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- PDB-9e22: Cryo-EM structure of human cytoplasmic dynein-1 bound to LIS1 in ... -

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Basic information

Entry
Database: PDB / ID: 9.0E+22
TitleCryo-EM structure of human cytoplasmic dynein-1 bound to LIS1 in the presence of ATP
Components
  • Cytoplasmic dynein 1 heavy chain 1
  • Platelet-activating factor acetylhydrolase IB subunit beta
KeywordsMOTOR PROTEIN / human / complex
Function / homology
Function and homology information


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 / maintenance of centrosome location / platelet activating factor metabolic process / radial glia-guided pyramidal neuron migration / acrosome assembly / central region of growth cone ...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 / maintenance of centrosome location / platelet activating factor metabolic process / radial glia-guided pyramidal neuron migration / acrosome assembly / central region of growth cone / cerebral cortex neuron differentiation / establishment of centrosome localization / microtubule sliding / positive regulation of cytokine-mediated signaling pathway / positive regulation of embryonic development / microtubule organizing center organization / interneuron migration / layer formation in cerebral cortex / astral microtubule / auditory receptor cell development / nuclear membrane disassembly / positive regulation of intracellular transport / cortical microtubule organization / positive regulation of dendritic spine morphogenesis / reelin-mediated signaling pathway / myeloid leukocyte migration / regulation of metaphase plate congression / positive regulation of spindle assembly / establishment of spindle localization / osteoclast development / stereocilium / microtubule plus-end binding / brain morphogenesis / vesicle transport along microtubule / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / kinesin complex / P-body assembly / negative regulation of JNK cascade / minus-end-directed microtubule motor activity / microtubule associated complex / cytoplasmic dynein complex / dynein light intermediate chain binding / motile cilium / neuromuscular process controlling balance / stem cell division / nuclear migration / cell leading edge / dynein intermediate chain binding / germ cell development / transmission of nerve impulse / dynein complex binding / establishment of mitotic spindle orientation / dynactin binding / protein secretion / cochlea development / neuroblast proliferation / positive regulation of axon extension / microtubule-based process / lipid catabolic process / COPI-mediated anterograde transport / phospholipase binding / cytoplasmic microtubule / JNK cascade / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / axon cytoplasm / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / stress granule assembly / 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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / regulation of microtubule cytoskeleton organization / regulation of mitotic spindle organization / AURKA Activation by TPX2 / adult locomotory behavior / mitotic spindle organization / filopodium / hippocampus development / phosphoprotein binding / RHO GTPases Activate Formins / cerebral cortex development / modulation of chemical synaptic transmission / kinetochore / microtubule cytoskeleton organization / Schaffer collateral - CA1 synapse / neuron migration / HCMV Early Events / Aggrephagy / azurophil granule lumen / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition
Similarity search - Function
: / : / PAC1 LisH domain / Dynein regulator LIS1 / LIS1, N-terminal / 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 ...: / : / PAC1 LisH domain / Dynein regulator LIS1 / LIS1, N-terminal / 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 heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsNguyen, K.H.V. / Kendrick, A.A. / Leschziner, A.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM139795 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM145296 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Pre-Chi dynein bound to Lis1
Authors: Nguyen, K.H.V. / Kendrick, A.A. / Leschziner, A.E.
History
DepositionOct 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: FSC / Part number: 1 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: FSC / Part number: 2 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Cytoplasmic dynein 1 heavy chain 1
E: Platelet-activating factor acetylhydrolase IB subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)602,7427
Polymers600,8492
Non-polymers1,8935
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

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


Mass: 554126.250 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
#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: 46722.918 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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: Human Cytoplasmic dynein-1 bound to LIS1 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3250 nm / Nominal defocus min: 610 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69831 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325086
ELECTRON MICROSCOPYf_angle_d0.61834123
ELECTRON MICROSCOPYf_dihedral_angle_d6.3573575
ELECTRON MICROSCOPYf_chiral_restr0.0433917
ELECTRON MICROSCOPYf_plane_restr0.0054441

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