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- EMDB-1309: Human kinetochore-associated kinesin CENP-E visualized at 17 A re... -

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Basic information

Entry
Database: EMDB / ID: EMD-1309
TitleHuman kinetochore-associated kinesin CENP-E visualized at 17 A resolution bound to microtubules.
Map dataKinetochore-associated kinesin CENP-E motors bound to microtubules
Sample
  • Sample: Human Kinetochore-associated Kinesin CENP-E bound to Microtubules
  • Protein or peptide: Polymerized Tubulin
  • Protein or peptide: Human kinetochore-associated kinesin CENP-E motors
Biological speciesBos taurus (cattle) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsNeumann E / Garcia-Saez I / DeBonis S / Wade RH / Kozielski F / Conway JF
CitationJournal: J Mol Biol / Year: 2006
Title: Human kinetochore-associated kinesin CENP-E visualized at 17 A resolution bound to microtubules.
Authors: E Neumann / I Garcia-Saez / S DeBonis / R H Wade / F Kozielski / J F Conway /
Abstract: The highly dynamic process of cell division is effected, in part, by molecular motors that generate the forces necessary for its enactment. Several members of the kinesin superfamily of motor ...The highly dynamic process of cell division is effected, in part, by molecular motors that generate the forces necessary for its enactment. Several members of the kinesin superfamily of motor proteins are implicated in mitosis, such as CENP-E, which plays essential roles in cell division, including association with the kinetochore to stabilize attachment of chromosomes to microtubules prior to and during their separation. Neither the functional assembly state of CENP-E nor its direction of motion along the polar microtubule are certain. To determine the mode of interaction between CENP-E and microtubules, we have used cryo-electron microscopy to visualize CENP-E motor domains complexed with microtubules and calculated a density map of the complex to 17 A resolution by combining helical and single-particle reconstruction methods. The interface between the motor domain and microtubules was modeled by docking atomic-resolution models of the subunits into the cryoEM density map. Our results support a plus end motion for CENP-E, consistent with features of the crystallographic structure. Despite considerable functional differences from the monomeric transporter kinesin KIF1A and the oppositely directed ncd kinesin, CENP-E appears to share many features of the intermolecular interactions, suggesting that differences in motor function are governed by small variations in the loops at the microtubule interface.
History
DepositionNov 28, 2006-
Header (metadata) releaseDec 11, 2006-
Map releaseDec 11, 2006-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: -35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: -35
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1309.gif

Downloads & links

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Map

FileDownload / File: emd_1309.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationKinetochore-associated kinesin CENP-E motors bound to microtubules
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
3.56 Å/pix.
x 128 pix.
= 455.68 Å		3.56 Å/pix.
x 128 pix.
= 455.68 Å		3.56 Å/pix.
x 128 pix.
= 455.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.56 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 87.0 / Movie #1: -35
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-87.432599999999994 (±41.033900000000003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-63-63-63
Dimensions128128128
Spacing128128128
CellA=B=C: 455.68 Å
α=β=γ: 90 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z3.563.563.56
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z455.680455.680455.680
α/β/γ90.00090.00090.000
start NX/NY/NZ-63-63-63
NX/NY/NZ128128128
MAP C/R/S312
start NC/NR/NS-63-63-63
NC/NR/NS128128128
D min/max/mean-128.000127.000-87.433

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Supplemental data

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Sample components

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Entire : Human Kinetochore-associated Kinesin CENP-E bound to Microtubules

EntireName: Human Kinetochore-associated Kinesin CENP-E bound to Microtubules
Components
  • Sample: Human Kinetochore-associated Kinesin CENP-E bound to Microtubules
  • Protein or peptide: Polymerized Tubulin
  • Protein or peptide: Human kinetochore-associated kinesin CENP-E motors

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Supramolecule #1000: Human Kinetochore-associated Kinesin CENP-E bound to Microtubules

SupramoleculeName: Human Kinetochore-associated Kinesin CENP-E bound to Microtubules
type: sample / ID: 1000
Oligomeric state: One CENP-E motor domain binds to a tubulin heterodimer
Number unique components: 2

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Macromolecule #1: Polymerized Tubulin

MacromoleculeName: Polymerized Tubulin / type: protein_or_peptide / ID: 1 / Name.synonym: Microtubules / Details: cat. no. TL238, Cytoskeleton Inc, Denver CO, USA / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (cattle) / synonym: Cattle / Tissue: Brain

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Macromolecule #2: Human kinetochore-associated kinesin CENP-E motors

MacromoleculeName: Human kinetochore-associated kinesin CENP-E motors / type: protein_or_peptide / ID: 2 / Name.synonym: Mitotic Kinesins / Details: Monomeric Form / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6
Details: 20 mM sodium phosphate, 50 mM NaCl, 1 mM MgCl2, 1 mM EGTA
GridDetails: Holey carbon grid
VitrificationCryogen name: ETHANE / Details: Vitrification carried out in nitrogen atmosphere / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200T
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 7 µm / Number real images: 21 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 39325 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: MRC and Spider
CTF correctionDetails: CTFMIX

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Atomic model buiding 1

SoftwareName: Situs, URO
DetailsThe cryoEM map and the atomic structures of CENP-E and the tubulin dimer were visualized together using the program "O". An initial manual fit was straightforward, and subsequently refined using CoLoRes from the SITUS package, and URO.
RefinementProtocol: RIGID BODY FIT

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