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- EMDB-3529: Ustilago maydis kinesin-5 motor domain in the AMPPNP state bound ... -

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Basic information

Entry
Database: EMDB / ID: 3529
TitleUstilago maydis kinesin-5 motor domain in the AMPPNP state bound to microtubules
Map datamicrotubule decorated with Ustillago maydis kinesin-5 motor domain in the AMPPNP state
SampleTernary complex of alpha-beta-tubulin stabilized by taxol and decorated with Ustilago maydis kinesin-5:
Ustilago maydis kinesin-5 / alpha-beta-tubulin / kinesin-5Kinesin family member 11 / Tubulin alpha-1A chain / Tubulin beta chain / (ligand) x 5
Function / homologyBeta tubulin, autoregulation binding site / Tubulin subunits alpha, beta, and gamma signature. / Kinesin motor domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, C-terminal domain superfamily / Kinesin motor domain superfamily / Tubulin/FtsZ, GTPase domain superfamily / Kinesin-like protein / P-loop containing nucleoside triphosphate hydrolase / Tubulin, C-terminal ...Beta tubulin, autoregulation binding site / Tubulin subunits alpha, beta, and gamma signature. / Kinesin motor domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, C-terminal domain superfamily / Kinesin motor domain superfamily / Tubulin/FtsZ, GTPase domain superfamily / Kinesin-like protein / P-loop containing nucleoside triphosphate hydrolase / Tubulin, C-terminal / Kinesin motor domain, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, conserved site / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, GTPase domain / Beta tubulin / Alpha tubulin / Kinesin motor domain / Tubulin / Tubulin-beta mRNA autoregulation signal. / Kinesin motor domain signature. / Kinesin motor domain profile. / Tubulin C-terminal domain / ATP-dependent microtubule motor activity, plus-end-directed / kinesin complex / microtubule-based movement / mitotic spindle assembly / microtubule-based process / structural constituent of cytoskeleton / chromosome segregation / microtubule binding / microtubule / GTPase activity / GTP binding / ATP binding / cytoplasm / Uncharacterized protein / Tubulin alpha-1A chain / Tubulin beta chain
Function and homology information
SourceUstilago maydis (strain 521 / FGSC 9021) (fungus) / Sus scrofa (pig) / pig (pig)
Methodsingle particle reconstruction / cryo EM / 4.5 Å resolution
AuthorsMoores CA / von Loeffelholz O
CitationJournal: To Be Published
Title: Ustilago maydis kinesin-5 motor domain in the AMPPNP state bound to microtubules
Authors: Moores CA / von Loeffelholz O
Validation ReportPDB-ID: 5mm4

SummaryFull reportAbout validation report
DateDeposition: Dec 8, 2016 / Header (metadata) release: Jan 11, 2017 / Map release: Jun 27, 2018 / Last update: Jun 27, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0171
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0171
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5mm4
  • Surface level: 0.0171
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5mm4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3529.map.gz (map file in CCP4 format, 2061 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
87 pix
1.39 Å/pix.
= 120.93 Å
74 pix
1.39 Å/pix.
= 102.86 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:0.0171 (by author), 0.0171 (movie #1):
Minimum - Maximum-0.1280504 - 0.17425705
Average (Standard dev.)0.0031008606 (0.025597509)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions748087
Origin0.0.0.
Limit73.79.86.
Spacing807487
CellA: 111.2 Å / B: 102.86 Å / C: 120.93 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/z807487
origin x/y/z0.0000.0000.000
length x/y/z111.200102.860120.930
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS807487
D min/max/mean-0.1280.1740.003

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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
Number of components: 11

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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
Recombinant expression: No

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Component #2: protein, Ustilago maydis kinesin-5

ProteinName: Ustilago maydis kinesin-5 / Recombinant expression: No
SourceSpecies: Ustilago maydis (strain 521 / FGSC 9021) (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, alpha-beta-tubulin

ProteinName: alpha-beta-tubulin / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)

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Component #4: protein, kinesin-5

ProteinName: kinesin-5Kinesin family member 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.103312 kDa
SourceSpecies: Ustilago maydis (strain 521 / FGSC 9021) (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Tubulin alpha-1A chain

ProteinName: Tubulin alpha-1A chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.769988 kDa
SourceSpecies: pig (pig)

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Component #6: protein, Tubulin beta chain

ProteinName: Tubulin beta chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.940945 kDa
SourceSpecies: pig (pig)

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Component #7: ligand, MAGNESIUM ION

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

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Component #8: 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 #9: 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 #10: ligand, TAXOL

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

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Component #11: 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: 13581
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Details: 13x symmetrisation

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Atomic model buiding

Output model

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