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Yorodumi- PDB-3jaw: Atomic model of a microtubule seam based on a cryo-EM reconstruct... -
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-Basic information
Entry | Database: PDB / ID: 3jaw | ||||||
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Title | Atomic model of a microtubule seam based on a cryo-EM reconstruction of the EB3-bound microtubule (merged dataset containing tubulin bound to GTPgammaS, GMPCPP, and GDP) | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / microtubule / EB3 / seam | ||||||
Function / homology | Function and homology information Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / microtubule / GTPase activity / GTP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Zhang, R. / Nogales, E. | ||||||
Citation | Journal: Cell / Year: 2015 Title: Mechanistic Origin of Microtubule Dynamic Instability and Its Modulation by EB Proteins. Authors: Rui Zhang / Gregory M Alushin / Alan Brown / Eva Nogales / Abstract: Microtubule (MT) dynamic instability is driven by GTP hydrolysis and regulated by microtubule-associated proteins, including the plus-end tracking end-binding protein (EB) family. We report six cryo- ...Microtubule (MT) dynamic instability is driven by GTP hydrolysis and regulated by microtubule-associated proteins, including the plus-end tracking end-binding protein (EB) family. We report six cryo-electron microscopy (cryo-EM) structures of MTs, at 3.5 Å or better resolution, bound to GMPCPP, GTPγS, or GDP, either decorated with kinesin motor domain after polymerization or copolymerized with EB3. Subtle changes around the E-site nucleotide during hydrolysis trigger conformational changes in α-tubulin around an "anchor point," leading to global lattice rearrangements and strain generation. Unlike the extended lattice of the GMPCPP-MT, the EB3-bound GTPγS-MT has a compacted lattice that differs in lattice twist from that of the also compacted GDP-MT. These results and the observation that EB3 promotes rapid hydrolysis of GMPCPP suggest that EB proteins modulate structural transitions at growing MT ends by recognizing and promoting an intermediate state generated during GTP hydrolysis. Our findings explain both EBs end-tracking behavior and their effect on microtubule dynamics. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3jaw.cif.gz | 349.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jaw.ent.gz | 279.2 KB | Display | PDB format |
PDBx/mmJSON format | 3jaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jaw_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3jaw_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3jaw_validation.xml.gz | 51.2 KB | Display | |
Data in CIF | 3jaw_validation.cif.gz | 76.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/3jaw ftp://data.pdbj.org/pub/pdb/validation_reports/ja/3jaw | HTTPS FTP |
-Related structure data
Related structure data | 6354MC 6347C 6348C 6349C 6350C 6351C 6352C 6353C 6355C 3jakC 3jalC 3jarC 3jasC 3jatC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 1 / Rise per n subunits: 9.44 Å / Rotation per n subunits: -27.71 °) |
-Components
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4 #2: Protein | Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554 #3: Chemical | #4: Chemical | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 14.6 MDa / Experimental value: NO | |||||||||||||||||||||||||
Buffer solution | Name: BRB80 / pH: 6.8 Details: 80 mM PIPES, 1 mM EGTA, 1 mM MgCl2, 1 mM DTT, 0.05% Nonidet P-40 | |||||||||||||||||||||||||
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: 400 mesh C-flat 1.2/1.3 EM grid, glow discharged in Ar/O2 gas (Solarus, Gatan Inc) | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temp: 90.4 K / Humidity: 95 % Details: Blot once for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK II). Method: Blot once for 4 seconds before plunging. |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN / Date: May 16, 2013 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 27500 X / Calibrated magnification: 27500 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Gatan 626 holder / Temperature: 90 K |
Image recording | Electron dose: 27.6 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) Details: The camera was operated in counting mode with a dose rate of ~8 electrons/pixel/s. A total exposure time of 6 seconds was fractionated into 20 movie frames. |
Image scans | Num. digital images: 922 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: CTFFIND4, each particle | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 27.71 ° / Axial rise/subunit: 9.44 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Method: projection matching / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79702 / Nominal pixel size: 1.32 Å / Actual pixel size: 1.32 Å / Details: asymmetric (C1) reconstruction / Symmetry type: HELICAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.9→118.8 Å / Cor.coef. Fo:Fc: 0.881 / SU B: 52.885 / SU ML: 0.722 / σ(F): 0 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 288.25 Å2 / Biso mean: 72.487 Å2 / Biso min: 18.5 Å2
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Refinement step | Cycle: LAST / Resolution: 3.9→118.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.9→4.001 Å / Total num. of bins used: 20
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