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- EMDB-55444: Cryo-EM reconstruction of the Kinesin KIF5A motor domain decorate... -

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Basic information

Entry
Database: EMDB / ID: EMD-55444
TitleCryo-EM reconstruction of the Kinesin KIF5A motor domain decorated GMPCPP microtubule (14-3)
Map data
Sample
  • Complex: Microtubule (14-3) complex of kinesin KIF5A motor domain with GMPCPP alpha/beta-tubulin.
    • Complex: Alpha/beta-tubulin
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin beta-2B chain
    • Complex: Kinesin heavy chain isoform 5A
      • Protein or peptide: Kinesin heavy chain isoform 5A
KeywordsMicrotubule 14-3. Binding motor domain. Tubulin dimer. / STRUCTURAL PROTEIN
Biological speciesBos taurus (domestic cattle) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsMunoz-Hernandez H / Wieczorek M
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_208120 Switzerland
Swiss National Science FoundationTMSGI3_211309 Switzerland
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2026
Title: A cryo-EM processing pipeline for microtubules using CryoSPARC.
Authors: Daniel Zhang / Hugo Muñoz-Hernández / Pavel Filipcik / Kushal Sejwal / Yixin Xu / Sung Ryul Choi / Michel O Steinmetz / Michal Wieczorek /
Abstract: Microtubules are cytoskeletal filaments that are typically characterized by a discontinuous helical lattice of α/β-tubulin heterodimers. Microtubules can also adopt variable lattice architectures ...Microtubules are cytoskeletal filaments that are typically characterized by a discontinuous helical lattice of α/β-tubulin heterodimers. Microtubules can also adopt variable lattice architectures both in vitro and in cellular contexts. Pseudo-helical averaging processing strategies have been developed to generate cryo-EM reconstructions of microtubules with and without decorating protein-binding partners, but these pipelines can be difficult to implement for the average user, especially for undecorated filaments. Here, we describe MiCSPARC, a cryo-EM processing pipeline developed around CryoSPARC [Punjani et al. (2017), Nat. Methods, 14, 290-296], which leverages automated particle picking and fast 3D refinement times in CryoSPARC to determine the structures of both decorated and undecorated microtubules. We generate reconstructions of undecorated GDP microtubules, as well as kinesin-1 motor domain-decorated GMPCPP filaments, at resolutions of up to 2.8 Å, demonstrating the robustness of the pipeline. Based on its convenient implementation and its ability to routinely generate high-resolution, seam-corrected microtubule reconstructions, MiCSPARC should provide a valuable tool for understanding microtubule dynamics, microtubule-associated proteins and microtubule-targeting agents.
History
DepositionOct 21, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55444.png

Downloads & links

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Map

FileDownload / File: emd_55444.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.28 Å/pix.
x 512 pix.
= 655.36 Å		1.28 Å/pix.
x 512 pix.
= 655.36 Å		1.28 Å/pix.
x 512 pix.
= 655.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.814
Minimum - Maximum-0.1193245 - 7.7782464
Average (Standard dev.)0.06859998 (±0.3773965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 655.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55444_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_55444_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55444_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Microtubule (14-3) complex of kinesin KIF5A motor domain with GMP...

EntireName: Microtubule (14-3) complex of kinesin KIF5A motor domain with GMPCPP alpha/beta-tubulin.
Components
  • Complex: Microtubule (14-3) complex of kinesin KIF5A motor domain with GMPCPP alpha/beta-tubulin.
    • Complex: Alpha/beta-tubulin
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin beta-2B chain
    • Complex: Kinesin heavy chain isoform 5A
      • Protein or peptide: Kinesin heavy chain isoform 5A

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Supramolecule #1: Microtubule (14-3) complex of kinesin KIF5A motor domain with GMP...

SupramoleculeName: Microtubule (14-3) complex of kinesin KIF5A motor domain with GMPCPP alpha/beta-tubulin.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Alpha/beta-tubulin

SupramoleculeName: Alpha/beta-tubulin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #3: Kinesin heavy chain isoform 5A

SupramoleculeName: Kinesin heavy chain isoform 5A / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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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: Bos taurus (domestic cattle)
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVD LEPTVIDEVR TGTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL D RIRKLADQ CTGLQGFLVF HSFGGGTGSG FTSLLMERLS VDYGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVD LEPTVIDEVR TGTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL D RIRKLADQ CTGLQGFLVF HSFGGGTGSG FTSLLMERLS VDYGKKSKLE FSIYPAPQVS TA VVEPYNS ILTTHTTLEH SDCAFMVDNE AIYDICRRNL DIERPTYTNL NRLISQIVSS ITA SLRFDG ALNVDLTEFQ TNLVPYPRIH FPLATYAPVI SAEKAYHEQL SVAEITNACF EPAN QMVKC DPRHGKYMAC CLLYRGDVVP KDVNAAIATI KTKRSIQFVD WCPTGFKVGI NYQPP TVVP GGDLAKVQRA VCMLSNTTAI AEAWARLDHK FDLMYAKRAF VHWYVGEGME EGEFSE ARE DMAALEKDYE EVGVDSV

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Macromolecule #2: Tubulin beta-2B chain

MacromoleculeName: Tubulin beta-2B chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLE PGTMDSVRSG PFGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV V RKESESCD CLQGFQLTHS LGGGTGSGMG TLLISKIREE YPDRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLE PGTMDSVRSG PFGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV V RKESESCD CLQGFQLTHS LGGGTGSGMG TLLISKIREE YPDRIMNTFS VMPSPKVSDT VV EPYNATL SVHQLVENTD ETYCIDNEAL YDICFRTLKL TTPTYGDLNH LVSATMSGVT TCL RFPGQL NADLRKLAVN MVPFPRLHFF MPGFAPLTSR GSQQYRALTV PELTQQMFDS KNMM AACDP RHGRYLTVAA IFRGRMSMKE VDEQMLNVQN KNSSYFVEWI PNNVKTAVCD IPPRG LKMS ATFIGNSTAI QELFKRISEQ FTAMFRRKAF LHWYTGEGMD EMEFTEAESN MNDLVS EYQ QYQD

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Macromolecule #3: Kinesin heavy chain isoform 5A

MacromoleculeName: Kinesin heavy chain isoform 5A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAETNNECSI KVLCRFRPLN QAEILRGDKF IPIFQGDDSV VIGGKPYVFD RVFPPNTTQE QVYHACAMQ IVKDVLAGYN GTIFAYGQTS SGKTHTMEGK LHDPQLMGII PRIARDIFNH I YSMDENLE FHIKVSYFEI YLDKIRDLLD VTKTNLSVHE DKNRVPFVKG ...String:
MAETNNECSI KVLCRFRPLN QAEILRGDKF IPIFQGDDSV VIGGKPYVFD RVFPPNTTQE QVYHACAMQ IVKDVLAGYN GTIFAYGQTS SGKTHTMEGK LHDPQLMGII PRIARDIFNH I YSMDENLE FHIKVSYFEI YLDKIRDLLD VTKTNLSVHE DKNRVPFVKG CTERFVSSPE EI LDVIDEG KSNRHVAVTN MNEHSSRSHS IFLINIKQEN METEQKLSGK LYLVDLAGSE KVS KTGAEG AVLDEAKNIN KSLSALGNVI SALAEGTKSY VPYRDSKMTR ILQDSLGGNC RTTM FICCS PSSYNDAETK STLMFGQRAK T

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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

BufferpH: 6.8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 78125
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionDetails: MiCSPARC - our new pipeline presented with this deposition
CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
In silico model: MiCSPARC - our new pipeline presented with this deposition
Details: MiCSPARC - our new pipeline presented with this deposition
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: MiCSPARC - processing pipeline with the associated deposition was used to correct the seam of the KIF5A decorated GMPcPP microtubule (14-3)
Number images used: 11523
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9t17


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT

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