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- EMDB-2006: Asymmetric reconstruction of GDP microtubules decorated with mono... -

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Basic information

Entry
Database: EMDB / ID: EMD-2006
TitleAsymmetric reconstruction of GDP microtubules decorated with monomeric Mal3
Map dataAsymmetric reconstruction of GDP microtubules decorated with monomeric Mal3
Sample
  • Sample: GDP microtubules decorated with monomeric Mal3
  • Protein or peptide: Alpha tubulin
  • Protein or peptide: Beta tubulin
  • Protein or peptide: Mal3
  • Ligand: guanosine 5'-O-diphosphate
Keywordscytoskeleton / GTPase / end binding / calponin homology
Function / homology: / microtubule-based movement
Function and homology information
Biological speciesSus scrofa (pig) / Schizosaccharomyces pombe (fission yeast) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsMaurer SP / Fourniol FJ / Bohner G / Moores CA / Surrey T
CitationJournal: Cell / Year: 2012
Title: EBs recognize a nucleotide-dependent structural cap at growing microtubule ends.
Authors: Sebastian P Maurer / Franck J Fourniol / Gergő Bohner / Carolyn A Moores / Thomas Surrey /
Abstract: Growing microtubule ends serve as transient binding platforms for essential proteins that regulate microtubule dynamics and their interactions with cellular substructures. End-binding proteins (EBs) ...Growing microtubule ends serve as transient binding platforms for essential proteins that regulate microtubule dynamics and their interactions with cellular substructures. End-binding proteins (EBs) autonomously recognize an extended region at growing microtubule ends with unknown structural characteristics and then recruit other factors to the dynamic end structure. Using cryo-electron microscopy, subnanometer single-particle reconstruction, and fluorescence imaging, we present a pseudoatomic model of how the calponin homology (CH) domain of the fission yeast EB Mal3 binds to the end regions of growing microtubules. The Mal3 CH domain bridges protofilaments except at the microtubule seam. By binding close to the exchangeable GTP-binding site, the CH domain is ideally positioned to sense the microtubule's nucleotide state. The same microtubule-end region is also a stabilizing structural cap protecting the microtubule from depolymerization. This insight supports a common structural link between two important biological phenomena, microtubule dynamic instability and end tracking.
History
DepositionDec 5, 2011-
Header (metadata) releaseJan 6, 2012-
Map releaseMay 31, 2012-
UpdateMay 31, 2012-
Current statusMay 31, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

2006.jpg

Downloads & links

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Map

FileDownload / File: emd_2006.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric reconstruction of GDP microtubules decorated with monomeric Mal3
Voxel sizeX=Y=Z: 1.88 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.03621116 - 0.09649521
Average (Standard dev.)0.00096966 (±0.0142878)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 601.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.881.881.88
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z601.600601.600601.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.0360.0960.001

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Supplemental data

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Sample components

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Entire : GDP microtubules decorated with monomeric Mal3

EntireName: GDP microtubules decorated with monomeric Mal3
Components
  • Sample: GDP microtubules decorated with monomeric Mal3
  • Protein or peptide: Alpha tubulin
  • Protein or peptide: Beta tubulin
  • Protein or peptide: Mal3
  • Ligand: guanosine 5'-O-diphosphate

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Supramolecule #1000: GDP microtubules decorated with monomeric Mal3

SupramoleculeName: GDP microtubules decorated with monomeric Mal3 / type: sample / ID: 1000
Details: tubulin was mixed with GMPCPP microtubule seeds, GTP and monomeric Mal3, and incubated 1-5min at 37degC
Oligomeric state: 13-protofilament microtubule / Number unique components: 3

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Macromolecule #1: Alpha tubulin

MacromoleculeName: Alpha tubulin / type: protein_or_peptide / ID: 1 / Name.synonym: Alpha tubulin / Oligomeric state: Dimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Sus scrofa (pig) / synonym: Pig / Tissue: Brain / Location in cell: cytoplasmic
Molecular weightExperimental: 50 KDa / Theoretical: 50 KDa
SequenceGO: GO: 0006184

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Macromolecule #2: Beta tubulin

MacromoleculeName: Beta tubulin / type: protein_or_peptide / ID: 2 / Name.synonym: Beta tubulin / Oligomeric state: Dimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Sus scrofa (pig) / synonym: Pig / Tissue: Brain / Location in cell: cytoplasmic
Molecular weightExperimental: 100 KDa / Theoretical: 100 KDa
SequenceGO: GO: 0006184

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Macromolecule #4: Mal3

MacromoleculeName: Mal3 / type: protein_or_peptide / ID: 4 / Name.synonym: Mal3 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast) / synonym: fission yeast / Location in cell: cytoplasmic
Molecular weightExperimental: 16 KDa / Theoretical: 16 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceGO: microtubule-based movement

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Macromolecule #3: guanosine 5'-O-diphosphate

MacromoleculeName: guanosine 5'-O-diphosphate / type: ligand / ID: 3 / Name.synonym: GDP / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: unidentified (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.8 / Details: 40mM Pipes, 1mM MgCl2, 1mM EGTA
GridDetails: 300 mesh lacey carbon grid
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot (FEI) / Method: Chamber at 37 degrees C, blot 2s

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 88 K / Max: 98 K / Average: 93 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 208 / Average electron dose: 20 e/Å2 / Details: sampling size 1.88 A per pixel
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: FREALIGN
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, FREALIGN
Details: approximately 173000 tubulin dimers were averaged together in the final map

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