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- EMDB-3527: S. pombe microtubule decorated with Cut7 motor domain in the AMPP... -

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Entry
Database: EMDB / ID: EMD-3527
TitleS. pombe microtubule decorated with Cut7 motor domain in the AMPPNP state
Map data
Sample
  • Complex: Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-B
    • Complex: Alpha tubulin, Beta tubulin
      • Protein or peptide: Tubulin alpha-1 chain
      • Protein or peptide: Tubulin beta chain
    • Complex: Cut7
      • Protein or peptide: Kinesin-like protein cut7
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: 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
KeywordsS. pombe / microtubule / kinesin-5 / Cut7 motor domain / motor protein
Function / homology
Function and homology information


mitotic spindle pole body duplication / Sealing of the nuclear envelope (NE) by ESCRT-III / Cilium Assembly / Platelet degranulation / RHO GTPases activate IQGAPs / mitotic spindle formation (spindle phase one) / mitotic spindle elongation (spindle phase three) / Kinesins / initial mitotic spindle pole body separation / microtubule plus-end directed mitotic chromosome migration ...mitotic spindle pole body duplication / Sealing of the nuclear envelope (NE) by ESCRT-III / Cilium Assembly / Platelet degranulation / RHO GTPases activate IQGAPs / mitotic spindle formation (spindle phase one) / mitotic spindle elongation (spindle phase three) / Kinesins / initial mitotic spindle pole body separation / microtubule plus-end directed mitotic chromosome migration / COPI-mediated anterograde transport / nuclear migration by microtubule mediated pushing forces / Neutrophil degranulation / meiotic spindle pole / meiotic spindle assembly / nuclear division / mitotic spindle pole body / mitotic spindle midzone assembly / mitotic spindle elongation / mitotic spindle midzone / spindle elongation / astral microtubule / polar microtubule / minus-end-directed microtubule motor activity / plus-end-directed microtubule motor activity / meiotic spindle / microtubule associated complex / microtubule motor activity / intracellular distribution of mitochondria / mitotic spindle assembly / cytoplasmic microtubule / cytoplasmic microtubule organization / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / mitotic spindle / spindle / microtubule cytoskeleton organization / kinetochore / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / cell division / response to antibiotic / GTPase activity / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Tubulin-beta mRNA autoregulation signal. ...: / : / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tubulin alpha-1 chain / Tubulin beta chain / Kinesin-like protein cut7
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972 (yeast) / Schizosaccharomyces pombe 972h-
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsMoores CA / von Loeffelholz O
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilL00190X/1 United Kingdom
CitationJournal: J Mol Biol / Year: 2020
Title: Corrigendum to "Cryo-EM Structure (4.5 Å) of Yeast Kinesin-5-Microtubule Complex Reveals a Distinct Binding Footprint and Mechanism of Drug Resistance" [J. Mol. Biol. 431 (2019) 864-872] ...Title: Corrigendum to "Cryo-EM Structure (4.5 Å) of Yeast Kinesin-5-Microtubule Complex Reveals a Distinct Binding Footprint and Mechanism of Drug Resistance" [J. Mol. Biol. 431 (2019) 864-872] https://doi.org/10.1016/j.jmb.2019.01.011.
Authors: Ottilie von Loeffelholz / Alejandro Peña / Douglas Robert Drummond / Robert Cross / Carolyn Ann Moores /
History
DepositionDec 7, 2016-
Header (metadata) releaseJan 11, 2017-
Map releaseAug 8, 2018-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0811
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0811
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5mlv
  • Surface level: 0.0811
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6s8m
  • Surface level: 0.0811
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6s8m
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3527.png

Downloads & links

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Map

FileDownload / File: emd_3527.map.gz / Format: CCP4 / Size: 1.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 0.0811 / Movie #1: 0.0811
Minimum - Maximum-0.26908487 - 0.4405258
Average (Standard dev.)0.015761957 (±0.045668256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions135125211
Spacing125135211
CellA: 173.75 Å / B: 187.65 Å / C: 293.29 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z125135211
origin x/y/z0.0000.0000.000
length x/y/z173.750187.650293.290
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS125135211
D min/max/mean-0.2690.4410.016

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Supplemental data

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Additional map: #1

Fileemd_3527_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_3527_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-B

EntireName: Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-B
Components
  • Complex: Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-B
    • Complex: Alpha tubulin, Beta tubulin
      • Protein or peptide: Tubulin alpha-1 chain
      • Protein or peptide: Tubulin beta chain
    • Complex: Cut7
      • Protein or peptide: Kinesin-like protein cut7
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: 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

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Supramolecule #1: Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-B

SupramoleculeName: Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-B
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Alpha tubulin, Beta tubulin

SupramoleculeName: Alpha tubulin, Beta tubulin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3
Source (natural)Organism: Schizosaccharomyces pombe 972 (yeast)

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Supramolecule #3: Cut7

SupramoleculeName: Cut7 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Schizosaccharomyces pombe 972 (yeast)

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Macromolecule #1: Tubulin alpha-1 chain

MacromoleculeName: Tubulin alpha-1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe 972h-
Molecular weightTheoretical: 51.20318 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe
SequenceString: MREVISVHVG QAGVQIGNAC WELYCLEHGI GPDGFPTENS EVHKNNSYLN DGFGTFFSET GQGKFVPRSI YVDLEPNVID QVRTGPYKD LFHPEQMVTG KEDASNNYAR GHYTVGKEMI DSVLERIRRM ADNCSGLQGF LVFHSFGGGT GSGLGALLLE R LNMEYGKK ...String:
MREVISVHVG QAGVQIGNAC WELYCLEHGI GPDGFPTENS EVHKNNSYLN DGFGTFFSET GQGKFVPRSI YVDLEPNVID QVRTGPYKD LFHPEQMVTG KEDASNNYAR GHYTVGKEMI DSVLERIRRM ADNCSGLQGF LVFHSFGGGT GSGLGALLLE R LNMEYGKK SNLQFSVYPA PQVSTSVVEP YNSVLTTHAT LDNSDCTFMV DNEACYDICR RNLDIERPTY ENLNRLIAQV VS SITASLR FAGSLNVDLN EFQTNLVPYP RIHFPLVTYS PIVSAAKAFH ESNSVQEITN QCFEPYNQMV KCDPRTGRYM ATC LLYRGD VIPRDVQAAV TSIKSRRTIQ FVDWCPTGFK IGICYEPPQH VPGSGIAKVN RAVCMLSNTT SIAEAWSRLD HKFD LMYSK RAFVHWYVGE GMEEGEFSEA REDLAALERD YEEVGQDSMD NEMYEADEEY

UniProtKB: Tubulin alpha-1 chain

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Macromolecule #2: Kinesin-like protein cut7

MacromoleculeName: Kinesin-like protein cut7 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe 972h-
Molecular weightTheoretical: 47.589062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAPRVAPGGS QQFLGKQGLK AKNPVSTPNS HFRSASNPRK RREPPTIDTG YPDRSDTNSP TDHALHDENE TNINVVVRVR GRTDQEVRD NSSLAVSTSG AMGAELAIQS DPSSMLVTKT YAFDKVFGPE ADQLMLFENS VAPMLEQVLN GYNCTIFAYG Q TGTGKTYT ...String:
MAPRVAPGGS QQFLGKQGLK AKNPVSTPNS HFRSASNPRK RREPPTIDTG YPDRSDTNSP TDHALHDENE TNINVVVRVR GRTDQEVRD NSSLAVSTSG AMGAELAIQS DPSSMLVTKT YAFDKVFGPE ADQLMLFENS VAPMLEQVLN GYNCTIFAYG Q TGTGKTYT MSGDLSDSDG ILSEGAGLIP RALYQLFSSL DNSNQEYAVK CSYYELYNEE IRDLLVSEEL RKPARVFEDT SR RGNVVIT GIEESYIKNA GDGLRLLREG SHRRQVAATK CNDLSSRSHS IFTITLHRKV SSGMTDETNS LTINNNSDDL LRA SKLHMV DLAGSENIGR SGAENKRARE TGMINQSLLT LGRVINALVE KAHHIPYRES KLTRLLQDSL GGKTKTSMIV TVSS TNTNL EETISTLEYA ARAKSIRNKP QNNQLVF

UniProtKB: Kinesin-like protein cut7

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Macromolecule #3: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe 972h-
Molecular weightTheoretical: 49.518359 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe
SequenceString: MREIVHIQAG QCGNQVGAAF WSTIADEHGL DSAGIYHGTS EAQHERLNVY FNEAAGGKYV PRAVLVDLEP GTMDAVKSGK FGNLFRPDN IIYGQSGAGN IWAKGHYTEG AELADAVLDV VRREAEACDA LQGFQLTHSL GGGTGSGMGT LLLSKIREEY P DRMMATFS ...String:
MREIVHIQAG QCGNQVGAAF WSTIADEHGL DSAGIYHGTS EAQHERLNVY FNEAAGGKYV PRAVLVDLEP GTMDAVKSGK FGNLFRPDN IIYGQSGAGN IWAKGHYTEG AELADAVLDV VRREAEACDA LQGFQLTHSL GGGTGSGMGT LLLSKIREEY P DRMMATFS VAPAPKSSDT VVEPYNATLS MHQLVENSDE TFCIDNEALS SIFANTLKIK SPSYDDLNHL VSAVMAGVTT SF RFPGELN SDLRKLAVNM VPFPRLHFFM VGFAPLAAIG SSSFQAVSVP ELTQQMFDAN NMMVAADPRH GRYLTVAALF RGK VSMKEV DEQIRSVQTK NSAYFVEWIP DNVLKAVCSV PPKDLKMSAT FIGNSTSIQE IFRRLGDQFS AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QEAGIDEGDE DYEIEEEKEP LEY

UniProtKB: Tubulin beta chain

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 6 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #7: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 6 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

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Macromolecule #8: 7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-T...

MacromoleculeName: 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
type: ligand / ID: 8 / Number of copies: 6 / Formula: EPB
Molecular weightTheoretical: 507.683 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 6.5
Sugar embeddingMaterial: vitreous ice
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN
Details: reference was low-pass filtered to 8 Angstroms in the final round of alignment.
Number images used: 12543

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