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- EMDB-1036: Structure of a fast kinesin: implications for ATPase mechanism an... -

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Entry
Database: EMDB / ID: EMD-1036
TitleStructure of a fast kinesin: implications for ATPase mechanism and interactions with microtubules.
Map dataNeurospora crassa kinesin monomer (nK355) AMP-PNP state
Sample
  • Sample: neurospora crassa kinesin monomer
  • Protein or peptide: neurospora crassakinesin
  • Protein or peptide: tubulin
Biological speciesNeurospora crassa (fungus)
Methodhelical reconstruction / cryo EM / negative staining / Resolution: 25.0 Å
AuthorsKrebs A
CitationJournal: EMBO J / Year: 2001
Title: Structure of a fast kinesin: implications for ATPase mechanism and interactions with microtubules.
Authors: Y H Song / A Marx / J Müller / G Woehlke / M Schliwa / A Krebs / A Hoenger / E Mandelkow /
Abstract: We determined the crystal structure of the motor domain of the fast fungal kinesin from Neurospora crassa (NcKin). The structure has several unique features. (i) Loop 11 in the switch 2 region is ...We determined the crystal structure of the motor domain of the fast fungal kinesin from Neurospora crassa (NcKin). The structure has several unique features. (i) Loop 11 in the switch 2 region is ordered and enables one to describe the complete nucleotide-binding pocket, including three inter-switch salt bridges between switch 1 and 2. (ii) Loop 9 in the switch 1 region bends outwards, making the nucleotide-binding pocket very wide. The displacement in switch 1 resembles that of the G-protein ras complexed with its guanosine nucleotide exchange factor. (iii) Loop 5 in the entrance to the nucleotide-binding pocket is remarkably long and interacts with the ribose of ATP. (iv) The linker and neck region is not well defined, indicating that it is mobile. (v) Image reconstructions of ice-embedded microtubules decorated with NcKin show that it interacts with several tubulin subunits, including a central beta-tubulin monomer and the two flanking alpha-tubulin monomers within the microtubule protofilament. Comparison of NcKin with other kinesins, myosin and G-proteins suggests that the rate-limiting step of ADP release is accelerated in the fungal kinesin and accounts for the unusually high velocity and ATPase activity.
History
DepositionFeb 27, 2003-
Header (metadata) releaseFeb 27, 2003-
Map releaseFeb 27, 2003-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 53.068715402
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 53.068715402
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1036.gif

Downloads & links

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Map

FileDownload / File: emd_1036.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNeurospora crassa kinesin monomer (nK355) AMP-PNP state
Voxel sizeX=Y=Z: 5.526 Å
Density
Contour Level1: 64.5 / Movie #1: 53.0687154
Minimum - Maximum0.0 - 100.0
Average (Standard dev.)42.953899999999997 (±9.965009999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 552.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.5265.5265.526
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z552.600552.600552.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean0.000100.00042.954

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Supplemental data

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Sample components

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Entire : neurospora crassa kinesin monomer

EntireName: neurospora crassa kinesin monomer
Components
  • Sample: neurospora crassa kinesin monomer
  • Protein or peptide: neurospora crassakinesin
  • Protein or peptide: tubulin

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Supramolecule #1000: neurospora crassa kinesin monomer

SupramoleculeName: neurospora crassa kinesin monomer / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 2

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Macromolecule #1: neurospora crassakinesin

MacromoleculeName: neurospora crassakinesin / type: protein_or_peptide / ID: 1 / Name.synonym: molecular motor / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: Neurospora crassa (fungus) / synonym: neurospora

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Macromolecule #2: tubulin

MacromoleculeName: tubulin / type: protein_or_peptide / ID: 2 / Name.synonym: microtubules / Number of copies: 1 / Oligomeric state: hetero dimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Neurospora crassa (fungus) / synonym: neurospora / Tissue: brain / Cell: neuronal cells / Location in cell: cytoplasm

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 6.9
Details: Pipes 20mM, 50 mM NaCl, 5mM mgcl,1mM Mg-ATP, 20um taxol.
StainingType: NEGATIVE / Details: ice-embedded
GridDetails: holey grids
VitrificationCryogen name: PROPANE / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: self made

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Electron microscopy

MicroscopeFEI/PHILIPS CM120T
Electron beamAcceleration voltage: 100 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 37000
Sample stageSpecimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 21 µm / Number real images: 18 / Average electron dose: 5 e/Å2 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Phoelix, Suprim
Details: Final maps from 36 averaged datasets = 18 helical tubes

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