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- PDB-5syc: Near-atomic resolution cryo-EM reconstruction of peloruside-stabi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5syc | ||||||||||||
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Title | Near-atomic resolution cryo-EM reconstruction of peloruside-stabilized microtubule | ||||||||||||
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Function / homology | ![]() Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Kellogg, E.H. / Nogales, E. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures. Authors: Elizabeth H Kellogg / Nisreen M A Hejab / Stuart Howes / Peter Northcote / John H Miller / J Fernando Díaz / Kenneth H Downing / Eva Nogales / ![]() ![]() ![]() Abstract: A number of microtubule (MT)-stabilizing agents (MSAs) have demonstrated or predicted potential as anticancer agents, but a detailed structural basis for their mechanism of action is still lacking. ...A number of microtubule (MT)-stabilizing agents (MSAs) have demonstrated or predicted potential as anticancer agents, but a detailed structural basis for their mechanism of action is still lacking. We have obtained high-resolution (3.9-4.2Å) cryo-electron microscopy (cryo-EM) reconstructions of MTs stabilized by the taxane-site binders Taxol and zampanolide, and by peloruside, which targets a distinct, non-taxoid pocket on β-tubulin. We find that each molecule has unique distinct structural effects on the MT lattice structure. Peloruside acts primarily at lateral contacts and has an effect on the "seam" of heterologous interactions, enforcing a conformation more similar to that of homologous (i.e., non-seam) contacts by which it regularizes the MT lattice. In contrast, binding of either Taxol or zampanolide induces MT heterogeneity. In doubly bound MTs, peloruside overrides the heterogeneity induced by Taxol binding. Our structural analysis illustrates distinct mechanisms of these drugs for stabilizing the MT lattice and is of relevance to the possible use of combinations of MSAs to regulate MT activity and improve therapeutic potential. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182 KB | Display | ![]() |
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PDB format | ![]() | 140.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8320MC ![]() 8321C ![]() 8322C ![]() 8323C ![]() 5syeC ![]() 5syfC ![]() 5sygC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 26 / Rise per n subunits: 9.38 Å / Rotation per n subunits: -27.7 °) |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 48679.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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#2: Protein | Mass: 47825.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-Non-polymers , 4 types, 4 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/POU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/POU.gif)
#3: Chemical | ChemComp-GTP / ![]() |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-GDP / ![]() |
#6: Chemical | ChemComp-POU / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: Ternary complex of peloruside-stabilized microtubule lattice, alpha-tubulin, and beta-tubulin Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 6.8 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Protochips CF-1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K Details: Blot for 4 seconds, blot force 10, before plunging into liquid ethane (FEI VITROBOT MARK IV). |
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Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Temperature (max): 93 K / Temperature (min): 93 K |
Image recording | Average exposure time: 0.3 sec. / Electron dose: 8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 312 |
Image scans | Sampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 20 / Used frames/image: 1-20 |
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Processing
EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -27.7 ° / Axial rise/subunit: 9.38 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 27275 Details: Microtubule filaments were manually selected using manualpicker.py. | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17069 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: correlation coefficient |