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- PDB-5mlv: S. pombe microtubule decorated with Cut7 motor domain in the AMPP... -

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Basic information

Entry
Database: PDB / ID: 5mlv
TitleS. pombe microtubule decorated with Cut7 motor domain in the AMPPNP state
Components
  • Kinesin-like protein cut7
  • Tubulin alpha-1 chain
  • Tubulin beta chain
KeywordsMOTOR PROTEIN / S. pombe / microtubule / kinesin-5 / Cut7 motor domain / motor protein
Function / homologyTubulin / Kinesin-like protein / Kinesin motor domain / Alpha tubulin / Beta tubulin / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain ...Tubulin / Kinesin-like protein / Kinesin motor domain / Alpha tubulin / Beta tubulin / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Kinesin motor domain, conserved site / Tubulin, C-terminal / P-loop containing nucleoside triphosphate hydrolase / 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. / Neutrophil degranulation / Kinesins / nuclear migration by microtubule mediated pushing forces / mitotic spindle pole body duplication / mitotic spindle pole body separation / microtubule plus-end directed mitotic chromosome migration / establishment or maintenance of cell polarity regulating cell shape / mitotic spindle pole body / mitotic spindle midzone assembly / mitotic spindle midzone / astral microtubule / condensed nuclear chromosome kinetochore / intracellular distribution of mitochondria / ATP-dependent microtubule motor activity, plus-end-directed / cytoplasmic microtubule organization / meiotic spindle / microtubule associated complex / kinesin complex / cytoplasmic microtubule / microtubule cytoskeleton organization / microtubule-based movement / structural constituent of cytoskeleton / spindle microtubule / microtubule cytoskeleton / microtubule / microtubule binding / GTPase activity / cell division / response to antibiotic / GTP binding / ATP binding / nucleus / cytosol / cytoplasm / Tubulin alpha-1 chain / Tubulin beta chain / Kinesin-like protein cut7
Function and homology information
Specimen sourceSchizosaccharomyces pombe 972h- (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.5 Å resolution
AuthorsMoores, C.A. / von Loeffelholz, O.
CitationJournal: To Be Published
Title: S. pombe microtubule decorated with Cut7 motor domain in the AMPPNP state
Authors: Moores, C.A. / von Loeffelholz, O.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 7, 2016 / Release: Aug 8, 2018

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
E: Tubulin alpha-1 chain
G: Kinesin-like protein cut7
I: Tubulin beta chain
O: Kinesin-like protein cut7
A: Kinesin-like protein cut7
D: Kinesin-like protein cut7
J: Kinesin-like protein cut7
P: Kinesin-like protein cut7
M: Tubulin alpha-1 chain
B: Tubulin alpha-1 chain
H: Tubulin alpha-1 chain
K: Tubulin alpha-1 chain
Q: Tubulin alpha-1 chain
N: Tubulin beta chain
C: Tubulin beta chain
F: Tubulin beta chain
L: Tubulin beta chain
R: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)901,89148
Polyers889,86418
Non-polymers12,02730
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein/peptide , 3 types, 18 molecules EMBHKQGOADJPINCFLR

#1: Protein/peptide
Tubulin alpha-1 chain


Mass: 51203.180 Da / Num. of mol.: 6 / Source: (gene. exp.) Schizosaccharomyces pombe 972h- / Gene: nda2, SPBC16A3.15c / Production host: Schizosaccharomyces pombe / References: UniProt: P04688
#2: Protein/peptide
Kinesin-like protein cut7 / Cell untimely torn protein 7


Mass: 47589.062 Da / Num. of mol.: 6 / Source: (gene. exp.) Schizosaccharomyces pombe 972h- / Gene: cut7, SPAC25G10.07c / Production host: Escherichia coli (E. coli) / References: UniProt: P24339
#3: Protein/peptide
Tubulin beta chain / Beta-tubulin


Mass: 49518.359 Da / Num. of mol.: 6 / Source: (gene. exp.) Schizosaccharomyces pombe 972h- / Gene: nda3, alp12, SPBC26H8.07c / Production host: Schizosaccharomyces pombe / References: UniProt: P05219

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Non-polymers , 5 types, 30 molecules

#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Formula: Mg / Magnesium
#6: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


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


Mass: 443.201 Da / Num. of mol.: 6 / Formula: C10H15N5O11P2 / Guanosine diphosphate / Comment: GDP (energy-carrying molecule) *YM
#8: Chemical
ChemComp-EPB / 7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE / EPOTHILONE B


Mass: 507.683 Da / Num. of mol.: 6 / Formula: C27H41NO6S / Epothilone

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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
1Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-BCOMPLEX1, 2, 30MULTIPLE SOURCES
2Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-BCOMPLEX1,31RECOMBINANT
3Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-BCOMPLEX21RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12284812Schizosaccharomyces pombe 972 (yeast)
23284812Schizosaccharomyces pombe 972 (yeast)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
124896Schizosaccharomyces pombe (fission yeast)
23562Escherichia coli (E. coli)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: vitreous ice
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
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM softwareName: FREALIGN / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 12543
Details: reference was low-pass filtered to 8 Angstroms in the final round of alignment.
Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00758068
ELECTRON MICROSCOPYf_angle_d0.97978720
ELECTRON MICROSCOPYf_dihedral_angle_d6.94334974
ELECTRON MICROSCOPYf_chiral_restr0.0638670
ELECTRON MICROSCOPYf_plane_restr0.00710572

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