pathway / positive regulation of embryonic development / microtubule organizing center organization / interneuron migration / layer formation in cerebral cortex / microtubule plus-end / auditory receptor cell development / astral microtubule / nuclear membrane disassembly / cortical microtubule organization / positive regulation of intracellular transport / XBP1(S) activates chaperone genes / positive regulation of microtubule nucleation / positive regulation of dendritic spine morphogenesis / myeloid leukocyte migration / reelin-mediated signaling pathway / regulation of metaphase plate congression / positive regulation of spindle assembly / melanosome transport / establishment of spindle localization / osteoclast development / stereocilium / microtubule plus-end binding / non-motile cilium assembly / brain morphogenesis / vesicle transport along microtubule / dynein complex / retrograde transport, endosome to Golgi / COPI-independent Golgi-to-ER retrograde traffic / kinesin complex / retrograde axonal transport / P-body assembly / microtubule motor activity / negative regulation of JNK cascade / microtubule associated complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / motile cilium / neuromuscular process controlling balance / microtubule-based movement / stem cell division / neuromuscular process / nuclear migration / neuromuscular junction development / germ cell development / cell leading edge / motor behavior / dynein intermediate chain binding / dynein complex binding / transmission of nerve impulse / dynactin binding / establishment of mitotic spindle orientation / protein secretion / cochlea development / neuroblast proliferation / positive regulation of axon extension / microtubule-based process / intercellular bridge / lipid catabolic process / COPI-mediated anterograde transport / phospholipase binding / cytoplasmic microtubule / JNK cascade / cytoplasmic microtubule organization / axon cytoplasm / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / neuron projection maintenance / positive regulation of microtubule polymerization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / centriole / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Mitotic Prometaphase / positive regulation of mitotic cell cycle / Recruitment of NuMA to mitotic centrosomes
Similarity search - Function
: / : / PAC1 LisH domain / 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. ...: / : / PAC1 LisH domain / 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 / LIS1 homology (LisH) motif profile. / LIS1 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 / : / 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 / Platelet-activating factor acetylhydrolase IB subunit beta / Cytoplasmic dynein 1 intermediate chain 2 / Dynactin subunit 1 / Cytoplasmic dynein 1 heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.26 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: To Be Published
Title: Motor domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B and LIS1
Authors: Rao, Q. / Yang, J. / Chai, P. / Zhang, K.
History
DepositionOct 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic dynein 1 heavy chain 1
B: Platelet-activating factor acetylhydrolase IB subunit beta
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: Cytoplasmic dynein 1 intermediate chain 2
G: Cytoplasmic dynein 1 intermediate chain 2
H: Dynactin subunit 1
I: Dynactin subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,148,88415
Polymers1,147,0479
Non-polymers1,8376
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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Cytoplasmic dynein 1 ... , 2 types, 3 molecules AFG

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


Mass: 533083.250 Da / Num. of mol.: 1
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 BCDEHI

#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 / DAP-150 / DP-150 / p135 / p150-glued


Mass: 142015.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCTN1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14203

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Non-polymers , 3 types, 6 molecules

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


Mass: 427.201 Da / Num. of mol.: 3 / 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.: 1 / 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.: 2 / 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 domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B and LIS1
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
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: 4.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37109 / Symmetry type: POINT

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