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- EMDB-3620: Microtubule-bound MKLP2 motor domain in the presence of ADP -

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Basic information

Entry
Database: EMDB / ID: 3620
TitleMicrotubule-bound MKLP2 motor domain in the presence of ADP
SampleComplex of 14pf microtubule with bound MKLP2 motor domain in the presence of ADP
SourceMus musculus / mammal / ハツカネズミ, はつかねずみ /
Bos taurus / mammal / ウシ /
Map dataMicrotubule-bound MKLP2 motor domain in the presence of ADP
Methodsingle particle reconstruction, at 5.8 Å resolution
AuthorsAtherton J / Yu IM
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
The divergent mitotic kinesin MKLP2 exhibits atypical structure and mechanochemistry.
Joseph Atherton / I-Mei Yu / Alexander Cook / Joseph M Muretta / Agnel Joseph / Jennifer Major / Yannick Sourigues / Jeffrey Clause / Maya Topf / Steven S Rosenfeld / Anne Houdusse / Carolyn A Moores

Validation ReportPDB-ID: 5nd2

SummaryFull reportAbout validation report
DateDeposition: Mar 7, 2017 / Header (metadata) release: Apr 5, 2017 / Map release: Oct 4, 2017 / Last update: Oct 4, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.027
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5nd2
  • Surface level: 0.027
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3620.map.gz (map file in CCP4 format, 14323 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
161 pix
1.53 Å/pix.
= 246.33 Å
139 pix
1.53 Å/pix.
= 212.67 Å
160 pix
1.53 Å/pix.
= 244.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.53 Å
Density
Contour Level:0.027 (by author), 0.027 (movie #1):
Minimum - Maximum-0.028648652 - 0.09889488
Average (Standard dev.)0.0022059928 (0.00960581)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions139160161
Origin7058123
Limit208217283
Spacing160139161
CellA: 244.79999 Å / B: 212.67 Å / C: 246.33 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.531.531.53
M x/y/z160139161
origin x/y/z0.0000.0000.000
length x/y/z244.800212.670246.330
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS5870123
NC/NR/NS160139161
D min/max/mean-0.0290.0990.002

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Supplemental data

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Sample components

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Entire Complex of 14pf microtubule with bound MKLP2 motor domain in the ...

EntireName: Complex of 14pf microtubule with bound MKLP2 motor domain in the presence of ADP
Details: Microtubule bound to taxol and GMPCPP / Number of components: 11

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Component #1: protein, Complex of 14pf microtubule with bound MKLP2 motor domai...

ProteinName: Complex of 14pf microtubule with bound MKLP2 motor domain in the presence of ADP
Details: Microtubule bound to taxol and GMPCPP / Recombinant expression: No

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Component #2: protein, Kinesin-like protein KIF20A

ProteinName: Kinesin-like protein KIF20A / Details: Microtubule bound to taxol and GMPCPP / Recombinant expression: No
SourceSpecies: Mus musculus / mammal / ハツカネズミ, はつかねずみ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #3: protein, Tubulin alpha and beta chains

ProteinName: Tubulin alpha and beta chains / Details: Microtubule bound to taxol and GMPCPP / Recombinant expression: No
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #4: protein, Kinesin-like protein KIF20A

ProteinName: Kinesin-like protein KIF20A / Details: MKLP2 25-520 with bound ADP / Recombinant expression: No
MassTheoretical: 56.021332 kDa
Source (engineered)Expression System: Mus musculus / mammal / ハツカネズミ, はつかねずみ /

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Component #5: protein, Tubulin alpha chain

ProteinName: Tubulin alpha chain / Details: Alpha-tubulin / Recombinant expression: No
MassTheoretical: 50.107238 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #6: protein, Tubulin beta-2B chain

ProteinName: Tubulin beta-2B chain / Recombinant expression: No
MassTheoretical: 49.90777 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #7: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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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, GUANOSINE-5'-TRIPHOSPHATE

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

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

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

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Component #11: ligand, TAXOL

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

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Experimental details

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Sample preparation

Specimen statefilament
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: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 9842
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Gold-standard FSCtrue using noise substitution test (Chen et al., 2014)

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Atomic model buiding

Output model

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