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- EMDB-64192: Cryo-EM structure of the heterotrimeric kinesin-2 from Caenorhabd... -

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Basic information

Entry
Database: EMDB / ID: EMD-64192
TitleCryo-EM structure of the heterotrimeric kinesin-2 from Caenorhabditis elegans
Map data
Sample
  • Complex: Ternary complex of the Caenorhabditis elegans KAP-1 in complex with two hetero-paired tails from kinesin-2 KLP-20 and KLP-11
    • Protein or peptide: Kinesin-associated protein KAP-1
    • Protein or peptide: Kinesin-like protein KLP-20
    • Protein or peptide: Kinesin-like protein KLP-11
KeywordsKinesin / TRANSPORT PROTEIN
Function / homology
Function and homology information


axonemal heterotrimeric kinesin-II complex / kinesin II complex / negative regulation of non-motile cilium assembly / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Intraflagellar transport / intraciliary anterograde transport / positive regulation of non-motile cilium assembly / ciliary transition zone / cilium organization ...axonemal heterotrimeric kinesin-II complex / kinesin II complex / negative regulation of non-motile cilium assembly / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Intraflagellar transport / intraciliary anterograde transport / positive regulation of non-motile cilium assembly / ciliary transition zone / cilium organization / anterograde axonal transport / non-motile cilium / kinesin complex / microtubule motor activity / microtubule-based movement / kinesin binding / axoneme / cilium assembly / axon cytoplasm / microtubule binding / microtubule / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Kinesin-associated protein 3 / Kinesin-associated protein (KAP) / Kinesin-associated protein (KAP) / 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-associated protein 3 / Kinesin-associated protein (KAP) / Kinesin-associated protein (KAP) / 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 / 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-associated protein / Kinesin-like protein / Kinesin-like protein klp-20
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.39 Å
AuthorsRen JQ / Zhao LY / Feng W
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: A mutual co-recognition mechanism ensures the proper assembly of heterotrimeric kinesin-2 for intraflagellar transport.
Authors: Jinqi Ren / Lingyan Zhao / Guanghan Chen / Guangshuo Ou / Wei Feng /
Abstract: Heterotrimeric kinesin-2, composed of two distinct kinesin motors and a kinesin-associated protein (KAP), is essential for intraflagellar transport and ciliogenesis. KAP specifically recognizes the ...Heterotrimeric kinesin-2, composed of two distinct kinesin motors and a kinesin-associated protein (KAP), is essential for intraflagellar transport and ciliogenesis. KAP specifically recognizes the hetero-paired motor tails for the holoenzyme assembly, but the underlying mechanism remains unclear. Here, we determine the structure of KAP-1 in complex with the hetero-paired tails from kinesin-2 motors KLP-20 and KLP-11. KAP-1 forms an elongated superhelical structure characterized by a central groove and a C-terminal helical (CTH)-hook. The two motor tails fold together and are co-recognized by the central groove of KAP-1. The adjacent hetero-pairing trigger sequences preceding the two tails form an intertwined heterodimer, which co-captures the CTH-hook of KAP-1 to complete the holoenzyme assembly. Mutations in the interfaces between KAP-1 and the two tails disrupt the heterotrimeric kinesin-2 complex and impair kinesin-2-mediated intraflagellar transport. Thus, KAP-1 and the hetero-paired motors are mutually co-recognized, ensuring the proper assembly of heterotrimeric kinesin-2 for cargo transport.
History
DepositionApr 15, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64192.png

Downloads & links

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Map

FileDownload / File: emd_64192.map.gz / Format: CCP4 / Size: 28.7 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.)
1 Å/pix.
x 196 pix.
= 196. Å		1 Å/pix.
x 196 pix.
= 196. Å		1 Å/pix.
x 196 pix.
= 196. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0838
Minimum - Maximum-0.1570385 - 0.41715035
Average (Standard dev.)0.0016919259 (±0.0138043035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 196.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64192_msk_1.map
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Half map: #1

Fileemd_64192_half_map_1.map
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Half map: #2

Fileemd_64192_half_map_2.map
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Sample components

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Entire : Ternary complex of the Caenorhabditis elegans KAP-1 in complex wi...

EntireName: Ternary complex of the Caenorhabditis elegans KAP-1 in complex with two hetero-paired tails from kinesin-2 KLP-20 and KLP-11
Components
  • Complex: Ternary complex of the Caenorhabditis elegans KAP-1 in complex with two hetero-paired tails from kinesin-2 KLP-20 and KLP-11
    • Protein or peptide: Kinesin-associated protein KAP-1
    • Protein or peptide: Kinesin-like protein KLP-20
    • Protein or peptide: Kinesin-like protein KLP-11

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Supramolecule #1: Ternary complex of the Caenorhabditis elegans KAP-1 in complex wi...

SupramoleculeName: Ternary complex of the Caenorhabditis elegans KAP-1 in complex with two hetero-paired tails from kinesin-2 KLP-20 and KLP-11
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Kinesin-associated protein KAP-1

MacromoleculeName: Kinesin-associated protein KAP-1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString: MNQVSIDAHP SDQAIIVRFE QSPSSSAGIS IKKRASSANV ESLGHQKIIH LKEMSLDVDI RALSNVILQK CLFIPATSRS QLEQVLFYIQ KRGNQRISAR SRSSSAVSFD RRPIHSPTIS AELGKIDEYI ECFYGETSVE KNKGAVALYE LSKNPQNLTQ LVNNETLMMA ...String:
MNQVSIDAHP SDQAIIVRFE QSPSSSAGIS IKKRASSANV ESLGHQKIIH LKEMSLDVDI RALSNVILQK CLFIPATSRS QLEQVLFYIQ KRGNQRISAR SRSSSAVSFD RRPIHSPTIS AELGKIDEYI ECFYGETSVE KNKGAVALYE LSKNPQNLTQ LVNNETLMMA LARVFREDWK KHFEVGTNIM NLFVNISKFS CLHGILLHHK IGTLCVNAME HETKRYDFWI AEMKKTDQET LRKLKTAIRK QAMLLAACVT FLTNLATDIS VELKMVRRNL VALLVKCLQM SSESTSSLTT ATIKFLLKLS IFDENKIVME QNGTIEKLLK LFPIQDPELR KAVIMLLFNF SFDSKNLPKM VNGGLVPHMA SLLDSDTKAL NMMYLLSCND DAKAMLAYTD AIKLLMKDVL SGTGSEVTKA VLLNICLEKR NAQLVCGQRG QGLDLLMEMS INSRDLMLIK VVRAISSHEG ATQNMFLKWI ETLIGIAKNE GADNSESKSS FGLECMGTVA ELKVAPWAKI IQSENLVPWM KTQLQEGIDE SEEVTVLRDI KPLQLQIVIA CGTMARQLDA ARLLAPLIDT FVQLLQSCQI DDEFVVQLLY VFLQFLKHKE LSARLMTQDS ALGAHMIDLM HDANAVVREV CDNALLIMGE HSKEWAKRIA GERFKWHNAQ WLEMVERDDS EFVDYDDEDF GADLKFDHYD DGFDMNEPLF

UniProtKB: Kinesin-associated protein

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Macromolecule #2: Kinesin-like protein KLP-20

MacromoleculeName: Kinesin-like protein KLP-20 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GGENLLEKVE EQAKLLEVNN KELEQSKFQE AHLRTQLEER TAVKVEIEER YSSLQEEAFV KSKKIKKVSN ELKDARAELK DLEEDHQRQV EAMLDDIRQL RKELLLNIAI IDEYIPVEHV ELIEKYVSWS EEHGDWQLKA IAYTGNNMRA SAPPAKKEFS NNNQTVPMYY ...String:
GGENLLEKVE EQAKLLEVNN KELEQSKFQE AHLRTQLEER TAVKVEIEER YSSLQEEAFV KSKKIKKVSN ELKDARAELK DLEEDHQRQV EAMLDDIRQL RKELLLNIAI IDEYIPVEHV ELIEKYVSWS EEHGDWQLKA IAYTGNNMRA SAPPAKKEFS NNNQTVPMYY SYRADLGAST AEHRPRTSSK KHRASIRLQQ LLT

UniProtKB: Kinesin-like protein klp-20

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Macromolecule #3: Kinesin-like protein KLP-11

MacromoleculeName: Kinesin-like protein KLP-11 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSEEDGRLES RTKEQHAQLE KKRRELAEQK RREREMVEAL ERQEEDTVDL KQTFSDLRTE VEAKTKKLKK MLIKLRQARN EIRDVSGAYS DERQDLDQTI AEVSKELKLK LLIVENFIPR DVSERIKERA EWNEDSFEWN VNAFQSTSSN SSTPLNNTIE VNEDGVFTRS ...String:
GSEEDGRLES RTKEQHAQLE KKRRELAEQK RREREMVEAL ERQEEDTVDL KQTFSDLRTE VEAKTKKLKK MLIKLRQARN EIRDVSGAYS DERQDLDQTI AEVSKELKLK LLIVENFIPR DVSERIKERA EWNEDSFEWN VNAFQSTSSN SSTPLNNTIE VNEDGVFTRS SGADSGVSVS GGNGTPATSQ FLDKRLVATP GCRRPMSMCE RMLVETAREQ FGAQRRPPIS GSGSFVEATI PEETIRFCGE NVVVFSALER FVPEVTDSDP STFSNSMMMS ARRPSIENLT IDASKVLVPI LNQSTMILKN SKNGQARNDT MPPNGSMRRS QN

UniProtKB: Kinesin-like protein

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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

Concentration0.1 mg/mL
BufferpH: 8
GridModel: Homemade / Material: NICKEL/TITANIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Number grids imaged: 2 / Number real images: 3137 / Average exposure time: 5.2 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2134786
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 76259
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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