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- PDB-8v3l: Microtubule inner proteins in the 48-nm doublet microtubule from ... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8v3l
TitleMicrotubule inner proteins in the 48-nm doublet microtubule from the proximal region of Tetrahymena thermophila strain K40R
Components
  • BMIP1
  • CCDC81B
KeywordsSTRUCTURAL PROTEIN / Cilia / Axoneme / Doublet Microtubule / Microtubule Inner Protein
Function / homology
Function and homology information


calcium ion binding / nucleoplasm
Similarity search - Function
CCDC81, HU domain 1 / CCDC81, HU domain 2 / CCDC81 eukaryotic HU domain 1 / CCDC81 eukaryotic HU domain 2 / : / EF hand / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...CCDC81, HU domain 1 / CCDC81, HU domain 2 / CCDC81 eukaryotic HU domain 1 / CCDC81 eukaryotic HU domain 2 / : / EF hand / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
EF-hand protein / Uncharacterized protein
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsLegal, T. / Bui, K.H.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-190195 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-04774 Canada
CitationJournal: To Be Published
Title: 48-nm doublet microtubule from the proximal region of Tetrahymena thermophila strain K40R
Authors: Bui, K.H.
History
DepositionNov 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CCDC81B
A1: BMIP1


Theoretical massNumber of molelcules
Total (without water)207,8772
Polymers207,8772
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein CCDC81B


Mass: 179311.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: K40R / References: UniProt: I7M688
#2: Protein BMIP1


Mass: 28564.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: K40R / References: UniProt: I7MB72

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 48-nm proximal repeat unit of microtubule doublet from Tetrahymena thermophila strain K40R
Type: ORGANELLE OR CELLULAR COMPONENT
Details: Single Particle Analysis of the proximal 48-nm repeating unit of the axoneme from intact cilia purified from Tetrahymena strain K40R
Entity ID: all / Source: NATURAL
Molecular weightValue: 7.6 MDa / Experimental value: YES
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: K40R / Organelle: Cilia
Buffer solutionpH: 7.4
SpecimenConc.: 2.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7UCSF ChimeraXmodel fitting
10RELION3.1final Euler assignment
11cryoSPARC2.3final Euler assignment
14PHENIXmodel refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45618 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 32 / Num. of volumes extracted: 2608
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
ID 3D fitting-IDAccession codeChain-IDInitial refinement model-IDSource nameType
11I7MB72A11AlphaFoldin silico model
21I7M688A2AlphaFoldin silico model

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