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Yorodumi- PDB-3nrx: Insights into anti-parallel microtubule crosslinking by PRC1, a c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nrx | ||||||
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Title | Insights into anti-parallel microtubule crosslinking by PRC1, a conserved non-motor microtubule binding protein | ||||||
Components | Protein regulator of cytokinesis 1 | ||||||
Keywords | PROTEIN BINDING / spectrin fold / microtubule binding domain | ||||||
Function / homology | Function and homology information contractile ring / mitotic spindle midzone assembly / mitotic spindle elongation / mitotic spindle midzone / RHO GTPases activate CIT / intercellular bridge / kinesin binding / regulation of cytokinesis / spindle microtubule / spindle pole ...contractile ring / mitotic spindle midzone assembly / mitotic spindle elongation / mitotic spindle midzone / RHO GTPases activate CIT / intercellular bridge / kinesin binding / regulation of cytokinesis / spindle microtubule / spindle pole / microtubule cytoskeleton organization / spindle / chromosome / microtubule cytoskeleton / midbody / microtubule binding / cell division / positive regulation of cell population proliferation / protein kinase binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Kapoor, T.M. / Subramanian, R. / Wilson-Kubalek, E.M. / Arthur, C.P. / Bick, M.J. / Campbell, E.A. / Darst, S.A. / Milligan, R.A. | ||||||
Citation | Journal: Cell / Year: 2010 Title: Insights into antiparallel microtubule crosslinking by PRC1, a conserved nonmotor microtubule binding protein. Authors: Radhika Subramanian / Elizabeth M Wilson-Kubalek / Christopher P Arthur / Matthew J Bick / Elizabeth A Campbell / Seth A Darst / Ronald A Milligan / Tarun M Kapoor / Abstract: Formation of microtubule architectures, required for cell shape maintenance in yeast, directional cell expansion in plants and cytokinesis in eukaryotes, depends on antiparallel microtubule ...Formation of microtubule architectures, required for cell shape maintenance in yeast, directional cell expansion in plants and cytokinesis in eukaryotes, depends on antiparallel microtubule crosslinking by the conserved MAP65 protein family. Here, we combine structural and single molecule fluorescence methods to examine how PRC1, the human MAP65, crosslinks antiparallel microtubules. We find that PRC1's microtubule binding is mediated by a structured domain with a spectrin-fold and an unstructured Lys/Arg-rich domain. These two domains, at each end of a homodimer, are connected by a linkage that is flexible on single microtubules, but forms well-defined crossbridges between antiparallel filaments. Further, we show that PRC1 crosslinks are compliant and do not substantially resist filament sliding by motor proteins in vitro. Together, our data show how MAP65s, by combining structural flexibility and rigidity, tune microtubule associations to establish crosslinks that selectively "mark" antiparallel overlap in dynamic cytoskeletal networks. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nrx.cif.gz | 117.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nrx.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 3nrx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nrx_validation.pdf.gz | 436.3 KB | Display | wwPDB validaton report |
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Full document | 3nrx_full_validation.pdf.gz | 439.2 KB | Display | |
Data in XML | 3nrx_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 3nrx_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/3nrx ftp://data.pdbj.org/pub/pdb/validation_reports/nr/3nrx | HTTPS FTP |
-Related structure data
Related structure data | 5205C 5212C 3nrySC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15838.070 Da / Num. of mol.: 2 / Fragment: UNP residues 341-466 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRC1 / Production host: Escherichia coli (E. coli) / References: UniProt: O43663 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.88 % |
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Crystal grow | Temperature: 277 K / pH: 9.5 Details: 1:1 v/v of protein ( 50 mg/ml in 80 mM PIPES, pH6.8, 1 mM MgCl2, 1 mM EDTA and 150 mM KCl) and reservoir buffer (100 mM CHES, pH 9.5, 30% PEG3000), VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 173 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2009 | |||||||||||||||
Radiation | Monochromator: SINGLE CRYSTAL SIDE-BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.75→25 Å / Num. obs: 24182 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 31.4 | |||||||||||||||
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 2.62 / Rsym value: 0.361 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NRY Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.196 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.79 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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