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- PDB-9e28: Cryo-EM structure of Phi dynein tail -

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Basic information

Entry
Database: PDB / ID: 9.0E+28
TitleCryo-EM structure of Phi dynein tail
Components
  • (Cytoplasmic dynein 1 ...) x 2
  • (Dynein light chain ...) x 3
  • Isoform 2C of Cytoplasmic dynein 1 intermediate chain 2
KeywordsMOTOR PROTEIN / human / complex
Function / homology
Function and homology information


intracellular transport of viral protein in host cell / secretory vesicle / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / transport along microtubule / intraciliary retrograde transport / visual behavior / dynein light chain binding / dynein heavy chain binding / motile cilium assembly ...intracellular transport of viral protein in host cell / secretory vesicle / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / transport along microtubule / intraciliary retrograde transport / visual behavior / dynein light chain binding / dynein heavy chain binding / motile cilium assembly / Activation of BIM and translocation to mitochondria / negative regulation of phosphorylation / ciliary tip / Intraflagellar transport / positive regulation of intracellular transport / regulation of metaphase plate congression / establishment of spindle localization / positive regulation of spindle assembly / regulation of G protein-coupled receptor signaling pathway / microtubule-dependent intracellular transport of viral material towards nucleus / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / minus-end-directed microtubule motor activity / P-body assembly / microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / centrosome localization / dynein intermediate chain binding / nuclear migration / microtubule-based movement / Macroautophagy / establishment of mitotic spindle orientation / enzyme inhibitor activity / tertiary granule membrane / ficolin-1-rich granule membrane / cytoplasmic microtubule / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / axon cytoplasm / Mitotic Prometaphase / substantia nigra development / 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 / Recruitment of NuMA to mitotic centrosomes / regulation of mitotic spindle organization / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / cellular response to nerve growth factor stimulus / kinetochore / negative regulation of neurogenesis / spindle / microtubule cytoskeleton organization / HCMV Early Events / Aggrephagy / mitotic spindle / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / late endosome / nervous system development / host cell / site of double-strand break / positive regulation of cold-induced thermogenesis / cell cortex / secretory granule lumen / vesicle / microtubule / ficolin-1-rich granule lumen / cytoskeleton / cilium / symbiont entry into host cell / cell division / apoptotic process / centrosome / DNA damage response / Neutrophil degranulation / Golgi apparatus / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Dynein 1 light intermediate chain / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Dynein light chain Tctex-1 like / Dynein light chain roadblock-type 1/2 / Tctex-1-like superfamily / Tctex-1 family / Dynein light chain, type 1/2, conserved site ...Dynein 1 light intermediate chain / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Dynein light chain Tctex-1 like / Dynein light chain roadblock-type 1/2 / Tctex-1-like superfamily / Tctex-1 family / 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 / 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 / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / 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 / 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
Cytoplasmic dynein 1 light intermediate chain 2 / 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: 4.4 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: 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic dynein 1 heavy chain 1
B: Cytoplasmic dynein 1 light intermediate chain 2
C: Cytoplasmic dynein 1 light intermediate chain 2
D: Isoform 2C of Cytoplasmic dynein 1 intermediate chain 2
E: Dynein light chain roadblock-type 1
F: Dynein light chain roadblock-type 1
G: Cytoplasmic dynein 1 heavy chain 1
H: Isoform 2C of Cytoplasmic dynein 1 intermediate chain 2
d: Dynein light chain 1, cytoplasmic
e: Cytoplasmic dynein 1 heavy chain 1
f: Cytoplasmic dynein 1 heavy chain 1
g: Isoform 2C of Cytoplasmic dynein 1 intermediate chain 2
h: Isoform 2C of Cytoplasmic dynein 1 intermediate chain 2
i: Dynein light chain 1, cytoplasmic
k: Dynein light chain Tctex-type 1
v: Dynein light chain Tctex-type 1


Theoretical massNumber of molelcules
Total (without water)2,666,17716
Polymers2,666,17716
Non-polymers00
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, 6 molecules AGefBC

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


Mass: 554126.250 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
#2: 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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Protein , 1 types, 4 molecules DHgh

#3: Protein
Isoform 2C of Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein intermediate chain 2 / Dynein intermediate chain 2 / cytosolic / DH IC-2


Mass: 68442.141 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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Dynein light chain ... , 3 types, 6 molecules EFdikv

#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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Details

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 / Type: COMPLEX / Entity ID: #4, #3, #5-#6, #2, #1 / 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: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21400 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00221221
ELECTRON MICROSCOPYf_angle_d0.40928212
ELECTRON MICROSCOPYf_dihedral_angle_d4.2434706
ELECTRON MICROSCOPYf_chiral_restr0.0442313
ELECTRON MICROSCOPYf_plane_restr0.0024706

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