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- EMDB-10061: Cryo-EM structure of mouse cytoplasmic dynein-1 microtubule bindi... -

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Basic information

Entry
Database: EMDB / ID: EMD-10061
TitleCryo-EM structure of mouse cytoplasmic dynein-1 microtubule binding domain bound to microtubules
Map data
SampleMouse cytoplasmic dynein-1 microtubule binding domain decorating microtubules:
Tubulin / dynein-1 microtubule binding / Tubulin alpha-1B chain / Tubulin beta chain / MKIAA0325 protein / (ligand) x 4
Function / homology
Function and homology information


manchette / cilium movement / positive regulation of intracellular transport / positive regulation of spindle assembly / minus-end-directed vesicle transport along microtubule / establishment of spindle localization / ATP-dependent microtubule motor activity, minus-end-directed / cytoplasmic mRNA processing body assembly / dynein light intermediate chain binding / regulation of metaphase plate congression ...manchette / cilium movement / positive regulation of intracellular transport / positive regulation of spindle assembly / minus-end-directed vesicle transport along microtubule / establishment of spindle localization / ATP-dependent microtubule motor activity, minus-end-directed / cytoplasmic mRNA processing body assembly / dynein light intermediate chain binding / regulation of metaphase plate congression / cytoplasmic dynein complex / dynein complex / retrograde axonal transport / dynein intermediate chain binding / nuclear migration / regulation of mitotic spindle organization / stress granule assembly / cytoplasmic microtubule organization / microtubule motor activity / microtubule-based movement / cytoplasmic microtubule / axon cytoplasm / cellular response to interleukin-4 / microtubule-based process / filopodium / structural constituent of cytoskeleton / neuron migration / microtubule cytoskeleton organization / positive regulation of cold-induced thermogenesis / nuclear envelope / cell cortex / double-stranded RNA binding / mitotic cell cycle / microtubule / GTPase activity / cell division / centrosome / axon / GTP binding / neuronal cell body / ubiquitin protein ligase binding / go:0005623: / ATP binding / cytoplasm
Tubulin, conserved site / Tubulin/FtsZ, C-terminal / Beta tubulin / Tubulin, C-terminal / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / P-loop containing nucleoside triphosphate hydrolase / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Tubulin/FtsZ, 2-layer sandwich domain / Dynein heavy chain, ATP-binding dynein motor region ...Tubulin, conserved site / Tubulin/FtsZ, C-terminal / Beta tubulin / Tubulin, C-terminal / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / P-loop containing nucleoside triphosphate hydrolase / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Tubulin/FtsZ, 2-layer sandwich domain / Dynein heavy chain, ATP-binding dynein motor region / Tubulin/FtsZ, GTPase domain / Alpha tubulin / AAA+ ATPase domain / Dynein heavy chain region D6 P-loop domain / Tubulin/FtsZ, GTPase domain superfamily / Tubulin / Tubulin/FtsZ, C-terminal domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, domain-2 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain, domain-1 / Dynein heavy chain, domain 2, C-terminal / Dynein heavy chain, C-terminal domain, barrel region / Beta tubulin, autoregulation binding site / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain AAA lid domain / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain, C-terminal domain
Tubulin beta chain / Tubulin alpha-1B chain / MKIAA0325 protein / Cytoplasmic dynein 1 heavy chain 1
Biological speciesSus scrofa (pig) / Mus musculus (house mouse) / Pig (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLacey SE / He S / Scheres SHW / Carter AP
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_A025_1011 United Kingdom
Wellcome TrustWT210711 United Kingdom
CitationJournal: Elife / Year: 2019
Title: Cryo-EM of dynein microtubule-binding domains shows how an axonemal dynein distorts the microtubule.
Authors: Samuel E Lacey / Shaoda He / Sjors Hw Scheres / Andrew P Carter /
Abstract: Dyneins are motor proteins responsible for transport in the cytoplasm and the beating of axonemes in cilia and flagella. They bind and release microtubules via a compact microtubule-binding domain ...Dyneins are motor proteins responsible for transport in the cytoplasm and the beating of axonemes in cilia and flagella. They bind and release microtubules via a compact microtubule-binding domain (MTBD) at the end of a coiled-coil stalk. We address how cytoplasmic and axonemal dynein MTBDs bind microtubules at near atomic resolution. We decorated microtubules with MTBDs of cytoplasmic dynein-1 and axonemal dynein DNAH7 and determined their cryo-EM structures using helical Relion. The majority of the MTBD is rigid upon binding, with the transition to the high-affinity state controlled by the movement of a single helix at the MTBD interface. DNAH7 contains an 18-residue insertion, found in many axonemal dyneins, that contacts the adjacent protofilament. Unexpectedly, we observe that DNAH7, but not dynein-1, induces large distortions in the microtubule cross-sectional curvature. This raises the possibility that dynein coordination in axonemes is mediated via conformational changes in the microtubule.
Validation ReportPDB-ID: 6rzb

SummaryFull reportAbout validation report
History
DepositionJun 13, 2019-
Header (metadata) releaseJul 3, 2019-
Map releaseJul 10, 2019-
UpdateJul 17, 2019-
Current statusJul 17, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rzb
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rzb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10061.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 512 pix.
= 532.48 Å
1.04 Å/pix.
x 512 pix.
= 532.48 Å
1.04 Å/pix.
x 512 pix.
= 532.48 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.04034018 - 0.07079709
Average (Standard dev.)0.00039506593 (±0.0031434344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 532.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z532.480532.480532.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0400.0710.000

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Supplemental data

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Segmentation: #1

Fileemd_10061_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_10061_additional.map
Projections & Slices
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Half map: #1

Fileemd_10061_half_map_1.map
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Half map: #2

Fileemd_10061_half_map_2.map
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Sample components

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Entire Mouse cytoplasmic dynein-1 microtubule binding domain decorating ...

EntireName: Mouse cytoplasmic dynein-1 microtubule binding domain decorating microtubules
Number of components: 10

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Component #1: protein, Mouse cytoplasmic dynein-1 microtubule binding domain de...

ProteinName: Mouse cytoplasmic dynein-1 microtubule binding domain decorating microtubules
Recombinant expression: No

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Component #2: protein, Tubulin

ProteinName: Tubulin / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)

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Component #3: protein, dynein-1 microtubule binding

ProteinName: dynein-1 microtubule binding / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)

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Component #4: protein, Tubulin alpha-1B chain

ProteinName: Tubulin alpha-1B chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.679051 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: Brain

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Component #5: protein, Tubulin beta chain

ProteinName: Tubulin beta chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.825859 kDa
SourceSpecies: Pig (pig)

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Component #6: protein, MKIAA0325 protein

ProteinName: MKIAA0325 protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.893574 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Component #8: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #9: ligand, GUANOSINE-5'-DIPHOSPHATE

LigandName: GUANOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.443201 kDa

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Component #10: ligand, TAXOL

LigandName: TAXOLPaclitaxel / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.853906 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 59100
3D reconstructionSoftware: RELION / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible
Output model

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