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- PDB-7rik: Magic-Angle-Spinning NMR Structure of Kinesin-1 Motor Domain Asse... -

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Basic information

Entry
Database: PDB / ID: 7rik
TitleMagic-Angle-Spinning NMR Structure of Kinesin-1 Motor Domain Assembled with Microtubules
ComponentsKinesin-1 heavy chain
KeywordsMOTOR PROTEIN / kinesin-1 motor domain / Kif5b / microtubules / MTs / integrated structural biology
Function / homology
Function and homology information


cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization ...cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization / positive regulation of potassium ion transport / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / stress granule disassembly / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / centrosome localization / microtubule motor activity / ciliary rootlet / natural killer cell mediated cytotoxicity / kinesin complex / synaptic vesicle transport / Insulin processing / microtubule-based movement / centriolar satellite / axon cytoplasm / phagocytic vesicle / MHC class II antigen presentation / dendrite cytoplasm / regulation of membrane potential / axon guidance / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / cellular response to type II interferon / Signaling by ALK fusions and activated point mutants / microtubule binding / vesicle / microtubule / cadherin binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / simulated annealing
AuthorsZhang, C. / Guo, C. / Russell, R.W. / Quinn, C.M. / Li, M. / Williams, J.C. / Gronenborn, A.M. / Polenova, T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE0959496 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110758 United States
CitationJournal: Nat Commun / Year: 2022
Title: Magic-angle-spinning NMR structure of the kinesin-1 motor domain assembled with microtubules reveals the elusive neck linker orientation
Authors: Zhang, C. / Guo, C. / Russell, R.W. / Quinn, C.M. / Li, M. / Williams, J.C. / Gronenborn, A.M. / Polenova, T.
History
DepositionJul 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)39,3181
Polymers39,3181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, EMD-6187
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 22000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Kinesin-1 heavy chain / Conventional kinesin heavy chain / Ubiquitous kinesin heavy chain / UKHC


Mass: 39318.406 Da / Num. of mol.: 1 / Fragment: Kinesin motor domain residues 1-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF5B, KNS, KNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P33176

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic12D 13C-detected CORD
124isotropic22D 13C-detected CORD
135isotropic12D 13C-detected CORD
146isotropic22D 13C-detected CORD
154isotropic22D NCACX
174isotropic23D NCACX
164isotropic23D NCOCX

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
gel solid39.1 % w/w [U-100% 13C; U-100% 15N] Apo-Kif5b, 16.4 % w/w Porcine-alpha-tubulin, 16.4 % w/w Porcine-beta-tubulin, 5 uM TAXOL, 1 mM GUANOSINE-5'-TRIPHOSPHATE, 1 mM GUANOSINE-5'-DIPHOSPHATE, 58.1 % w/w Buffer, 100% H2OU-13C,15N-enriched Kif5b/MT100% H2O
gel solid58.2 % w/w [1,6-13C-glucose; U-100% 15N] Apo-Kif5b, 16.4 % w/w Porcine-alpha-tubulin, 16.4 % w/w Porcine-beta-tubulin, 5 uM TAXOL, 1 mM GUANOSINE-5'-TRIPHOSPHATE, 1 mM GUANOSINE-5'-DIPHOSPHATE, 59 % w/w Buffer, 100% H2O[1,6-13C],[U,15N]-enriched Kif5b/MT100% H2O
gel solid67.6 % w/w [2-13C-glucose; U-100% 15N] Apo-Kif5b, 16.4 % w/w Porcine-alpha-tubulin, 16.4 % w/w Porcine-beta-tubulin, 5 uM TAXOL, 1 mM GUANOSINE-5'-TRIPHOSPHATE, 1 mM GUANOSINE-5'-DIPHOSPHATE, 59.6 % w/w Buffer, 100% H2O[2-13C],[U,15N]-enriched Kif5b/MT100% H2O
gel solid49.1 % w/w [U-100% 13C; U-100% 15N] Apo-Kif5b, 16.4 % w/w Porcine-alpha-tubulin, 16.4 % w/w Porcine-beta-tubulin, 5 uM TAXOL, 1 mM GUANOSINE-5'-TRIPHOSPHATE, 1 mM GUANOSINE-5'-DIPHOSPHATE, 58.1 % w/w Buffer, 100% H2OU-13C,15N-enriched Kif5b/MT_cryo100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
9.1 % w/wApo-Kif5b[U-100% 13C; U-100% 15N]3
16.4 % w/wPorcine-alpha-tubulinnatural abundance3
16.4 % w/wPorcine-beta-tubulinnatural abundance3
5 uMTAXOLnatural abundance3
1 mMGUANOSINE-5'-TRIPHOSPHATEnatural abundance3
1 mMGUANOSINE-5'-DIPHOSPHATEnatural abundance3
58.1 % w/wBuffernatural abundance3
8.2 % w/wApo-Kif5b[1,6-13C-glucose; U-100% 15N]5
16.4 % w/wPorcine-alpha-tubulinnatural abundance5
16.4 % w/wPorcine-beta-tubulinnatural abundance5
5 uMTAXOLnatural abundance5
1 mMGUANOSINE-5'-TRIPHOSPHATEnatural abundance5
1 mMGUANOSINE-5'-DIPHOSPHATEnatural abundance5
59 % w/wBuffernatural abundance5
7.6 % w/wApo-Kif5b[2-13C-glucose; U-100% 15N]6
16.4 % w/wPorcine-alpha-tubulinnatural abundance6
16.4 % w/wPorcine-beta-tubulinnatural abundance6
5 uMTAXOLnatural abundance6
1 mMGUANOSINE-5'-TRIPHOSPHATEnatural abundance6
1 mMGUANOSINE-5'-DIPHOSPHATEnatural abundance6
59.6 % w/wBuffernatural abundance6
9.1 % w/wApo-Kif5b[U-100% 13C; U-100% 15N]4
16.4 % w/wPorcine-alpha-tubulinnatural abundance4
16.4 % w/wPorcine-beta-tubulinnatural abundance4
5 uMTAXOLnatural abundance4
1 mMGUANOSINE-5'-TRIPHOSPHATEnatural abundance4
1 mMGUANOSINE-5'-DIPHOSPHATEnatural abundance4
58.1 % w/wBuffernatural abundance4
Sample conditionsDetails: All the NMR samples were prepared under same condition.
Ionic strength: 100 mM / Label: conditions_all / pH: 7.4 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III8501
Bruker AVANCE NEOBrukerAVANCE NEO6002CryoProbe

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNpeak picking
CcpNmr AnalysisCCPNchemical shift assignment
TALOS-NCornilescu, Delaglio and Baxchemical shift calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 8 / Details: torsion angle dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 22000 / Conformers submitted total number: 22

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