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- EMDB-4303: Cryo-EM subtomogram average of IFT complex B and inhibited dynein... -

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Basic information

Entry
Database: EMDB / ID: EMD-4303
TitleCryo-EM subtomogram average of IFT complex B and inhibited dynein-1b in anterograde IFT trains (Chlamydomonas reinhardtii)
Map dataCryo-EM stubtomogram average of IFT complex B and inhibited dynein-1b in anterograde IFT trains (Chlamydomonas reinhardtii)
Sample
  • Complex: Intraflagellar transport complex B and inhibited dynein-1b
Function / homology
Function and homology information


intraciliary transport involved in cilium assembly / nitric-oxide synthase inhibitor activity / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / negative regulation of phosphorylation / intraciliary retrograde transport / visual behavior / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / intraciliary transport ...intraciliary transport involved in cilium assembly / nitric-oxide synthase inhibitor activity / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / negative regulation of phosphorylation / intraciliary retrograde transport / visual behavior / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / intraciliary transport / dynein light chain binding / regulation of cilium assembly / ciliary transition zone / dynein heavy chain binding / Activation of BIM and translocation to mitochondria / embryonic skeletal system morphogenesis / motile cilium assembly / ciliary tip / Intraflagellar transport / negative regulation of nitric oxide biosynthetic process / cell projection organization / ciliary plasm / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / determination of left/right symmetry / microtubule motor activity / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / motile cilium / microtubule-based movement / Macroautophagy / ciliary base / pericentriolar material / dynein intermediate chain binding / tertiary granule membrane / axoneme / ficolin-1-rich granule membrane / cilium assembly / spermatid development / enzyme inhibitor activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / axon cytoplasm / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / centriole / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / substantia nigra development / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / filopodium / RHO GTPases Activate Formins / kinetochore / apical part of cell / HCMV Early Events / Aggrephagy / mitotic spindle / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / site of double-strand break / scaffold protein binding / nuclear membrane / methylation / microtubule / cytoskeleton / nuclear speck / nuclear body / cilium / ciliary basal body / DNA repair / apoptotic process / DNA damage response / centrosome / Neutrophil degranulation / protein-containing complex binding / nucleolus / enzyme binding / Golgi apparatus / ATP hydrolysis activity / mitochondrion / extracellular space / DNA binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Cytoplasmic dynein 2 light intermediate chain 1 / Cytoplasmic dynein 2 intermediate chain 1 / : / Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase domain / Dynein light chain roadblock-type 1/2 / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily ...Cytoplasmic dynein 2 light intermediate chain 1 / Cytoplasmic dynein 2 intermediate chain 1 / : / Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase domain / Dynein light chain roadblock-type 1/2 / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Dynein light chain, type 1/2, conserved site / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / 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, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / : / Dynein heavy chain, ATPase lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / 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 / Winged helix-like DNA-binding domain superfamily / 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 2 heavy chain 1 / Methylated-DNA--protein-cysteine methyltransferase / Dynein light chain 1, cytoplasmic / Cytoplasmic dynein 2 light intermediate chain 1 / Cytoplasmic dynein 2 intermediate chain 1 / Cytoplasmic dynein 2 intermediate chain 2 / Dynein light chain roadblock-type 1
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 37.0 Å
AuthorsPigino G / Jordan MA
CitationJournal: Nat Cell Biol / Year: 2018
Title: The cryo-EM structure of intraflagellar transport trains reveals how dynein is inactivated to ensure unidirectional anterograde movement in cilia.
Authors: Mareike A Jordan / Dennis R Diener / Ludek Stepanek / Gaia Pigino /
Abstract: Movement of cargos along microtubules plays key roles in diverse cellular processes, from signalling to mitosis. In cilia, rapid movement of ciliary components along the microtubules to and from the ...Movement of cargos along microtubules plays key roles in diverse cellular processes, from signalling to mitosis. In cilia, rapid movement of ciliary components along the microtubules to and from the assembly site is essential for the assembly and disassembly of the structure itself. This bidirectional transport, known as intraflagellar transport (IFT), is driven by the anterograde motor kinesin-2 and the retrograde motor dynein-1b (dynein-2 in mammals). However, to drive retrograde transport, dynein-1b must first be delivered to the ciliary tip by anterograde IFT. Although, the presence of opposing motors in bidirectional transport processes often leads to periodic stalling and slowing of cargos, IFT is highly processive. Using cryo-electron tomography, we show that a tug-of-war between kinesin-2 and dynein-1b is prevented by loading dynein-1b onto anterograde IFT trains in an autoinhibited form and by positioning it away from the microtubule track to prevent binding. Once at the ciliary tip, dynein-1b must transition into an active form and engage microtubules to power retrograde trains. These findings provide a striking example of how coordinated structural changes mediate the behaviour of complex cellular machinery.
History
DepositionFeb 21, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseOct 31, 2018-
UpdateNov 7, 2018-
Current statusNov 7, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.414
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.414
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6sc2
  • Surface level: 0.414
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6sc2
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4303_1.png

emd_4303_2.png

Downloads & links

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Map

FileDownload / File: emd_4303.map.gz / Format: CCP4 / Size: 306.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM stubtomogram average of IFT complex B and inhibited dynein-1b in anterograde IFT trains (Chlamydomonas reinhardtii)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.13 Å/pix.
x 54 pix.
= 763.02 Å		14.13 Å/pix.
x 44 pix.
= 621.72 Å		14.13 Å/pix.
x 33 pix.
= 466.29 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 14.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.414 / Movie #1: 0.414
Minimum - Maximum-2.6620708 - 3.8092673
Average (Standard dev.)0.032200836 (±0.5031689)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-21-250
Dimensions443354
Spacing334454
CellA: 466.29 Å / B: 621.72003 Å / C: 763.02 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z14.1314.1314.13
M x/y/z334454
origin x/y/z0.0000.0000.000
length x/y/z466.290621.720763.020
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS-25-210
NC/NR/NS334454
D min/max/mean-2.6623.8090.032

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Supplemental data

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Sample components

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Entire : Intraflagellar transport complex B and inhibited dynein-1b

EntireName: Intraflagellar transport complex B and inhibited dynein-1b
Components
  • Complex: Intraflagellar transport complex B and inhibited dynein-1b

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Supramolecule #1: Intraflagellar transport complex B and inhibited dynein-1b

SupramoleculeName: Intraflagellar transport complex B and inhibited dynein-1b
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-124

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state2D array

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R3.5/1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 2.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 37.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET (ver. 1.11.0) / Number subtomograms used: 750
ExtractionNumber tomograms: 15 / Number images used: 750 / Software - Name: IMOD (ver. 4.9.2)
CTF correctionSoftware - Name: CTFPHASEFLIP
Final angle assignmentType: NOT APPLICABLE

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