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- EMDB-5931: Dictyostelium dynein microtubule binding domain bound to a 15-pro... -

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Basic information

Entry
Database: EMDB / ID: EMD-5931
TitleDictyostelium dynein microtubule binding domain bound to a 15-protofilament microtubule
Map data3D reconstruction of dynein microtubule binding domain-microtubule complex
Sample
  • Sample: Dictyostelium dynein microtubule binding domain bound to a 15-protofilament microtubule
  • Protein or peptide: Dynein microtubule binding domain
  • Protein or peptide: Tubulin dimer
KeywordsMotor protein / Cytoskeleton / Retrograde transport / Nuclear segregation / AAA+ ATPase / GTPase
Function / homology
Function and homology information


minus-end-directed vesicle transport along microtubule / early phagosome membrane / COPI-mediated anterograde transport / Aggrephagy / phagolysosome membrane / CTPase activity / Neutrophil degranulation / phagosome maturation / minus-end-directed microtubule motor activity / cytoplasmic dynein complex ...minus-end-directed vesicle transport along microtubule / early phagosome membrane / COPI-mediated anterograde transport / Aggrephagy / 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 / cytoplasmic microtubule / endocytic vesicle / mitotic spindle assembly / cytoplasmic microtubule organization / tubulin binding / mitotic spindle organization / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / cell cortex / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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, 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, 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 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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
Tubulin alpha-1A chain / Tubulin beta chain / Dynein heavy chain, cytoplasmic
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote) / Caenorhabditis elegans (invertebrata)
Methodhelical 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, 2014-
Header (metadata) releaseDec 24, 2014-
Map releaseDec 31, 2014-
UpdateApr 8, 2015-
Current statusApr 8, 2015Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.106
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.106
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j6p
  • Surface level: 0.106
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5931.gif

Downloads & links

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Map

FileDownload / File: emd_5931.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of dynein microtubule binding domain-microtubule complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 100 pix.
= 137. Å		1.37 Å/pix.
x 100 pix.
= 137. Å		1.37 Å/pix.
x 100 pix.
= 137. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.106 / Movie #1: 0.106
Minimum - Maximum-0.16258945 - 0.38901326
Average (Standard dev.)0.00914535 (±0.03653634)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 137.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z137.000137.000137.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-108-108-54
NX/NY/NZ10810854
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.1630.3890.009

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Supplemental data

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Sample components

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Entire : Dictyostelium dynein microtubule binding domain bound to a 15-pro...

EntireName: Dictyostelium dynein microtubule binding domain bound to a 15-protofilament microtubule
Components
  • Sample: Dictyostelium dynein microtubule binding domain bound to a 15-protofilament microtubule
  • Protein or peptide: Dynein microtubule binding domain
  • Protein or peptide: Tubulin dimer

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Supramolecule #1000: Dictyostelium dynein microtubule binding domain bound to a 15-pro...

SupramoleculeName: Dictyostelium dynein microtubule binding domain bound to a 15-protofilament microtubule
type: sample / ID: 1000
Oligomeric state: one trimer of microtubule binding domain bound to a 15-protofilament microtubule
Number unique components: 2

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Macromolecule #1: Dynein microtubule binding domain

MacromoleculeName: Dynein microtubule binding domain / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Dictyostelium discoideum (eukaryote)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #2: Tubulin dimer

MacromoleculeName: Tubulin dimer / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
Details: 20mM PIPES-KOH, 10mM K-acetate, 4mM MgSO4, 1mM EGTA
GridDetails: Quantifoil holey carbon molybdenum grid (R1.2/1.3, Quantifoil)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II / Method: Blot for 3.5 seconds before plunging

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureAverage: 50 K
Specialist opticsEnergy filter - Name: Omega filter
DateNov 5, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Number real images: 1407 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 109489 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 11.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 23.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: OTHER / Software - Name: SPIDER
CTF correctionDetails: CTFFIND3 Each particle

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Atomic model buiding 1

Initial modelPDB ID:

3vkh

SoftwareName: DireX
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-3j6p:
Pseudo-atomic model of dynein microtubule binding domain-tubulin complex based on a cryoEM map

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