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- PDB-5mm4: Ustilago maydis kinesin-5 motor domain in the AMPPNP state bound ... -

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Basic information

Entry
Database: PDB / ID: 5mm4
TitleUstilago maydis kinesin-5 motor domain 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 / 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
Specimen sourceUstilago maydis (fungus)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.5 Å resolution
AuthorsMoores, C.A. / 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 Report
SummaryFull reportAbout validation report
DateDeposition: Dec 8, 2016 / Release: Jun 27, 2018

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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)141,1899
Polyers138,8143
Non-polymers2,3756
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11670
ΔGint (kcal/M)-64
Surface area (Å2)52370
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: 42103.312 Da / Num. of mol.: 1 / Fragment: motor domain, UNP residues 73-457
Source: (gene. exp.) Ustilago maydis (strain 521 / FGSC 9021) (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: (natural) Sus scrofa (pig) / References: UniProt: P02550
#3: Protein/peptide Tubulin beta chain / Beta-tubulin


Mass: 47940.945 Da / Num. of mol.: 1 / Source: (natural) 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-5COMPLEX1, 2, 30MULTIPLE SOURCES
2Ustilago maydis kinesin-5COMPLEX11RECOMBINANT
3alpha-beta-tubulinCOMPLEX2,31NATURAL
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12237631Ustilago maydis (strain 521 / FGSC 9021) (fungus)
239823Sus scrofa (pig)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 13581 / Details: 13x symmetrisation / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0089975
ELECTRON MICROSCOPYf_angle_d1.04513544
ELECTRON MICROSCOPYf_dihedral_angle_d6.2926032
ELECTRON MICROSCOPYf_chiral_restr0.0581501
ELECTRON MICROSCOPYf_plane_restr0.0081811

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