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- EMDB-55425: Cryo-EM reconstruction of the Kinesin KIF5A motor domain decorate... -

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Basic information

Entry
Database: EMDB / ID: EMD-55425
TitleCryo-EM reconstruction of the Kinesin KIF5A motor domain decorated GMPCPP microtubule
Map data
Sample
  • Complex: Microtubule 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
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
KeywordsMicrotubule-binding motor domain. Tubulin dimer. / STRUCTURAL PROTEIN
Function / homology
Function and homology information


plus-end-directed kinesin ATPase / anterograde dendritic transport of neurotransmitter receptor complex / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / ciliary rootlet / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / Kinesins / positive regulation of axon guidance / microtubule motor activity ...plus-end-directed kinesin ATPase / anterograde dendritic transport of neurotransmitter receptor complex / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / ciliary rootlet / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / Kinesins / positive regulation of axon guidance / microtubule motor activity / kinesin complex / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / Insulin processing / synaptic vesicle transport / cytoskeletal motor activity / kinesin binding / postsynaptic cytosol / microtubule-based process / cytoplasmic microtubule / vesicle-mediated transport / axon cytoplasm / MHC class II antigen presentation / cellular response to interleukin-4 / dendrite cytoplasm / axon guidance / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / microtubule binding / chemical synaptic transmission / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / perikaryon / cilium / protein heterodimerization activity / GTPase activity / ubiquitin protein ligase binding / GTP binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / Kinesin-like protein / 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 / Alpha tubulin ...: / Kinesin-like protein / 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 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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-1B chain / Kinesin heavy chain isoform 5A / Tubulin beta-2B chain
Similarity search - Component
Biological speciesBos taurus (domestic cattle) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 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_55425.png

Downloads & links

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Map

FileDownload / File: emd_55425.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 512 pix.
= 327.68 Å		0.64 Å/pix.
x 512 pix.
= 327.68 Å		0.64 Å/pix.
x 512 pix.
= 327.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.12222061 - 0.33633482
Average (Standard dev.)0.0007475676 (±0.008670748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 327.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened Map

Fileemd_55425_additional_1.map
AnnotationSharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: KIF5A decorated Microtubule (14-3)

Fileemd_55425_additional_2.map
AnnotationKIF5A decorated Microtubule (14-3)
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Half map A related to KIF5A decorated Microtubule (14-3)

Fileemd_55425_additional_3.map
AnnotationHalf map A related to KIF5A decorated Microtubule (14-3)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Half map B related to KIF5A decorated Microtubule (14-3)

Fileemd_55425_additional_4.map
AnnotationHalf map B related to KIF5A decorated Microtubule (14-3)
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55425_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55425_half_map_2.map
Projections & Slices
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Sample components

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Entire : Microtubule complex of kinesin KIF5A motor domain with GMPCPP alp...

EntireName: Microtubule complex of kinesin KIF5A motor domain with GMPCPP alpha/beta-tubulin.
Components
  • Complex: Microtubule 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
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER

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Supramolecule #1: Microtubule complex of kinesin KIF5A motor domain with GMPCPP alp...

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

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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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 48.966324 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLISQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRSIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSV

UniProtKB: Tubulin alpha-1B chain

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Macromolecule #2: Tubulin beta-2B chain

MacromoleculeName: Tubulin beta-2B chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 48.033062 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VMPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDSK NMMAACDPRH GRYLTVAAIF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QD

UniProtKB: Tubulin beta-2B chain

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Macromolecule #3: Kinesin heavy chain isoform 5A

MacromoleculeName: Kinesin heavy chain isoform 5A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: plus-end-directed kinesin ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.544531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAETNNECSI KVLCRFRPLN QAEILRGDKF IPIFQGDDSV VIGGKPYVFD RVFPPNTTQE QVYHACAMQI VKDVLAGYNG TIFAYGQTS SGKTHTMEGK LHDPQLMGII PRIARDIFNH IYSMDENLEF HIKVSYFEIY LDKIRDLLDV TKTNLSVHED K NRVPFVKG ...String:
MAETNNECSI KVLCRFRPLN QAEILRGDKF IPIFQGDDSV VIGGKPYVFD RVFPPNTTQE QVYHACAMQI VKDVLAGYNG TIFAYGQTS SGKTHTMEGK LHDPQLMGII PRIARDIFNH IYSMDENLEF HIKVSYFEIY LDKIRDLLDV TKTNLSVHED K NRVPFVKG CTERFVSSPE EILDVIDEGK SNRHVAVTNM NEHSSRSHSI FLINIKQENM ETEQKLSGKL YLVDLAGSEK VS KTGAEGA VLDEAKNINK SLSALGNVIS ALAEGTKSYV PYRDSKMTRI LQDSLGGNCR TTMFICCSPS SYNDAETKST LMF GQRAKT

UniProtKB: Kinesin heavy chain isoform 5A

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

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

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: G2P
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

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Macromolecule #7: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / type: ligand / ID: 7 / Number of copies: 1 / Formula: ACP
Molecular weightTheoretical: 505.208 Da
Chemical component information

ChemComp-ACP:
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / AMP-PCP, energy-carrying molecule analogue*YM

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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: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 117345
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 modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9t17:
Cryo-EM reconstruction of the Kinesin KIF5A motor domain decorated GMPCPP microtubule

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