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- PDB-6ojq: Monomeric kinesin-1 motor domain in no-nucleotide state bound to ... -

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Basic information

Entry
Database: PDB / ID: 6ojq
TitleMonomeric kinesin-1 motor domain in no-nucleotide state bound to GMPCPP-stabilized microtubule
Components
  • Kinesin-1 heavy chain
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsMOTOR PROTEIN / Kinesin / Microtubule
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 / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / mitocytosis / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / ciliary rootlet ...regulation of modification of synapse structure, modulating synaptic transmission / plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / mitocytosis / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / ciliary rootlet / lysosome localization / positive regulation of potassium ion transport / plus-end-directed microtubule motor activity / vesicle transport along microtubule / RHO GTPases activate KTN1 / Kinesins / positive regulation of axon guidance / kinesin complex / microtubule motor activity / centrosome localization / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / stress granule disassembly / natural killer cell mediated cytotoxicity / Insulin processing / synaptic vesicle transport / postsynaptic cytosol / microtubule-based process / cytoplasmic microtubule / phagocytic vesicle / axon cytoplasm / MHC class II antigen presentation / cellular response to interleukin-4 / dendrite cytoplasm / axon guidance / positive regulation of synaptic transmission, GABAergic / regulation of membrane potential / positive regulation of protein localization to plasma membrane / cellular response to type II interferon / structural constituent of cytoskeleton / centriolar satellite / microtubule cytoskeleton organization / neuron migration / Signaling by ALK fusions and activated point mutants / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / nuclear membrane / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / vesicle / microtubule / cilium / cadherin binding / protein heterodimerization activity / GTPase activity / ubiquitin protein ligase binding / GTP binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Kinesin motor domain / Kinesin / Kinesin-like protein / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. ...Kinesin motor domain / Kinesin / Kinesin-like protein / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase 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 / 60s Ribosomal Protein L30; Chain: A; / 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 / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Helix Hairpins / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GUANOSINE-5'-TRIPHOSPHATE / Kinesin-1 heavy chain / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsCha, H.K. / Debs, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM 110530-01 United States
CitationJournal: To Be Published
Title: Structural Intermediates of the Dimeric Kinesin Stepping Cycle Revealed by Cryo-EM
Authors: Cha, H.K. / Debs, G. / Liu, X. / Liu, D. / Sindelar, C.V.
History
DepositionApr 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

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Assembly

Deposited unit
B: Tubulin beta-2B chain
A: Tubulin alpha-1B chain
K: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,0307
Polymers131,9373
Non-polymers1,0934
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 3 molecules BAK

#1: Protein Tubulin beta-2B chain


Mass: 47825.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q6B856
#2: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 48665.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P81947
#3: Protein Kinesin-1 heavy chain / Conventional kinesin heavy chain / Ubiquitous kinesin heavy chain / UKHC


Mass: 35445.801 Da / Num. of mol.: 1
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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Non-polymers , 3 types, 4 molecules

#4: Chemical ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-CPP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Monomeric kinesin-1 motor domain in the no-nucleotide state bound to GMPCPP-stabilized microtubules
Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Source (natural)Organism: Bos taurus (domestic cattle)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.625 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.13_2998refinement
PHENIX1.13_2998refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 403424 / Symmetry type: POINT
RefinementStereochemistry target values: GeoStd + Monomer Library
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003218271
ELECTRON MICROSCOPYf_angle_d0.668232919
ELECTRON MICROSCOPYf_chiral_restr0.04371400
ELECTRON MICROSCOPYf_plane_restr0.00312762
ELECTRON MICROSCOPYf_dihedral_angle_d7.14587381

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