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- EMDB-72726: KIF1A R350W bound to microtubules in the apo state -

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Entry
Database: EMDB / ID: EMD-72726
TitleKIF1A R350W bound to microtubules in the apo state
Map dataKIF1A R350W bound to microtubules in the apo state
Sample
  • Complex: KIF1A R350W bound to microtubules in the apo state
    • Complex: KIF1A R350W mutant motor domain
      • Protein or peptide: Kinesin-like protein KIF1A
    • Complex: Tubulins
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin beta-2B chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
KeywordsKIF1A / Kinesin-3 superfamily / KIF1A R350W mutant / motor domain / Apo / MOTOR PROTEIN
Function / homology
Function and homology information


neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / plus-end-directed kinesin ATPase / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / regulation of dendritic spine development / regulation of dendritic spine morphogenesis / anterograde axonal transport / plus-end-directed microtubule motor activity / Kinesins ...neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / plus-end-directed kinesin ATPase / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / regulation of dendritic spine development / regulation of dendritic spine morphogenesis / anterograde axonal transport / plus-end-directed microtubule motor activity / Kinesins / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / kinesin complex / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / cytoskeletal motor activity / microtubule-based process / neuronal dense core vesicle / vesicle-mediated transport / axon cytoplasm / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule cytoskeleton / microtubule binding / microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / axon / GTPase activity / synapse / dendrite / GTP binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
: / : / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Kinesin-associated / Kinesin-associated / Forkhead associated domain / Forkhead-associated (FHA) domain profile. ...: / : / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Kinesin-associated / Kinesin-associated / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / SMAD/FHA domain superfamily / PH 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 / PH domain profile. / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Pleckstrin homology domain. / Tubulin/FtsZ, GTPase domain superfamily / Pleckstrin homology domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tubulin beta chain / Kinesin-like protein KIF1A / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesHomo sapiens (human) / Sus scrofa (pig)
Methodhelical reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsShatarupa A / Rao L / Asenjo AB / Gennerich A / Sosa H
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM147332 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM113164 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
CitationJournal: Nat Commun / Year: 2026
Title: Pathogenic KIF1A R350 mutations disrupt a conserved and conformation-dependent kinesin-tubulin salt bridge.
Authors: Abhipsa Shatarupa / Lu Rao / Ana B Asenjo / Arne Gennerich / Hernando Sosa /
Abstract: Pathogenic variants in the motor domain of the kinesin-3 motor protein KIF1A cause a range of neurodevelopmental and neurodegenerative conditions collectively termed KIF1A-associated neurological ...Pathogenic variants in the motor domain of the kinesin-3 motor protein KIF1A cause a range of neurodevelopmental and neurodegenerative conditions collectively termed KIF1A-associated neurological disorder (KAND). Among these, mutations at residue R350 are linked to hereditary spastic paraplegia and altered motor function. Yet, the structural basis for their pathogenicity remains unclear. Here, we present high-resolution cryo-electron microscopy (cryo-EM) structures of KIF1A R350G and R350W bound to microtubules in both the apo and AMP-PNP-bound states. We identify a salt bridge between KIF1A residue R350 and α-tubulin E415 that forms only in the open conformation of the motor domain and is disrupted in both mutants. The loss of this electrostatic interaction correlates with increased velocity, reduced processivity, and decreased microtubule affinity in the open, apo conformation, as demonstrated by single-molecule assays. Our results reveal an electrostatic interaction at the motor-microtubule interface that regulates KIF1A's motility behavior.
History
DepositionSep 15, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72726.png

Downloads & links

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Map

FileDownload / File: emd_72726.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKIF1A R350W bound to microtubules in the apo state
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 420 pix.
= 346.92 Å		0.83 Å/pix.
x 420 pix.
= 346.92 Å		0.83 Å/pix.
x 420 pix.
= 346.92 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.33347502 - 0.52283025
Average (Standard dev.)0.0013693037 (±0.009493153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 346.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72726_msk_1.map
Projections & Slices
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Mask #2

Fileemd_72726_msk_2.map
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Mask #3

Fileemd_72726_msk_3.map
Projections & Slices
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Additional map: This is a low pass filter map of...

Fileemd_72726_additional_1.map
AnnotationThis is a low pass filter map of the original map at 6 Ang to make figures.
Projections & Slices
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Additional map: This is a local resolution map.

Fileemd_72726_additional_2.map
AnnotationThis is a local resolution map.
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Half map: Half Map B

Fileemd_72726_half_map_1.map
AnnotationHalf Map B
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_72726_half_map_2.map
AnnotationHalf Map A
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Sample components

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Entire : KIF1A R350W bound to microtubules in the apo state

EntireName: KIF1A R350W bound to microtubules in the apo state
Components
  • Complex: KIF1A R350W bound to microtubules in the apo state
    • Complex: KIF1A R350W mutant motor domain
      • Protein or peptide: Kinesin-like protein KIF1A
    • Complex: Tubulins
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin beta-2B chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL

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Supramolecule #1: KIF1A R350W bound to microtubules in the apo state

SupramoleculeName: KIF1A R350W bound to microtubules in the apo state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 100.086 kDa/nm

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Supramolecule #2: KIF1A R350W mutant motor domain

SupramoleculeName: KIF1A R350W mutant motor domain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Tubulins

SupramoleculeName: Tubulins / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Sus scrofa (pig)

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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: Sus scrofa (pig)
Molecular weightTheoretical: 50.204445 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 GVDSVEGEGE EEGEEY

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: Sus scrofa (pig)
Molecular weightTheoretical: 49.999887 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 QDATADEQGE FEEEEGEDEA

UniProtKB: Tubulin beta chain

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Macromolecule #3: Kinesin-like protein KIF1A

MacromoleculeName: Kinesin-like protein KIF1A / 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: 49.317453 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAGASVKVAV RVRPFNSREM SRDSKCIIQM SGSTTTIVNP KQPKETPKSF SFDYSYWSHT SPEDINYASQ KQVYRDIGEE MLQHAFEGY NVCIFAYGQT GAGKSYTMMG KQEKDQQGII PQLCEDLFSR INDTTNDNMS YSVEVSYMEI YCERVRDLLN P KNKGNLRV ...String:
MAGASVKVAV RVRPFNSREM SRDSKCIIQM SGSTTTIVNP KQPKETPKSF SFDYSYWSHT SPEDINYASQ KQVYRDIGEE MLQHAFEGY NVCIFAYGQT GAGKSYTMMG KQEKDQQGII PQLCEDLFSR INDTTNDNMS YSVEVSYMEI YCERVRDLLN P KNKGNLRV REHPLLGPYV EDLSKLAVTS YNDIQDLMDS GNKARTVAAT NMNETSSRSH AVFNIIFTQK RHDAETNITT EK VSKISLV DLAGSERADS TGAKGTRLKE GANINKSLTT LGKVISALAE MDSGPNKNKK KKKTDFIPYR DSVLTWLLRE NLG GNSRTA MVAALSPADI NYDETLSTLR YADWAKQIRC NAVINEDPNN KLIRELKDEV TRLRDLLYAQ GLGDITDGAG VKQL EDKVE ELASKNYHLE NEVARLKKLV EFTSAWSHPQ FEK

UniProtKB: Kinesin-like protein KIF1A

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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: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

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

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Macromolecule #7: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 7 / Number of copies: 1 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.8
Component:
ConcentrationFormulaName
80.0 mMC8H18N2O6S2PIPES
2.0 mMMgCl2Magnesium Chloride
1.0 mMC14H24N2O10EGTA

Details: BRB80 buffer composed of 80 mM PIPES, 2 mM MgCl2, 1 mM EGTA, PH 6.8
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Details: The grid used was UltrAuFoil R0.6/1
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 4uL of a 6uM MT solution in BRB80 (80mM PIPES, 2mM MgCl2, 1mM EGTA pH 6.8) along with 20uM paclitaxel was added onto a plasma-cleaned grid. The MTs were incubated for 1 minute at room ...Details: 4uL of a 6uM MT solution in BRB80 (80mM PIPES, 2mM MgCl2, 1mM EGTA pH 6.8) along with 20uM paclitaxel was added onto a plasma-cleaned grid. The MTs were incubated for 1 minute at room temperature, and then the excess liquid was removed from the grid using Whatman #1 paper. Next, 4uL of a solution containing 17.5uM KIF1A-R350W in BRB80 supplemented with 20uM paclitaxel and 0.005 units per uL apyrase was added to the grid. The grid with the MT and kinesin mixture was then mounted into a Vitrobot, incubated for 1 minute at room temperature, and plunge-frozen into liquid nitrogen-cooled ethane..

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8344 / Average exposure time: 1.32 sec. / Average electron dose: 57.96 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.09 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

Final reconstructionNumber classes used: 4
Applied symmetry - Helical parameters - Δz: 5.571 Å
Applied symmetry - Helical parameters - Δ&Phi: 168.07 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 953398
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8uts

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8uts

chain_id: A, residue_range: 1-440, source_name: PDB, initial_model_type: experimental model

8uts

chain_id: B, residue_range: 1-433, source_name: PDB, initial_model_type: experimental model

8uts

chain_id: K, residue_range: 4-357, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 104.8
Output model

PDB-9yab:
KIF1A R350W bound to microtubules in the apo state

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