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- PDB-3j6p: Pseudo-atomic model of dynein microtubule binding domain-tubulin ... -

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Basic information

Entry
Database: PDB / ID: 3j6p
TitlePseudo-atomic model of dynein microtubule binding domain-tubulin complex based on a cryoEM map
Components
  • Dynein heavy chain, cytoplasmic
  • Tubulin alpha-1A chain
  • Tubulin beta chain
KeywordsMOTOR PROTEIN/STRUCTURAL PROTEIN / Motor Protein-Cytoskeleton Complex / MOTOR PROTEIN-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


minus-end-directed vesicle transport along microtubule / early phagosome membrane / COPI-mediated anterograde transport / phagolysosome membrane / CTPase activity / Neutrophil degranulation / phagosome maturation / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding ...minus-end-directed vesicle transport along microtubule / early phagosome membrane / COPI-mediated anterograde transport / phagolysosome membrane / CTPase activity / Neutrophil degranulation / phagosome maturation / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / nuclear migration / microtubule motor activity / dynein intermediate chain binding / ATPase complex / endocytic vesicle / mitotic spindle assembly / cytoplasmic microtubule / cytoplasmic microtubule organization / tubulin binding / mitotic spindle organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / cell cortex / microtubule binding / microtubule / hydrolase activity / GTPase activity / centrosome / GTP binding / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 ...Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / 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, 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 / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOL / Tubulin alpha-1A chain / Tubulin beta chain / Dynein heavy chain, cytoplasmic
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsUchimura, S. / Fujii, T. / Takazaki, H. / Ayukawa, R. / Nishikawa, Y. / Minoura, I. / Hachikubo, Y. / Kurisu, G. / Sutoh, K. / Kon, T. ...Uchimura, S. / Fujii, T. / Takazaki, H. / Ayukawa, R. / Nishikawa, Y. / Minoura, I. / Hachikubo, Y. / Kurisu, G. / Sutoh, K. / Kon, T. / Namba, K. / Muto, E.
CitationJournal: J Cell Biol / Year: 2015
Title: A flipped ion pair at the dynein-microtubule interface is critical for dynein motility and ATPase activation.
Authors: Seiichi Uchimura / Takashi Fujii / Hiroko Takazaki / Rie Ayukawa / Yosuke Nishikawa / Itsushi Minoura / You Hachikubo / Genji Kurisu / Kazuo Sutoh / Takahide Kon / Keiichi Namba / Etsuko Muto /
Abstract: Dynein is a motor protein that moves on microtubules (MTs) using the energy of adenosine triphosphate (ATP) hydrolysis. To understand its motility mechanism, it is crucial to know how the signal of ...Dynein is a motor protein that moves on microtubules (MTs) using the energy of adenosine triphosphate (ATP) hydrolysis. To understand its motility mechanism, it is crucial to know how the signal of MT binding is transmitted to the ATPase domain to enhance ATP hydrolysis. However, the molecular basis of signal transmission at the dynein-MT interface remains unclear. Scanning mutagenesis of tubulin identified two residues in α-tubulin, R403 and E416, that are critical for ATPase activation and directional movement of dynein. Electron cryomicroscopy and biochemical analyses revealed that these residues form salt bridges with the residues in the dynein MT-binding domain (MTBD) that work in concert to induce registry change in the stalk coiled coil and activate the ATPase. The R403-E3390 salt bridge functions as a switch for this mechanism because of its reversed charge relative to other residues at the interface. This study unveils the structural basis for coupling between MT binding and ATPase activation and implicates the MTBD in the control of directional movement.
History
DepositionMar 20, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_image_scans / em_single_particle_entity / em_software / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._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 / _em_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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Assembly

Deposited unit
D: Dynein heavy chain, cytoplasmic
A: Tubulin alpha-1A chain
B: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1877
Polymers112,3433
Non-polymers1,8454
Water0
1


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

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Components

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Protein , 3 types, 3 molecules DAB

#1: Protein Dynein heavy chain, cytoplasmic / Dynein heavy chain / cytosolic / DYHC


Mass: 12327.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB_G0276355, dhcA / Production host: Escherichia coli (E. coli) / References: UniProt: P34036
#2: Protein Tubulin alpha-1A chain / / Alpha-tubulin 1 / Tubulin alpha-1 chain


Mass: 50107.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02550
#3: Protein Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554

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Non-polymers , 4 types, 4 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-TA1 / TAXOL / Paclitaxel


Mass: 853.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication, chemotherapy*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Dictyostelium dynein microtubule binding domain bound to a 15-protofilament microtubule
Type: COMPLEX
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Method: Blot for 3.5 seconds before plunging

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC / Date: Nov 5, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 60000 X / Calibrated magnification: 109489 X / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm / Cs: 1.6 mm
Specimen holderTemperature: 50 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1DireXmodel fitting
2Flex-EMmodel fitting
3SPIDER3D reconstruction
CTF correctionDetails: CTFFIND3 Each particle
3D reconstructionMethod: Projection Matching / Resolution: 8.2 Å / Actual pixel size: 1.37 Å / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--Flexible fitting REFINEMENT PROTOCOL--Flexible fitting
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13VKH

3vkh

13VKH1PDBexperimental model
21JFF

1jff

11JFF2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms7440 0 123 0 7563

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