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

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Basic information

Entry
Database: PDB / ID: 5ucy
TitleCryo-EM map of protofilament of microtubule doublet
Components
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / cilia / doublet / protofilament / tubulin
Function / homologyBeta tubulin, autoregulation binding site / Tubulin C-terminal domain / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ, GTPase domain superfamily / Tubulin, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, conserved site / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, GTPase domain / Beta tubulin ...Beta tubulin, autoregulation binding site / Tubulin C-terminal domain / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ, GTPase domain superfamily / Tubulin, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, conserved site / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, GTPase domain / Beta tubulin / Alpha tubulin / Tubulin / Tubulin subunits alpha, beta, and gamma signature. / Tubulin-beta mRNA autoregulation signal. / Tubulin/FtsZ family, GTPase domain / microtubule-based process / structural constituent of cytoskeleton / microtubule / GTPase activity / GTP binding / cytoplasm / Tubulin alpha chain / Tubulin beta chain
Function and homology information
Specimen sourceTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.6 Å resolution
AuthorsIchikawa, M. / Liu, D. / Kastritis, P.L. / Basu, K. / Bui, K.H.
CitationJournal: Nat Commun / Year: 2017
Title: Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins.
Authors: Muneyoshi Ichikawa / Dinan Liu / Panagiotis L Kastritis / Kaustuv Basu / Tzu Chin Hsu / Shunkai Yang / Khanh Huy Bui
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 22, 2016 / Release: May 10, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 10, 2017Structure modelrepositoryInitial release
1.1May 17, 2017Structure modelDatabase references
1.2Sep 27, 2017Structure modelAuthor supporting evidence / Data collectionem_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization
1.3May 16, 2018Structure modelData collection / Derived calculationspdbx_point_symmetry / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list

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Structure visualization

Movie
  • Biological unit as complete point assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-8539
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-8539
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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

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

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


Theoretical massNumber of molelcules
Total (without water)293,36415
Polyers290,3926
Non-polymers2,9729
Water0
TypeNameSymmetry operationNumber
point symmetry operation3
2


  • idetical with deposited unit in distinct coordinate
  • point asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1

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Components

#1: Protein/peptide Tubulin alpha chain / Alpha-tubulin


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


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


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Mass: 443.201 Da / Num. of mol.: 1 / Formula: C10H15N5O11P2 / Guanosine diphosphate / Comment: GDP (energy-carrying molecule) *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Protofilament from ciliary microtubule doublet / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1, 2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB255
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 kelvins / Details: Blot force 3 for 5 seconds

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 / Nominal defocus max: 3800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.4 sec. / Electron dose: 45 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 4 / Number of real images: 5983
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 7 / Used frames/image: 1-7

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Processing

EM software
IDNameVersionCategory
1E2helixboxer2particle selection
2EPU1.6image acquisition
4ctffind4CTF correction
7Chimeramodel fitting
9PHENIXmodel refinement
10MATLABinitial Euler assignment
11Tom Av3final Euler assignment
13Tom AV33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 127428
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.6 Å / 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.
Symmetry type: POINT
Atomic model buildingRef protocol: BACKBONE TRACE / Ref space: REAL / Target criteria: minimization global

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