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- PDB-9pmb: Kinesin-1 heterotetramer -

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Basic information

Entry
Database: PDB / ID: 9pmb
TitleKinesin-1 heterotetramer
Components
  • Kinesin light chain 1
  • Kinesin-1 heavy chain
KeywordsMOTOR PROTEIN / Autoinhibited Kinesin-1 heterotetramer
Function / homology
Function and homology information


regulation of modification of synapse structure, modulating synaptic transmission / plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde axonal protein transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / ciliary rootlet ...regulation of modification of synapse structure, modulating synaptic transmission / plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde axonal protein transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / ciliary rootlet / lysosome localization / positive regulation of potassium ion transport / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / Kinesins / vesicle transport along microtubule / centrosome localization / natural killer cell mediated cytotoxicity / microtubule motor activity / kinesin complex / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / stress granule disassembly / Insulin processing / synaptic vesicle transport / cytoskeletal motor activity / kinesin binding / postsynaptic cytosol / centriolar satellite / phagocytic vesicle / axon cytoplasm / MHC class II antigen presentation / dendrite cytoplasm / positive regulation of synaptic transmission, GABAergic / axon guidance / sperm end piece / positive regulation of protein localization to plasma membrane / regulation of membrane potential / cellular response to type II interferon / Signaling by ALK fusions and activated point mutants / growth cone / nuclear membrane / cytoplasmic vesicle / microtubule binding / vesicle / microtubule / cell adhesion / cadherin binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / : / Tetratricopeptide repeat / Tetratricopeptide repeat / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain ...Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / : / Tetratricopeptide repeat / Tetratricopeptide repeat / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-1 heavy chain / Kinesin light chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å
AuthorsAshaduzzaman, M. / Al-Bassam, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM110283 United States
CitationJournal: To Be Published
Title: Kinesin-1 heterotetramer
Authors: Ashaduzzaman, M. / Al-Bassam, J.
History
DepositionJul 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Kinesin light chain 1
D: Kinesin light chain 1
A: Kinesin-1 heavy chain
B: Kinesin-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)398,7094
Polymers398,7094
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Kinesin light chain 1 / KLC 1


Mass: 62969.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLC1, KLC, KNS2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q07866
#2: Protein Kinesin-1 heavy chain / Conventional kinesin heavy chain / Ubiquitous kinesin heavy chain / UKHC


Mass: 136384.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF5B, KNS, KNS1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P33176
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Heterotetramer of Kinesin-1 KIF5B/KLC1 / Type: COMPLEX / Details: 2:2 complex of KIF5B/KLC1 / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.5 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.2
SpecimenConc.: 3.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30746 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 418.16 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002428313
ELECTRON MICROSCOPYf_angle_d0.524638036
ELECTRON MICROSCOPYf_chiral_restr0.03554146
ELECTRON MICROSCOPYf_plane_restr0.00475041
ELECTRON MICROSCOPYf_dihedral_angle_d4.97473797

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