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- EMDB-9004: Cryo-EM structure of C. elegans GDP-microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-9004
TitleCryo-EM structure of C. elegans GDP-microtubule
Map dataCryo-EM structure of C. elegans GDP-microtubules
Sample
  • Organelle or cellular component: microtubule
    • Protein or peptide: Tubulin alpha-2 chain
    • Protein or peptide: Tubulin beta-2 chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsCytoskeletal protein / STRUCTURAL PROTEIN
Function / homology
Function and homology information


COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Intraflagellar transport / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / meiotic spindle organization / embryo development ending in birth or egg hatching / centrosome localization / tubulin complex ...COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Intraflagellar transport / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / meiotic spindle organization / embryo development ending in birth or egg hatching / centrosome localization / tubulin complex / establishment of mitotic spindle orientation / regulation of cytokinesis / spindle microtubule / protein localization / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
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-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
Similarity search - Domain/homology
Tubulin alpha-2 chain / Tubulin beta-2 chain
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsChaaban S / Jariwala S
Funding support Canada, 3 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-137055 Canada
Canadian Institutes of Health Research (CIHR)PJT-148702 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)03791 Canada
CitationJournal: Dev Cell / Year: 2018
Title: The Structure and Dynamics of C. elegans Tubulin Reveals the Mechanistic Basis of Microtubule Growth.
Authors: Sami Chaaban / Shashank Jariwala / Chieh-Ting Hsu / Stefanie Redemann / Justin M Kollman / Thomas Müller-Reichert / David Sept / Khanh Huy Bui / Gary J Brouhard /
Abstract: The dynamic instability of microtubules is a conserved and fundamental mechanism in eukaryotes. Yet microtubules from different species diverge in their growth rates, lattice structures, and ...The dynamic instability of microtubules is a conserved and fundamental mechanism in eukaryotes. Yet microtubules from different species diverge in their growth rates, lattice structures, and responses to GTP hydrolysis. Therefore, we do not know what limits microtubule growth, what determines microtubule structure, or whether the mechanisms of dynamic instability are universal. Here, we studied microtubules from the nematode C. elegans, which have strikingly fast growth rates and non-canonical lattices in vivo. Using a reconstitution approach, we discovered that C. elegans microtubules combine intrinsically fast growth with very frequent catastrophes. We solved the structure of C. elegans microtubules to 4.8 Å and discovered sequence divergence in the lateral contact loops, one of which is ordered in C. elegans but unresolved in other species. We provide direct evidence that C. elegans tubulin has a higher free energy in solution and propose a model wherein the ordering of lateral contact loops activates tubulin for growth.
History
DepositionJul 27, 2018-
Header (metadata) releaseAug 8, 2018-
Map releaseOct 10, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 8.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6e88
  • Surface level: 8.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6e88
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9004.png

Downloads & links

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Map

FileDownload / File: emd_9004.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of C. elegans GDP-microtubules
Voxel sizeX=Y=Z: 1.373 Å
Density
Contour LevelBy AUTHOR: 8.039999999999999 / Movie #1: 8.04
Minimum - Maximum0.0 - 33.362082999999998
Average (Standard dev.)1.1610311 (±2.6082835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 343.25 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3731.3731.373
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z343.250343.250343.250
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean0.00033.3621.161

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Supplemental data

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Sample components

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Entire : microtubule

EntireName: microtubule
Components
  • Organelle or cellular component: microtubule
    • Protein or peptide: Tubulin alpha-2 chain
    • Protein or peptide: Tubulin beta-2 chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: microtubule

SupramoleculeName: microtubule / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: C. elegans microtubules polymerized in the presence of GTP
Source (natural)Organism: Caenorhabditis elegans (invertebrata) / Strain: N2
Molecular weightTheoretical: 165 kDa/nm

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Macromolecule #1: Tubulin alpha-2 chain

MacromoleculeName: Tubulin alpha-2 chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata) / Strain: N2
Molecular weightTheoretical: 48.467609 KDa
SequenceString: MREVISIHVG QAGVQIGNAC WELYCLEHGI QPDGTMPTQS TNEGESFTTF FSDTGSGRYV PRSIFVDLEP TVVDEIRTGT YKKLFHPEQ MITGKEDAAN NYARGHYTVG KELIDTVLDR IRRLADNCSG LQGFFVFHSF GGGTGSGFTS LLMERLSVDY G KKSKLEFS ...String:
MREVISIHVG QAGVQIGNAC WELYCLEHGI QPDGTMPTQS TNEGESFTTF FSDTGSGRYV PRSIFVDLEP TVVDEIRTGT YKKLFHPEQ MITGKEDAAN NYARGHYTVG KELIDTVLDR IRRLADNCSG LQGFFVFHSF GGGTGSGFTS LLMERLSVDY G KKSKLEFS IYPAPQVSTA VVEPYNSILT THTTLEHSDC AFMVDNEAIY DICRRNLDVE RPSYTNLNRI ISQVVSSITA SL RFDGALN VDLNEFQTNL VPYPRIHFPL AAYTPLISAE KAYHEALSVS DITNSCFEPA NQMVKCDPRH GKYMAVCLLY RGD VVPKDV NTAIAAIKTK RTIQFVDWCP TGFKVGINYQ PPTVVPGGDL AKVPRAVCML SNTTAIAEAW SRLDYKFDLM YAKR AFVHW YVGEGMEEGE FTEAREDLAA LEKDYEEVG

UniProtKB: Tubulin alpha-2 chain

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Macromolecule #2: Tubulin beta-2 chain

MacromoleculeName: Tubulin beta-2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata) / Strain: N2
Molecular weightTheoretical: 47.843988 KDa
SequenceString: MREIVHVQAG QCGNQIGSKF WEVISDEHGI QPDGTFKGET DLQLERIDVY YNEANNGKYV PRAVLVDLEP GTMDSVRSGP FGQLFRPDN FVFGQSGAGN NWAKGHYTEG AELVDNVLDV IRKEAEGCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMSSFS ...String:
MREIVHVQAG QCGNQIGSKF WEVISDEHGI QPDGTFKGET DLQLERIDVY YNEANNGKYV PRAVLVDLEP GTMDSVRSGP FGQLFRPDN FVFGQSGAGN NWAKGHYTEG AELVDNVLDV IRKEAEGCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMSSFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICYRTLKLT NPTYGDLNHL VSLTMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLSAKG TQAYRALTVA ELTQQMFDAK NMMAACDPRH GRYLTVAAMF RGR MSMREV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMAAT FVGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLISEYQQY Q

UniProtKB: Tubulin beta-2 chain

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Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

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Macromolecule #4: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.9
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 29.33 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16574
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6e88:
Cryo-EM structure of C. elegans GDP-microtubule

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