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- EMDB-58509: Discodermolide stabilised 13-protofilament microtubule C1 reconst... -

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Basic information

Entry
Database: EMDB / ID: EMD-58509
TitleDiscodermolide stabilised 13-protofilament microtubule C1 reconstruction
Map datadiscodermolide bound 13-protofilament microtubule C1 reconstruction - sharpened map
Sample
  • Organelle or cellular component: Microtubule
    • Protein or peptide: Tubulin alpha-1B chain
    • Protein or peptide: Tubulin beta chain
Keywordsmicrotubule / cytoskeleton / filament / compact / stable / chemotherapeutic / cell division / transport / Tubulin / alpha-tubulin / beta-tubulin / Heterodimer / Protofilament / GTP-binding protein / Cytoskeletal protein / Discodermolide / Polyketide natural product / Marine natural product / Taxane-site ligand / Microtubule-stabilizing agent / Lactone / Carbamate / Microtubule stabilization / Microtubule dynamics / Mitotic arrest / Cell cycle inhibition / Spindle assembly / Antimitotic agent / Cytoskeleton regulation / Tubulin polymerization / Anticancer / Antitumor / Cancer therapy / Drug-tubulin interaction / Chemotherapeutic agent / Cryo-EM / Helical reconstruction / Drug binding site / Protein-ligand complex / Taxane binding pocket / Lumenal binding / STRUCTURAL PROTEIN
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsGravett MSC / Howes SC / Pelster Jose A
Funding supportEuropean Union, Netherlands, 2 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission101153345European Union
Netherlands Organisation for Scientific Research (NWO)OCENW.XL21.XL21.048 Netherlands
CitationJournal: bioRxiv / Year: 2025
Title: Taxane-Induced Conformational Changes in the Microtubule Lattice Activate GEF-H1-Dependent RhoA Signaling
Authors: Meiring JCM / Mahapatra V / Liu RR / Gravett MSC / Morren D / Saunders HAJ / Choi SR / Pelster Jose A / Karhanova A / Metallidou I / Moore A / Spoelstra MFM / Grigoriev IS / Giono M / Iyer ...Authors: Meiring JCM / Mahapatra V / Liu RR / Gravett MSC / Morren D / Saunders HAJ / Choi SR / Pelster Jose A / Karhanova A / Metallidou I / Moore A / Spoelstra MFM / Grigoriev IS / Giono M / Iyer SS / Stehbens SJ / Diaz JF / Lansky Z / Stecker KE / Steinmetz MO / Howes SC / Kapitein LC / Akhmanova A
History
DepositionJun 11, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58509.png

Downloads & links

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Map

FileDownload / File: emd_58509.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdiscodermolide bound 13-protofilament microtubule C1 reconstruction - sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 576 pix.
= 489.024 Å		0.85 Å/pix.
x 576 pix.
= 489.024 Å		0.85 Å/pix.
x 576 pix.
= 489.024 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.849 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.045990724 - 0.15588206
Average (Standard dev.)0.0017443806 (±0.011514421)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 489.024 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58509_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: discodermolide bound 13-protofilament microtubule C1 reconstruction - unsharpened...

Fileemd_58509_additional_1.map
Annotationdiscodermolide bound 13-protofilament microtubule C1 reconstruction - unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: discodermolide bound 13-protofilament microtubule C1 reconstruction - half...

Fileemd_58509_half_map_1.map
Annotationdiscodermolide bound 13-protofilament microtubule C1 reconstruction - half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: discodermolide bound 13-protofilament microtubule C1 reconstruction - half...

Fileemd_58509_half_map_2.map
Annotationdiscodermolide bound 13-protofilament microtubule C1 reconstruction - half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Microtubule

EntireName: Microtubule
Components
  • Organelle or cellular component: Microtubule
    • Protein or peptide: Tubulin alpha-1B chain
    • Protein or peptide: Tubulin beta chain

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Supramolecule #1: Microtubule

SupramoleculeName: Microtubule / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 183 kDa/nm

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Macromolecule #1: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFLVFHS FGGGTGSGFT SLLMERLSVD YGKKSKLEFS ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFLVFHS FGGGTGSGFT SLLMERLSVD YGKKSKLEFS IYPAPQVSTA VVEPYNSILT THTTLEHSDC AFMVDNEAIY DICRRNLDIE RPTYTNLNRL ISQIVSSITA SLRFDGALNV DLTEFQTNLV PYPRIHFPLA TYAPVISAEK AYHEQLSVAE ITNACFEPAN QMVKCDPRHG KYMACCLLYR GDVVPKDVNA AIATIKTKRS IQFVDWCPTG FKVGINYQPP TVVPGGDLAK VQRAVCMLSN TTAIAEAWAR LDHKFDLMYA KRAFVHWYVG EGMEEGEFSE AREDMAALEK DYEEVGVDSV EGEGEEEGEE Y

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Macromolecule #2: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKESESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP DRIMNTFSVV ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKESESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP DRIMNTFSVV PSPKVSDTVV EPYNATLSVH QLVENTDETY CIDNEALYDI CFRTLKLTTP TYGDLNHLVS ATMSGVTTCL RFPGQLNADL RKLAVNMVPF PRLHFFMPGF APLTSRGSQQ YRALTVPELT QQMFDAKNMM AACDPRHGRY LTVAAVFRGR MSMKEVDEQM LNVQNKNSSY FVEWIPNNVK TAVCDIPPRG LKMSATFIGN STAIQELFKR ISEQFTAMFR RKAFLHWYTG EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEQGEFEEEG EEDEA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.22 mg/mL
BufferpH: 6.8
Component:
ConcentrationFormulaName
80.0 mMC8H18N2O6S2PIPES
1.0 mMC14H24N2O10EGTA
4.0 mMMgCl2Magnesium chloride
2.0 mMC10H16N5O14P3GTP
0.1 mMC33H55NO8discodermolide

Details: polymerised in MRB80 (80 mM Pipes, 1 mM EGTA, 4 mM MgCl2, pH 6.80 with KOH), 0.1 mM discodermolide and 2 mM GTP. Pelleted and resuspended in MRB80 and 0.1 mM discodermolide.
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 39.0 kPa / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 303.15 K / Instrument: LEICA EM GP / Details: Leica EM GP2 Back-side blotting 1.5s.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8513 / Average exposure time: 1.82 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 820009
Details: Separation distance set to the length of a single dimer 82 angstroms (0.33).
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: https://www.dropbox.com/scl/fi/c9cd7tbo184oe9lmqs6bv/14pf_apix2.8_box200.mrc?rlkey=x9i7vaq2k9xydnlrc60kvy7xe&dl=0 initial model provided by Rui Zhang, pixel and box size adjusted using relion image handler.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 164768
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC / Details: Initial angle assignment from filament tracer
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC
Details: Classification into different protofilament number classes (11-16). This map is the 14 protofilament class.
FSC plot (resolution estimation)

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