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- EMDB-3530: Ustilago maydis kinesin-5 motor domain with N-terminal extension ... -

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Basic information

Entry
Database: EMDB / ID: 3530
TitleUstilago maydis kinesin-5 motor domain with N-terminal extension in the AMPPNP state bound to microtubules
Map dataMicrotubule-bound Ustilago maydis kinesin-5 motor domain with N-terminal extension in the AMPPNP state
SampleTernary complex of alpha-beta-tubulin stabilized by taxol and decorated with Ustilago maydis kinesin-5 motordomain with N-terminal extension:
(kinesin-5Kinesin family member 11) x 2 / (Tubulin alpha-1A ...) x 2 / (Tubulin beta ...) x 2 / (ligand) x 5
Function / homologyBeta tubulin / P-loop containing nucleoside triphosphate hydrolase / Kinesin motor domain, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, conserved site / Beta tubulin, autoregulation binding site / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, GTPase domain / Kinesin-like protein / Alpha tubulin ...Beta tubulin / P-loop containing nucleoside triphosphate hydrolase / Kinesin motor domain, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, conserved site / Beta tubulin, autoregulation binding site / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, GTPase domain / Kinesin-like protein / Alpha tubulin / Kinesin motor domain / Tubulin / Tubulin/FtsZ, GTPase domain superfamily / Kinesin motor domain superfamily / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ family, GTPase domain / Kinesin motor domain / Tubulin C-terminal domain / Tubulin subunits alpha, beta, and gamma signature. / Tubulin-beta mRNA autoregulation signal. / Kinesin motor domain signature. / Kinesin motor domain profile. / Tubulin, C-terminal / ATP-dependent microtubule motor activity, plus-end-directed / kinesin complex / microtubule motor activity / microtubule-based movement / microtubule-based process / mitotic spindle assembly / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / spindle microtubule / mitotic cell cycle / microtubule / microtubule binding / ATPase activity / GTPase activity / GTP binding / ATP binding / nucleus / cytoplasm / Uncharacterized protein / Tubulin alpha-1A chain / Tubulin beta chain
Function and homology information
SourceUstilago maydis (fungus) / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / 5.1 Å resolution
AuthorsMoores CA / von Loeffelholz O
CitationJournal: Nat Commun / Year: 2017
Title: Nucleotide- and Mal3-dependent changes in fission yeast microtubules suggest a structural plasticity view of dynamics.
Authors: Ottilie von Loeffelholz / Neil A Venables / Douglas Robert Drummond / Miho Katsuki / Robert Cross / Carolyn A Moores
Validation ReportPDB-ID: 5mm7

SummaryFull reportAbout validation report
DateDeposition: Dec 8, 2016 / Header (metadata) release: Jan 11, 2017 / Map release: Aug 8, 2018 / Last update: Aug 8, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0535
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0535
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5mm7
  • Surface level: 0.0535
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5mm7
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3530.map.gz (map file in CCP4 format, 1767 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
1.39 Å/pix.
= 111.2 Å
69 pix
1.39 Å/pix.
= 95.91 Å
80 pix
1.39 Å/pix.
= 111.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour Level:0.0535 (by author), 0.0535 (movie #1):
Minimum - Maximum-0.049994238 - 0.19904202
Average (Standard dev.)0.028387314 (0.042107515)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions698080
Origin0.0.0.
Limit68.79.79.
Spacing806980
CellA: 111.2 Å / B: 95.909996 Å / C: 111.2 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z806980
origin x/y/z0.0000.0000.000
length x/y/z111.20095.910111.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS806980
D min/max/mean-0.0500.1990.028

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Supplemental data

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Sample components

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Entire Ternary complex of alpha-beta-tubulin stabilized by taxol and dec...

EntireName: Ternary complex of alpha-beta-tubulin stabilized by taxol and decorated with Ustilago maydis kinesin-5 motordomain with N-terminal extension
Number of components: 12

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Component #1: protein, Ternary complex of alpha-beta-tubulin stabilized by taxo...

ProteinName: Ternary complex of alpha-beta-tubulin stabilized by taxol and decorated with Ustilago maydis kinesin-5 motordomain with N-terminal extension
Recombinant expression: No

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Component #2: protein, kinesin-5

ProteinName: kinesin-5Kinesin family member 11 / Recombinant expression: No
SourceSpecies: Ustilago maydis (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Tubulin alpha-1A chain

ProteinName: Tubulin alpha-1A chain / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #4: protein, Tubulin beta chain

ProteinName: Tubulin beta chain / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #5: protein, kinesin-5

ProteinName: kinesin-5Kinesin family member 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.482207 kDa
SourceSpecies: Ustilago maydis (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Tubulin alpha-1A chain

ProteinName: Tubulin alpha-1A chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.769988 kDa
SourceSpecies: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #7: protein, Tubulin beta chain

ProteinName: Tubulin beta chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.940945 kDa
SourceSpecies: Sus scrofa (pig)
Source (engineered)Expression System: Sus scrofa (pig)

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Component #8: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #9: ligand, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.506196 kDa

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Component #10: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Component #11: ligand, TAXOL

LigandName: TAXOLPaclitaxel / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.853906 kDa

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Component #12: ligand, GUANOSINE-5'-DIPHOSPHATE

LigandName: GUANOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.443201 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Sample solutionpH: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 12629
3D reconstructionResolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Details: 13x symmetrisation

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Atomic model buiding

Output model

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