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- PDB-8sh7: TUBB4B and TUBA1A Heterodimer from Human Respiratory Doublet Micr... -

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Basic information

Entry
Database: PDB / ID: 8sh7
TitleTUBB4B and TUBA1A Heterodimer from Human Respiratory Doublet Microtubules
Components
  • Tubulin alpha-1A chain
  • Tubulin beta-4B chain
KeywordsSTRUCTURAL PROTEIN / Cilia / Axoneme / Microtubule
Function / homology
Function and homology information


Post-chaperonin tubulin folding pathway / axonemal microtubule / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / cytoskeleton-dependent intracellular transport / Sealing of the nuclear envelope (NE) by ESCRT-III ...Post-chaperonin tubulin folding pathway / axonemal microtubule / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / cytoskeleton-dependent intracellular transport / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / neuron projection arborization / Gap junction assembly / Formation of tubulin folding intermediates by CCT/TriC / cerebellar cortex morphogenesis / dentate gyrus development / COPI-independent Golgi-to-ER retrograde traffic / natural killer cell mediated cytotoxicity / pyramidal neuron differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / Assembly and cell surface presentation of NMDA receptors / centrosome cycle / motor behavior / COPI-dependent Golgi-to-ER retrograde traffic / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / intercellular bridge / startle response / microtubule polymerization / Recycling pathway of L1 / locomotory exploration behavior / RHO GTPases activate IQGAPs / MHC class I protein binding / Hedgehog 'off' state / response to tumor necrosis factor / microtubule-based process / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / response to mechanical stimulus / Mitotic Prometaphase / homeostasis of number of cells within a tissue / EML4 and NUDC in mitotic spindle formation / condensed chromosome / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / cellular response to calcium ion / MHC class II antigen presentation / adult locomotory behavior / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / synapse organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / neuron migration / visual learning / neuromuscular junction / PKR-mediated signaling / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / memory / mitotic spindle / microtubule cytoskeleton organization / recycling endosome / cerebral cortex development / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / extracellular vesicle / unfolded protein binding / double-stranded RNA binding / mitotic cell cycle / gene expression / neuron apoptotic process / microtubule / cytoskeleton / hydrolase activity / protein heterodimerization activity / cell division / GTPase activity / Neutrophil degranulation / protein-containing complex binding / GTP binding / structural molecule activity / extracellular exosome / extracellular region / identical protein binding / metal ion binding / nucleus
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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta-4B chain / Tubulin alpha-1A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsAnderson, J.R. / Gui, M. / Brown, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM141109 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5F30HL162128 United States
The Pew Charitable Trusts United States
CitationJournal: To Be Published
Title: TUBB4B variants specifically impact ciliary function, causing a ciliopathic spectrum
Authors: Anderson, J.R. / Gui, M. / Brown, A.
History
DepositionApr 13, 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

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Assembly

Deposited unit
A: Tubulin alpha-1A chain
B: Tubulin beta-4B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0575
Polymers100,0662
Non-polymers9913
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Tubulin alpha-1A chain / / Alpha-tubulin 3 / Tubulin B-alpha-1 / Tubulin alpha-3 chain


Mass: 50188.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Respiratory epithelial cells / References: UniProt: Q71U36
#2: Protein Tubulin beta-4B chain / / Tubulin beta-2 chain / Tubulin beta-2C chain


Mass: 49877.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Respiratory epithelial cells / References: UniProt: P68371
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: TUBB4B and TUBA1A Heterodimer from Human Respiratory Doublet Microtubules
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.0996 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.3
SpecimenEmbedding 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: 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: 64000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.5/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Linux / Type: package
EM software
IDNameCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208558 / Symmetry type: POINT

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