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Yorodumi- EMDB-40480: TUBB4B and TUBA1A Heterodimer from Human Respiratory Doublet Micr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40480 | ||||||||||||
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Title | TUBB4B and TUBA1A Heterodimer from Human Respiratory Doublet Microtubules | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Cilia / Axoneme / Microtubule / STRUCTURAL PROTEIN | ||||||||||||
Function / homology | Function and homology information Post-chaperonin tubulin folding pathway / axonemal microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport ...Post-chaperonin tubulin folding pathway / axonemal microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / neuron projection arborization / cytoskeleton-dependent intracellular transport / cerebellar cortex morphogenesis / Formation of tubulin folding intermediates by CCT/TriC / dentate gyrus development / Gap junction assembly / COPI-independent Golgi-to-ER retrograde traffic / pyramidal neuron differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / Hedgehog 'off' state / Assembly and cell surface presentation of NMDA receptors / centrosome cycle / motor behavior / COPI-dependent Golgi-to-ER retrograde traffic / natural killer cell mediated cytotoxicity / response to L-glutamate / smoothened signaling pathway / intercellular bridge / regulation of synapse organization / MHC class I protein binding / startle response / locomotory exploration behavior / Recycling pathway of L1 / microtubule polymerization / microtubule-based process / RHO GTPases activate IQGAPs / response to tumor necrosis factor / response to mechanical stimulus / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / condensed chromosome / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / homeostasis of number of cells within a tissue / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / cellular response to calcium ion / AURKA Activation by TPX2 / adult locomotory behavior / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / RHO GTPases Activate Formins / neuron migration / synapse organization / visual learning / neuromuscular junction / PKR-mediated signaling / recycling endosome / cerebral cortex development / mitotic spindle / structural constituent of cytoskeleton / memory / microtubule cytoskeleton organization / Aggrephagy / HCMV Early Events / cytoplasmic ribonucleoprotein granule / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / azurophil granule lumen / microtubule cytoskeleton / double-stranded RNA binding / Regulation of PLK1 Activity at G2/M Transition / unfolded protein binding / extracellular vesicle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / gene expression / neuron apoptotic process / microtubule / cytoskeleton / hydrolase activity / protein heterodimerization activity / cell division / GTPase activity / Neutrophil degranulation / GTP binding / protein-containing complex binding / structural molecule activity / extracellular exosome / extracellular region / identical protein binding / nucleus / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||
Authors | Anderson JR / Gui M / Brown A | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: To Be Published Title: TUBB4B variants specifically impact ciliary function, causing a ciliopathic spectrum Authors: Anderson JR / Gui M / Brown A | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40480.map.gz | 16.1 MB | EMDB map data format | |
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Header (meta data) | emd-40480-v30.xml emd-40480.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40480_fsc.xml | 17.9 KB | Display | FSC data file |
Images | emd_40480.png | 54.9 KB | ||
Masks | emd_40480_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-40480.cif.gz | 5.8 KB | ||
Others | emd_40480_half_map_1.map.gz emd_40480_half_map_2.map.gz | 408 MB 408.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40480 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40480 | HTTPS FTP |
-Validation report
Summary document | emd_40480_validation.pdf.gz | 723.3 KB | Display | EMDB validaton report |
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Full document | emd_40480_full_validation.pdf.gz | 722.8 KB | Display | |
Data in XML | emd_40480_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | emd_40480_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40480 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40480 | HTTPS FTP |
-Related structure data
Related structure data | 8sh7MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40480.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_40480_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40480_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40480_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TUBB4B and TUBA1A Heterodimer from Human Respiratory Doublet Micr...
Entire | Name: TUBB4B and TUBA1A Heterodimer from Human Respiratory Doublet Microtubules |
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Components |
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-Supramolecule #1: TUBB4B and TUBA1A Heterodimer from Human Respiratory Doublet Micr...
Supramolecule | Name: TUBB4B and TUBA1A Heterodimer from Human Respiratory Doublet Microtubules type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 99.6 KDa |
-Macromolecule #1: Tubulin alpha-1A chain
Macromolecule | Name: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50.188441 KDa |
Sequence | String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY UniProtKB: Tubulin alpha-1A chain |
-Macromolecule #2: Tubulin beta-4B chain
Macromolecule | Name: Tubulin beta-4B chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 49.877824 KDa |
Sequence | String: MREIVHLQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLERINVY YNEATGGKYV PRAVLVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String: MREIVHLQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLERINVY YNEATGGKYV PRAVLVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEGE FEEEAEEEVA UniProtKB: Tubulin beta-4B chain |
-Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ChemComp-GDP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.3 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |