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- PDB-9e14: Full-length human dynein-1 in phi-like comformation bound to a Li... -

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Basic information

Entry
Database: PDB / ID: 9.0E+14
TitleFull-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Nde1-Lis1 condition
Components
  • (Cytoplasmic dynein 1 ...) x 3
  • (Dynein light chain ...) x 3
  • Platelet-activating factor acetylhydrolase IB subunit beta
KeywordsMOTOR PROTEIN / dynein-1 / phi-like conformation / Lis1
Function / homology
Function and homology information


intracellular transport of viral protein in host cell / nitric-oxide synthase inhibitor activity / microtubule cytoskeleton organization involved in establishment of planar polarity / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / negative regulation of DNA strand resection involved in replication fork processing / secretory vesicle / corpus callosum morphogenesis / negative regulation of phosphorylation / maintenance of centrosome location ...intracellular transport of viral protein in host cell / nitric-oxide synthase inhibitor activity / microtubule cytoskeleton organization involved in establishment of planar polarity / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / negative regulation of DNA strand resection involved in replication fork processing / secretory vesicle / corpus callosum morphogenesis / negative regulation of phosphorylation / maintenance of centrosome location / ameboidal-type cell migration / intraciliary retrograde transport / platelet activating factor metabolic process / visual behavior / radial glia-guided pyramidal neuron migration / establishment of centrosome localization / central region of growth cone / cerebral cortex neuron differentiation / acrosome assembly / nuclear membrane disassembly / microtubule sliding / dynein light chain binding / transport along microtubule / dynein heavy chain binding / Activation of BIM and translocation to mitochondria / positive regulation of cytokine-mediated signaling pathway / motile cilium assembly / positive regulation of embryonic development / microtubule organizing center organization / interneuron migration / layer formation in cerebral cortex / astral microtubule / auditory receptor cell development / cortical microtubule organization / Intraflagellar transport / myeloid leukocyte migration / reelin-mediated signaling pathway / positive regulation of intracellular transport / regulation of metaphase plate congression / positive regulation of spindle assembly / positive regulation of dendritic spine morphogenesis / negative regulation of nitric oxide biosynthetic process / establishment of spindle localization / osteoclast development / regulation of G protein-coupled receptor signaling pathway / stereocilium / microtubule plus-end binding / microtubule-dependent intracellular transport of viral material towards nucleus / brain morphogenesis / motile cilium / vesicle transport along microtubule / retrograde axonal transport / COPI-independent Golgi-to-ER retrograde traffic / P-body assembly / minus-end-directed microtubule motor activity / microtubule associated complex / negative regulation of JNK cascade / centrosome localization / dynein light intermediate chain binding / cytoplasmic dynein complex / microtubule motor activity / kinesin complex / neuromuscular process controlling balance / stem cell division / microtubule-based movement / nuclear migration / Macroautophagy / establishment of mitotic spindle orientation / dynein intermediate chain binding / germ cell development / cell leading edge / transmission of nerve impulse / dynein complex binding / tertiary granule membrane / neuroblast proliferation / dynactin binding / cochlea development / ficolin-1-rich granule membrane / protein secretion / spermatid development / positive regulation of axon extension / microtubule-based process / lipid catabolic process / COPI-mediated anterograde transport / phospholipase binding / cytoplasmic microtubule / JNK cascade / cytoplasmic microtubule organization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / positive regulation of mitotic cell cycle / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / substantia nigra development / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation
Similarity search - Function
: / : / PAC1 LisH domain / Dynein 1 light intermediate chain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Dynein light chain roadblock-type 1/2 / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) ...: / : / PAC1 LisH domain / Dynein 1 light intermediate chain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Dynein light chain roadblock-type 1/2 / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein regulator LIS1 / LIS1, N-terminal / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / : / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Lissencephaly type-1-like homology motif / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / LIS1 homology (LisH) motif profile. / LIS1 homology motif / 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 / Cytoplasmic dynein 1 light intermediate chain 2 / Platelet-activating factor acetylhydrolase IB subunit beta / Dynein light chain 1, cytoplasmic / Dynein light chain Tctex-type 1 / Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein 1 heavy chain 1 / Dynein light chain roadblock-type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å
AuthorsYang, J. / 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: Nat Chem Biol / Year: 2026
Title: Nde1 promotes Lis1 binding to full-length autoinhibited human dynein 1.
Authors: Jun Yang / Yuanchang Zhao / Pengxin Chai / Ahmet Yildiz / Kai Zhang /
Abstract: Cytoplasmic dynein 1 (dynein) is the primary motor responsible for the retrograde transport of intracellular cargoes along microtubules. Activation of dynein requires the opening its autoinhibited ...Cytoplasmic dynein 1 (dynein) is the primary motor responsible for the retrograde transport of intracellular cargoes along microtubules. Activation of dynein requires the opening its autoinhibited Phi conformation, a process driven by Lis1 and Nde1/Ndel1. Using biochemical reconstitution and cryo-electron microscopy, we demonstrate that Nde1 enhances Lis1 binding to autoinhibited dynein and facilitates Phi opening. We identify a key intermediate in this activation pathway where a single Lis1 dimer binds between Phi-like (Phi) motor rings. In this 'Phi-Lis1' complex, Lis1 interacts with one motor domain through canonical sites at the AAA+ (adenosine triphosphatases associated with diverse cellular activities) ring and stalk, and with AAA5, AAA6 and linker regions of the other motor domain. Mutagenesis and motility assays confirm the critical role of the Phi-Lis1 interface in dynein activation. This intermediate forms rapidly in the presence of Nde1, although Nde1 is not part of Phi-Lis1. These findings provide key insights into how Nde1 promotes Lis1-mediated Phi opening.
History
DepositionOct 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / 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: Cytoplasmic dynein 1 heavy chain 1
C: Cytoplasmic dynein 1 intermediate chain 2
D: Cytoplasmic dynein 1 intermediate chain 2
E: Cytoplasmic dynein 1 light intermediate chain 2
F: Cytoplasmic dynein 1 light intermediate chain 2
G: Dynein light chain roadblock-type 1
H: Dynein light chain roadblock-type 1
I: Dynein light chain 1, cytoplasmic
J: Dynein light chain 1, cytoplasmic
K: Dynein light chain Tctex-type 1
L: Dynein light chain Tctex-type 1
O: Platelet-activating factor acetylhydrolase IB subunit beta
P: Platelet-activating factor acetylhydrolase IB subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,482,25726
Polymers1,478,58314
Non-polymers3,67512
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 ... , 3 types, 6 molecules ABCDEF

#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
#2: 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
#3: Protein Cytoplasmic dynein 1 light intermediate chain 2 / Dynein light intermediate chain 2 / cytosolic / LIC-2 / LIC53/55


Mass: 54173.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1LI2, DNCLI2, LIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43237

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Dynein light chain ... , 3 types, 6 molecules GHIJKL

#4: Protein Dynein light chain roadblock-type 1 / Bithoraxoid-like protein / BLP / Dynein light chain 2A / cytoplasmic / Dynein-associated protein ...Bithoraxoid-like protein / BLP / Dynein light chain 2A / cytoplasmic / Dynein-associated protein Km23 / Roadblock domain-containing protein 1


Mass: 10934.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLRB1, BITH, DNCL2A, DNLC2A, ROBLD1, HSPC162 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NP97
#5: Protein Dynein light chain 1, cytoplasmic / 8 kDa dynein light chain / DLC8 / Dynein light chain LC8-type 1 / Protein inhibitor of neuronal ...8 kDa dynein light chain / DLC8 / Dynein light chain LC8-type 1 / Protein inhibitor of neuronal nitric oxide synthase / PIN


Mass: 10381.899 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLL1, DLC1, DNCL1, DNCLC1, HDLC1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63167
#6: Protein Dynein light chain Tctex-type 1 / Protein CW-1 / T-complex testis-specific protein 1 homolog


Mass: 12461.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLT1, TCTEL1, TCTEX-1, TCTEX1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63172

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Protein , 1 types, 2 molecules OP

#7: 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.: 2
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

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Non-polymers , 3 types, 12 molecules

#8: 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
#9: 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
#10: 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: Full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Nde1-Lis1 condition
Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightValue: 1.5 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.2
Details: 25 mM HEPES pH 7.2, 150 mM KCl, 1 mM MgCl2, 5 mM DTT, 3 mM ATP
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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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
IDNameVersionCategory
11cryoSPARC4final Euler assignment
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61684 / Symmetry type: POINT

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