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- PDB-5ucy: Cryo-EM map of protofilament of microtubule doublet -

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Entry
Database: PDB / ID: 5ucy
TitleCryo-EM map of protofilament of microtubule doublet
DescriptorTubulin alpha chain, Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / cilia / doublet / protofilament / tubulin
Specimen sourceTetrahymena thermophila / eukaryote
MethodElectron microscopy (4.6 A resolution / Single particle)
AuthorsIchikawa, M. / Liu, D. / Kastritis, P.L. / Basu, K. / Bui, K.H.
CitationNat Commun, 2017, 8, 15035-15035

Nat Commun, 2017, 8, 15035-15035 StrPapers
Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins.
Muneyoshi Ichikawa / Dinan Liu / Panagiotis L Kastritis / Kaustuv Basu / Tzu Chin Hsu / Shunkai Yang / Khanh Huy Bui

DateDeposition: Dec 22, 2016 / Release: May 10, 2017 / Last modification: May 17, 2017

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Assembly

Deposited unit
A: Tubulin alpha chain
B: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7885
Polyers96,7972
Non-polymers9913
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Polypeptide(L)Tubulin alpha chain / Alpha-tubulin


Mass: 48788.254 Da / Num. of mol.: 1 / Source: (natural) Tetrahymena thermophila / eukaryote / References: UniProt: P41351
#2: Polypeptide(L)Tubulin beta chain / Beta-tubulin


Mass: 48009.199 Da / Num. of mol.: 1 / Source: (natural) Tetrahymena thermophila / eukaryote / References: UniProt: P41352
#3: ChemicalChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP *YM


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3
#4: ChemicalChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg
#5: ChemicalChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP *YM


Mass: 443.201 Da / Num. of mol.: 1 / Formula: C10H15N5O11P2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Protofilament from ciliary microtubule doublet / Type: ORGANELLE OR CELLULAR COMPONENT
Specimen supportGrid material: COPPER / Grid mesh size: 200 /inch. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 / Details: Blot force 3 for 5 seconds

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Processing

3D reconstructionResolution: 4.6 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 23
Details: 23 boxes of the protofilament are boxed out from the doublet map (EMD-8528), aligned and averaged using subtomogram averaging software.
Atomic model buildingRef protocol: BACKBONE TRACE / Ref space: REAL / Target criteria: minimization global

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