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- PDB-5mm7: Ustilago maydis kinesin-5 motor domain with N-terminal extension ... -

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Basic information

Entry
Database: PDB / ID: 5mm7
TitleUstilago maydis kinesin-5 motor domain with N-terminal extension in the AMPPNP state bound to microtubules
Components
  • Tubulin alpha-1A chain
  • Tubulin beta chain
  • kinesin-5Kinesin family member 11
KeywordsMOTOR PROTEIN / Ustilago maydis / kinesin-5 / motor protein
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 / mitotic spindle assembly / microtubule-based process / microtubule-based movement / structural constituent of cytoskeleton / chromosome segregation / microtubule / microtubule binding / GTPase activity / GTP binding / ATP binding / cytoplasm / Uncharacterized protein / Tubulin alpha-1A chain / Tubulin beta chain
Function and homology information
Specimen sourceUstilago maydis (fungus)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5.1 Å resolution
AuthorsMoores, C.A. / von Loeffelholz, O.
CitationJournal: To Be Published
Title: Ustilago maydis kinesin-5 motor domain in the AMPPNP state bound to microtubules
Authors: Moores, C.A. / von Loeffelholz, O.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 8, 2016 / Release: Aug 8, 2018

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
K: kinesin-5
A: Tubulin alpha-1A chain
B: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,5689
Polyers146,1933
Non-polymers2,3756
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)11500
ΔGint (kcal/M)-58
Surface area (Å2)52500
MethodPISA

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Components

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Protein/peptide , 3 types, 3 molecules KAB

#1: Protein/peptide kinesin-5 / Kinesin family member 11


Mass: 49482.207 Da / Num. of mol.: 1 / Fragment: motor domain, UNP residues 1-456 / Source: (gene. exp.) Ustilago maydis (fungus) / Gene: UMAG_10678 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D1DQH0
#2: Protein/peptide Tubulin alpha-1A chain / Alpha-tubulin 1 / Tubulin alpha-1 chain


Mass: 48769.988 Da / Num. of mol.: 1 / Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBA1A / Production host: Sus scrofa (pig) / References: UniProt: P02550
#3: Protein/peptide Tubulin beta chain / Beta-tubulin


Mass: 47940.945 Da / Num. of mol.: 1 / Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig) / References: UniProt: P02554

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Non-polymers , 5 types, 6 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Formula: C10H17N6O12P3 / Comment: AMP-PNP (energy-carrying molecule analogue) *YM
#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#7: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 1 / Formula: C47H51NO14 / Paclitaxel
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Mass: 443.201 Da / Num. of mol.: 1 / Formula: C10H15N5O11P2 / Guanosine diphosphate / Comment: GDP (energy-carrying molecule) *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Ternary complex of alpha-beta-tubulin stabilized by taxol and decorated with Ustilago maydis kinesin-5 motordomain with N-terminal extensionCOMPLEX1, 2, 30MULTIPLE SOURCES
2kinesin-5COMPLEX11RECOMBINANT
3Tubulin alpha-1A chainCOMPLEX21RECOMBINANT
4Tubulin beta chainCOMPLEX31RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
125270Ustilago maydis (fungus)
239823Sus scrofa (pig)
349823Sus scrofa (pig)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
12562Escherichia coli (E. coli)
239823Sus scrofa (pig)
349823Sus scrofa (pig)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 12629 / Details: 13x symmetrisation / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410098
ELECTRON MICROSCOPYf_angle_d0.86013708
ELECTRON MICROSCOPYf_dihedral_angle_d6.3086114
ELECTRON MICROSCOPYf_chiral_restr0.0521518
ELECTRON MICROSCOPYf_plane_restr0.0071835

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