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- PDB-3j68: Structural mechanism of the dynein powerstroke (pre-powerstroke state) -

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Entry
Database: PDB / ID: 3j68
TitleStructural mechanism of the dynein powerstroke (pre-powerstroke state)
ComponentsDynein motor domain
KeywordsMOTOR PROTEIN
Function / homology
Function and homology information


karyogamy / astral microtubule / establishment of mitotic spindle localization / nuclear migration along microtubule / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / nuclear migration / spindle pole body / dynein intermediate chain binding ...karyogamy / astral microtubule / establishment of mitotic spindle localization / nuclear migration along microtubule / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / nuclear migration / spindle pole body / dynein intermediate chain binding / cytoplasmic microtubule / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / cytoplasmic microtubule organization / Neutrophil degranulation / mitotic spindle organization / cell cortex / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
AAA+ lid domain / : / DYN1, AAA+ ATPase lid 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 ...AAA+ lid domain / : / DYN1, AAA+ ATPase lid 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynein heavy chain, cytoplasmic
Similarity search - Component
Biological speciesStrongylocentrotus purpuratus (purple sea urchin)
MethodELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 30 Å
AuthorsLin, J. / Okada, K. / Raytchev, M. / Smith, M.C. / Nicastro, D.
CitationJournal: Nat Cell Biol / Year: 2014
Title: Structural mechanism of the dynein power stroke.
Authors: Jianfeng Lin / Kyoko Okada / Milen Raytchev / Maria C Smith / Daniela Nicastro /
Abstract: Dyneins are large microtubule motor proteins required for mitosis, intracellular transport and ciliary and flagellar motility. They generate force through a power-stroke mechanism, which is an ATP- ...Dyneins are large microtubule motor proteins required for mitosis, intracellular transport and ciliary and flagellar motility. They generate force through a power-stroke mechanism, which is an ATP-consuming cycle of pre- and post-power-stroke conformational changes that cause relative motion between different dynein domains. However, key structural details of dynein's force generation remain elusive. Here, using cryo-electron tomography of intact, active (that is, beating), rapidly frozen sea urchin sperm flagella, we determined the in situ three-dimensional structures of all domains of both pre- and post-power-stroke dynein, including the previously unresolved linker and stalk of pre-power-stroke dynein. Our results reveal that the rotation of the head relative to the linker is the key action in dynein movement, and that there are at least two distinct pre-power-stroke conformations: pre-I (microtubule-detached) and pre-II (microtubule-bound). We provide three-dimensional reconstructions of native dyneins in three conformational states, in situ, allowing us to propose a molecular model of the structural cycle underlying dynein movement.
History
DepositionDec 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_imaging_optics / em_software
Item: _em_imaging_optics.energyfilter_name / _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
A: Dynein motor domain


Theoretical massNumber of molelcules
Total (without water)262,1221
Polymers262,1221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Dynein motor domain


Mass: 262122.234 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: P36022*PLUS
Sequence detailsTHE IMAGED DYNEIN WAS FROM STRONGYLOCENTROTUS PURPURATUS, BUT THE MODELED COORDINATES ARE DERIVED ...THE IMAGED DYNEIN WAS FROM STRONGYLOCENTROTUS PURPURATUS, BUT THE MODELED COORDINATES ARE DERIVED FROM SACCHAROMYCES CEREVISIAE. FULL-LENGTH PROTEIN WAS PRESENT IN THE SAMPLE, BUT N-TERMINAL RESIDUES WERE NOT MODELED.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: active sea urchin sperm flagella / Type: COMPLEX
Buffer solutionName: 360 mM NaCl, 50 mM MgCl2, 10 mM CaCl2, 10 mM KCl, 30 mM HEPES, pH 8.0
pH: 8
Details: 360 mM NaCl, 50 mM MgCl2, 10 mM CaCl2, 10 mM KCl, 30 mM HEPES, pH 8.0
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holey carbon grids Cu 200 mesh R2/2
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: Blot for 1.5-2.5 seconds before plunging in liquid ethane.
Method: Blot for 1.5-2.5 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Apr 7, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 13500 X / Nominal defocus max: 8000 nm / Nominal defocus min: 6000 nm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: GATAN LIQUID NITROGEN / Temperature: 80 K / Tilt angle max: 65 ° / Tilt angle min: -65 °
Image recordingElectron dose: 100 e/Å2 / Film or detector model: GENERIC GATAN (2k x 2k)
EM imaging opticsEnergyfilter name: GIF / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1IMOD3D reconstruction
2PEET3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: fiducial alignment and weighted back-projection / Resolution: 30 Å / Resolution method: FSC 0.5 CUT-OFF / Nominal pixel size: 9.856 Å / Actual pixel size: 9.856 Å
Details: Final maps were calculated by averaging 2800 particles from 41 tomograms. Axonemal repeats (96 nm long) from 41 tomograms (reconstructed using fiducial alignment and weighted backprojection, ...Details: Final maps were calculated by averaging 2800 particles from 41 tomograms. Axonemal repeats (96 nm long) from 41 tomograms (reconstructed using fiducial alignment and weighted backprojection, IMOD software, Kremer et al. 1996) were aligned and averaged using the PEET software (bio3d.colorado.edu, Nicastro et al. 2006). To obtain structures with consistent conformations, classification of the different conformational states of dynein was performed using a clustering approach implemented in PEET (Heumann et al. 2011).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Details: REFINEMENT PROTOCOL--rigid body DETAILS--Initial local fitting was done using Chimera and then manual adjustment was performed.
Atomic model buildingPDB-ID: 4AKI

4aki


Pdb chain-ID: A / Accession code: 4AKI / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms18105 0 0 0 18105

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