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- EMDB-65777: Cryo-EM structure of the mouse kinesin-2 tail in complex with KAP... -

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Basic information

Entry
Database: EMDB / ID: EMD-65777
TitleCryo-EM structure of the mouse kinesin-2 tail in complex with KAP3 adaptor
Map dataSharpened map
Sample
  • Complex: Ternary complex of kinesin-2 KIF3A/B and KAP3 adaptor
    • Protein or peptide: Kinesin-like protein KIF3A
    • Protein or peptide: Kinesin-like protein KIF3B
    • Protein or peptide: Kinesin-associated protein 3
KeywordsKinesin-2 motor Intracellular transport Kinesin-adaptor complex / MOTOR PROTEIN
Function / homology
Function and homology information


positive regulation of calcium-dependent cell-cell adhesion / opsin transport / epidermal stem cell homeostasis / kinesin II complex / anterograde dendritic transport / intraciliary transport particle B binding / periciliary membrane compartment / Activation of SMO / Intraflagellar transport / centriole-centriole cohesion ...positive regulation of calcium-dependent cell-cell adhesion / opsin transport / epidermal stem cell homeostasis / kinesin II complex / anterograde dendritic transport / intraciliary transport particle B binding / periciliary membrane compartment / Activation of SMO / Intraflagellar transport / centriole-centriole cohesion / anterograde dendritic transport of neurotransmitter receptor complex / positive regulation of keratinocyte proliferation / microtubule anchoring at centrosome / Kinesins / intraciliary transport / cilium movement / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / COPI-dependent Golgi-to-ER retrograde traffic / motile cilium assembly / Hedgehog 'off' state / dorsal/ventral neural tube patterning / dentate gyrus development / MHC class II antigen presentation / non-motile cilium assembly / negative regulation of thymocyte apoptotic process / dorsal/ventral pattern formation / determination of left/right symmetry / microtubule motor activity / anterior/posterior pattern specification / neural precursor cell proliferation / neural tube development / negative regulation of cardiac muscle cell apoptotic process / motile cilium / negative regulation of neuroblast proliferation / smoothened signaling pathway / spectrin binding / thymocyte apoptotic process / positive regulation of cytokinesis / heart looping / forebrain development / keratinocyte proliferation / axoneme / cilium assembly / neuroblast proliferation / mitotic spindle assembly / kinesin binding / epidermis development / photoreceptor outer segment / microtubule-based process / vesicle-mediated transport / cardiac muscle cell apoptotic process / photoreceptor inner segment / centriole / dendrite cytoplasm / positive regulation of epithelial cell proliferation / condensed nuclear chromosome / spindle microtubule / kidney development / small GTPase binding / intracellular protein localization / heart development / microtubule cytoskeleton / midbody / protein phosphatase binding / microtubule binding / dendritic spine / in utero embryonic development / microtubule / cell population proliferation / postsynapse / neuron projection / cilium / ciliary basal body / axon / apoptotic process / dendrite / centrosome / negative regulation of apoptotic process / glutamatergic synapse / endoplasmic reticulum / Golgi apparatus / ATP binding / cytosol
Similarity search - Function
Kinesin-associated protein 3 / Kinesin-associated protein (KAP) / Kinesin-associated protein (KAP) / Kinesin-like protein / Armadillo/plakoglobin ARM repeat profile. / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. ...Kinesin-associated protein 3 / Kinesin-associated protein (KAP) / Kinesin-associated protein (KAP) / Kinesin-like protein / Armadillo/plakoglobin ARM repeat profile. / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Armadillo/beta-catenin-like repeats / Armadillo / Kinesin motor domain superfamily / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-like protein KIF3A / Kinesin-associated protein 3 / Kinesin-like protein KIF3B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsJiang X / Danev R / Yanagisawa H / Kikkawa M
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJER2202 Japan
Japan Society for the Promotion of Science (JSPS)JP21H05247 Japan
Japan Society for the Promotion of Science (JSPS)JP24KF0141 Japan
Japan Society for the Promotion of Science (JSPS)JP24K18106 Japan
CitationJournal: Sci Adv / Year: 2025
Title: The hook-like adaptor and cargo-binding (HAC) domain in the kinesin-2 tail enables adaptor assembly and cargo recognition.
Authors: Xuguang Jiang / Radostin Danev / Sotaro Ichinose / Baichun Niu / Sumio Ohtsuki / Haruaki Yanagisawa / Satoru Nagatoishi / Kouhei Tsumoto / Nobutaka Hirokawa / Masahide Kikkawa /
Abstract: Intracellular transport relies on motor proteins such as kinesins to deliver cargo along microtubules, yet how they recognize cargo remains unclear. Here, we present high-resolution cryo-electron ...Intracellular transport relies on motor proteins such as kinesins to deliver cargo along microtubules, yet how they recognize cargo remains unclear. Here, we present high-resolution cryo-electron microscopy structures of the heterotrimeric kinesin-2 complex (KIF3A/KIF3B/KAP3) bound to the cargo protein APC. Our findings reveal a previously uncharacterized KIF3 tail hook-like motif, termed the "HAC" domain, which mediates binding to both KAP3 adaptor and APC cargo. Within this domain, the KIF3A helical regions ensure cargo specificity, while a β-hairpin and KIF3B provide structural support. Biochemical and neuronal experiments confirm its functional importance. Notably, the HAC/KAP3 structure resembles hook-like architectures seen in kinesin-1 and dynein, suggesting a shared cargo recognition framework. These findings also shed light on kinesin-2 cargo specificity and offer a structural framework for understanding related neuronal transport mechanisms.
History
DepositionAug 10, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65777.png

Downloads & links

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Map

FileDownload / File: emd_65777.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 400 pix.
= 228.4 Å		0.57 Å/pix.
x 400 pix.
= 228.4 Å		0.57 Å/pix.
x 400 pix.
= 228.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.571 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.07181345 - 1.3725488
Average (Standard dev.)0.00063273055 (±0.01408687)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 228.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65777_msk_1.map
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Additional map: Raw map

Fileemd_65777_additional_1.map
AnnotationRaw map
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Half map: Halfmap1

Fileemd_65777_half_map_1.map
AnnotationHalfmap1
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Half map: Halfmap2

Fileemd_65777_half_map_2.map
AnnotationHalfmap2
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Sample components

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Entire : Ternary complex of kinesin-2 KIF3A/B and KAP3 adaptor

EntireName: Ternary complex of kinesin-2 KIF3A/B and KAP3 adaptor
Components
  • Complex: Ternary complex of kinesin-2 KIF3A/B and KAP3 adaptor
    • Protein or peptide: Kinesin-like protein KIF3A
    • Protein or peptide: Kinesin-like protein KIF3B
    • Protein or peptide: Kinesin-associated protein 3

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Supramolecule #1: Ternary complex of kinesin-2 KIF3A/B and KAP3 adaptor

SupramoleculeName: Ternary complex of kinesin-2 KIF3A/B and KAP3 adaptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 145 KDa

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Macromolecule #1: Kinesin-like protein KIF3A

MacromoleculeName: Kinesin-like protein KIF3A / type: protein_or_peptide / ID: 1 / Details: Clone in pETDuet-1 MCS1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.706559 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGSSHHHHHH SQVIVGGVDL LAKAEEQEKL LEESNMELEE RRRRAEQLRK ELEEKEQERL DIEEKYTSLQ EEAQGKTKKL KKVWTMLMA AKSEMADLQQ EHQREIEGLL ENIRQLSREL RLQMLIIDNF IPQDYQEMIE NYVHWNEDIG EWQLKCVAYT G NNMRKQTP ...String:
MGSSHHHHHH SQVIVGGVDL LAKAEEQEKL LEESNMELEE RRRRAEQLRK ELEEKEQERL DIEEKYTSLQ EEAQGKTKKL KKVWTMLMA AKSEMADLQQ EHQREIEGLL ENIRQLSREL RLQMLIIDNF IPQDYQEMIE NYVHWNEDIG EWQLKCVAYT G NNMRKQTP VPDKKERDPF EVDLSHVYLA YTEESLRQSL MKLERPRTSK GKARPKMGRR KRSAKPETVI DSLLQ

UniProtKB: Kinesin-like protein KIF3A

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Macromolecule #2: Kinesin-like protein KIF3B

MacromoleculeName: Kinesin-like protein KIF3B / type: protein_or_peptide / ID: 2 / Details: Clone in pETDuet-1 MCS2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 31.857107 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: LVGGKNIVDH TNEQQKILEQ KRQEIAEQKR REREIQQQME SRDEETLELK ETYTSLQQEV DIKTKKLKKL FSKLQAVKAE IHDLQEEHI KERQELEQTQ NELTRELKLK HLIIENFIPL EEKNKIMNRS FFDDEEDHWK LHPITRLENQ QMMKRPVSAV G YKRPLSQH ...String:
LVGGKNIVDH TNEQQKILEQ KRQEIAEQKR REREIQQQME SRDEETLELK ETYTSLQQEV DIKTKKLKKL FSKLQAVKAE IHDLQEEHI KERQELEQTQ NELTRELKLK HLIIENFIPL EEKNKIMNRS FFDDEEDHWK LHPITRLENQ QMMKRPVSAV G YKRPLSQH ARMSMMIRPE PRYRAENIML LELDMPSRTT RDYEGPAISP KVQAALDAAL QDEDEIQVDA SSFESTASRK PK ARPKSGR KSGSSSSSSG NPASQFYPQS RGLVPK

UniProtKB: Kinesin-like protein KIF3B

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Macromolecule #3: Kinesin-associated protein 3

MacromoleculeName: Kinesin-associated protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 80.224148 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MQGEDARYLK RKVKGGNIDV HPSEKALIVQ YEVEATILGE MGDPMLGERK ECQKIIRLKS LNANTDITSL ARKVVEECKL IHPSKLSEV EQLLYYLQNR RDSLPGKEKK EKSSKPKDPP PFEGMEIDEV ANINDMDEYI ELLYEDIPDK VRGSALILQL A RNPDNLEE ...String:
MQGEDARYLK RKVKGGNIDV HPSEKALIVQ YEVEATILGE MGDPMLGERK ECQKIIRLKS LNANTDITSL ARKVVEECKL IHPSKLSEV EQLLYYLQNR RDSLPGKEKK EKSSKPKDPP PFEGMEIDEV ANINDMDEYI ELLYEDIPDK VRGSALILQL A RNPDNLEE LLLNETALGA LARVLREDWK QSVELATNII YIFFCFSSFS HFHGLITHYK IGALCMNIID HELKRHELWQ EE LSKKKKA VDEDLENQTL RKDYDKTFKK YQGLVVKQEQ LLRVALYLLL NLAEDTRTEL KMRNKNIVHM LVKALDRDNF ELL ILVVSF LKKLSIFMEN KNDMVEMDIV EKLVKMIPCE HEDLLNITLR LLLNLSFDTG LRNKMVQVGL LPKLTALLGN ENYK QIAMC VLYHISMDDR FKSMFAYTDC IPQLMKMLFE CSDERIDLEL ISFCINLAAN KRNVQLICEG NGLKMLMKRA LKLKD PLLM KMIRNISQHD GPTKNLFIDY VGDLAAQISS DEEEEFVIEC LGTLANLTIP DLDWELVLKE YKLVPFLKDK LKPGAA EDD LVLEVVIMIG TVSMDDSCAA LLAKSGIIPA LIELLNAQQE DDEFVCQIIY VFYQMVFHQA TRDVIIKETQ APAYLID LM HDKNNEIRKV CDNTLDIIAE YDEEWAKKIQ SEKFRWHNSQ WLEMVESRQL D

UniProtKB: Kinesin-associated protein 3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.75 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 34176 / Average electron dose: 65.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.55 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 80000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 9701817
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-Initio Reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 539244
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: ModelAngelo de novo model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9w9h:
Cryo-EM structure of the mouse kinesin-2 tail in complex with KAP3 adaptor

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