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- EMDB-5212: Structural insights into anti-parallel microtubule crosslinking b... -

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Basic information

Entry
Database: EMDB / ID: EMD-5212
TitleStructural insights into anti-parallel microtubule crosslinking by PRC1, a conserved non-motor microtubule associated protein.
Map dataThis is a 3D map of a truncated version of PRCI
Sample
  • Sample: Truncated form of PRC1
  • Protein or peptide: microtubule
Keywordsmember of MAP65 family
Biological speciesunidentified (others)
Methodhelical reconstruction / cryo EM / Resolution: 30.0 Å
AuthorsSuramanian R / Wilson-Kubalek EM / Arthur CP / Bick MJ / Campbell EA / Darst SA / Milligan RA / Kapoor TM
CitationJournal: 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
DepositionJul 15, 2010-
Header (metadata) releaseSep 10, 2010-
Map releaseSep 10, 2010-
UpdateNov 2, 2010-
Current statusNov 2, 2010Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 14
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5212_1.png

Downloads & links

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Map

FileDownload / File: emd_5212.map.gz / Format: CCP4 / Size: 11.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a 3D map of a truncated version of PRCI
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.5 Å/pix.
x 103 pix.
= 360.5 Å		3.5 Å/pix.
x 171 pix.
= 598.5 Å		3.5 Å/pix.
x 171 pix.
= 598.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 3.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 14
Minimum - Maximum-26.0 - 49.0
Average (Standard dev.)3.38414 (±9.65236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions171171103
Spacing171171103
CellA: 598.5 Å / B: 598.5 Å / C: 360.5 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.53.53.5
M x/y/z171171103
origin x/y/z0.0000.0000.000
length x/y/z598.500598.500360.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS171171103
D min/max/mean-26.00049.0003.384

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Supplemental data

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Sample components

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Entire : Truncated form of PRC1

EntireName: Truncated form of PRC1
Components
  • Sample: Truncated form of PRC1
  • Protein or peptide: microtubule

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Supramolecule #1000: Truncated form of PRC1

SupramoleculeName: Truncated form of PRC1 / type: sample / ID: 1000 / Details: complex of microtubule and protein / Number unique components: 2

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Macromolecule #1: microtubule

MacromoleculeName: microtubule / type: protein_or_peptide / ID: 1 / Name.synonym: tubulin / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: unidentified (others)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual

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Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: gatan side entry / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: phoelix
CTF correctionDetails: phoelix

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