+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44762 | |||||||||
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Title | Structure of alpha1B and betaI/IVb microtubule bound to GMPCPP | |||||||||
Map data | Full B-factor sharpened map of a1B/bI bIVb microtubule | |||||||||
Sample |
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Keywords | human microtubule / tubulin isoforms / cytoskeleton / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information odontoblast differentiation / Post-chaperonin tubulin folding pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / cytoskeleton-dependent intracellular transport / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly ...odontoblast differentiation / Post-chaperonin tubulin folding pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / cytoskeleton-dependent intracellular transport / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / COPI-independent Golgi-to-ER retrograde traffic / Kinesins / Hedgehog 'off' state / Assembly and cell surface presentation of NMDA receptors / GTPase activating protein binding / COPI-dependent Golgi-to-ER retrograde traffic / natural killer cell mediated cytotoxicity / intercellular bridge / regulation of synapse organization / nuclear envelope lumen / MHC class I protein binding / cytoplasmic microtubule / Recycling pathway of L1 / microtubule-based process / RHOH GTPase cycle / RHO GTPases activate IQGAPs / spindle assembly / cellular response to interleukin-4 / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / 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 / 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 / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / PKR-mediated signaling / mitotic spindle / structural constituent of cytoskeleton / 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / cell body / microtubule / Potential therapeutics for SARS / cytoskeleton / membrane raft / protein domain specific binding / cell division / GTPase activity / ubiquitin protein ligase binding / Neutrophil degranulation / GTP binding / protein-containing complex binding / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Zehr EA / Roll-Mecak A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Biorxiv / Year: 2023 Title: Cryo-EM structures of human alpha 1B/ beta I+ beta IVb microtubules shed light on isoform specific assembly Authors: Zehr EA / Roll-Mecak A | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44762.map.gz | 30 MB | EMDB map data format | |
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Header (meta data) | emd-44762-v30.xml emd-44762.xml | 25.8 KB 25.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44762_fsc.xml | 25.8 KB | Display | FSC data file |
Images | emd_44762.png | 46.3 KB | ||
Masks | emd_44762_msk_1.map | 699 MB | Mask map | |
Filedesc metadata | emd-44762.cif.gz | 6.9 KB | ||
Others | emd_44762_additional_1.map.gz emd_44762_additional_2.map.gz emd_44762_half_map_1.map.gz emd_44762_half_map_2.map.gz | 560.5 MB 8.8 MB 563.1 MB 562.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44762 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44762 | HTTPS FTP |
-Validation report
Summary document | emd_44762_validation.pdf.gz | 664.1 KB | Display | EMDB validaton report |
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Full document | emd_44762_full_validation.pdf.gz | 663.7 KB | Display | |
Data in XML | emd_44762_validation.xml.gz | 27 KB | Display | |
Data in CIF | emd_44762_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44762 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44762 | HTTPS FTP |
-Related structure data
Related structure data | 9bp6MC 42916 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_44762.map.gz / Format: CCP4 / Size: 699 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Full B-factor sharpened map of a1B/bI bIVb microtubule | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_44762_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Full raw map of a1B/bI bIVb microtubule
File | emd_44762_additional_1.map | ||||||||||||
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Annotation | Full raw map of a1B/bI bIVb microtubule | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Full map of a1B/bI bIVb microtubule modified with DeepEMhancer
File | emd_44762_additional_2.map | ||||||||||||
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Annotation | Full map of a1B/bI bIVb microtubule modified with DeepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: First half-map of a1B/bI bIVb microtubule
File | emd_44762_half_map_1.map | ||||||||||||
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Annotation | First half-map of a1B/bI bIVb microtubule | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Second half-map of a1B/bI bIVb microtubule
File | emd_44762_half_map_2.map | ||||||||||||
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Annotation | Second half-map of a1B/bI bIVb microtubule | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : alpha1B and betaI/IVb microtubule
Entire | Name: alpha1B and betaI/IVb microtubule |
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Components |
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-Supramolecule #1: alpha1B and betaI/IVb microtubule
Supramolecule | Name: alpha1B and betaI/IVb microtubule / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Microtubules were double-cycled with GMPCPP |
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Source (natural) | Organism: Homo sapiens (human) / Organ: kidney / Location in cell: cytoplasm |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: Tubulin alpha-1B chain
Macromolecule | Name: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) / Organ: kidney / Location in cell: cytoplasm |
Molecular weight | Theoretical: 50.204445 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 RLISQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRSIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY UniProtKB: Tubulin alpha-1B chain |
-Macromolecule #2: Tubulin beta chain
Macromolecule | Name: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) / Organ: kidney / Location in cell: cytoplasm |
Molecular weight | Theoretical: 49.717629 KDa |
Sequence | String: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQVFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMAVT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEED FGEEAEEEA UniProtKB: Tubulin beta chain |
-Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / 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: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
Macromolecule | Name: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: G2P |
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Molecular weight | Theoretical: 521.208 Da |
Chemical component information | ChemComp-G2P: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.1 mg/mL | |||||||||||||||
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Buffer | pH: 7 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 100 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 303 K / Instrument: LEICA EM GP Details: Double-cycled GMPCPP microtubules were diluted to 2.5uM in Brb80 buffer. 5 ul of microtubules were applied to glow-discharged cryo-EM grid and allowed to absorb for 30 sec.. | |||||||||||||||
Details | Microtubules were double-cycled with GMPCPP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Software | Name: SerialEM |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number real images: 6930 / Average exposure time: 7.8 sec. / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Residue range: 1-437 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Software | Name: Coot |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation |
Output model | PDB-9bp6: |