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- PDB-3x2t: Crystal Structure of the KIF5C Motor Domain With ADP -

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Basic information

Entry
Database: PDB / ID: 3x2t
TitleCrystal Structure of the KIF5C Motor Domain With ADP
ComponentsKinesin heavy chain isoform 5C
KeywordsMOTOR PROTEIN / kinesin / motor domain / ATPase / nucleotide binding / microtubule / transport protein
Function / homology
Function and homology information


distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / anterograde dendritic transport of neurotransmitter receptor complex / anterograde axonal protein transport / apolipoprotein receptor binding / intracellular mRNA localization / plus-end-directed microtubule motor activity / motor neuron axon guidance / postsynaptic cytosol / ciliary rootlet ...distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / anterograde dendritic transport of neurotransmitter receptor complex / anterograde axonal protein transport / apolipoprotein receptor binding / intracellular mRNA localization / plus-end-directed microtubule motor activity / motor neuron axon guidance / postsynaptic cytosol / ciliary rootlet / synaptic vesicle transport / kinesin complex / microtubule motor activity / mRNA transport / axonal growth cone / axon cytoplasm / dendrite cytoplasm / axon guidance / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / microtubule binding / microtubule / neuron projection / neuronal cell body / dendrite / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Kinesin motor domain / Kinesin / 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 ...Kinesin motor domain / Kinesin / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Kinesin heavy chain isoform 5C
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsInoue, S. / Nitta, R. / Hirokawa, N.
CitationJournal: EMBO J / Year: 2015
Title: X-ray and Cryo-EM structures reveal mutual conformational changes of Kinesin and GTP-state microtubules upon binding.
Authors: Manatsu Morikawa / Hiroaki Yajima / Ryo Nitta / Shigeyuki Inoue / Toshihiko Ogura / Chikara Sato / Nobutaka Hirokawa /
Abstract: The molecular motor kinesin moves along microtubules using energy from ATP hydrolysis in an initial step coupled with ADP release. In neurons, kinesin-1/KIF5C preferentially binds to the GTP-state ...The molecular motor kinesin moves along microtubules using energy from ATP hydrolysis in an initial step coupled with ADP release. In neurons, kinesin-1/KIF5C preferentially binds to the GTP-state microtubules over GDP-state microtubules to selectively enter an axon among many processes; however, because the atomic structure of nucleotide-free KIF5C is unavailable, its molecular mechanism remains unresolved. Here, the crystal structure of nucleotide-free KIF5C and the cryo-electron microscopic structure of nucleotide-free KIF5C complexed with the GTP-state microtubule are presented. The structures illustrate mutual conformational changes induced by interaction between the GTP-state microtubule and KIF5C. KIF5C acquires the 'rigor conformation', where mobile switches I and II are stabilized through L11 and the initial portion of the neck-linker, facilitating effective ADP release and the weak-to-strong transition of KIF5C microtubule affinity. Conformational changes to tubulin strengthen the longitudinal contacts of the GTP-state microtubule in a similar manner to GDP-taxol microtubules. These results and functional analyses provide the molecular mechanism of the preferential binding of KIF5C to GTP-state microtubules.
History
DepositionJan 2, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Nov 20, 2019Group: Database references / Category: pdbx_database_related / struct_ref_seq_dif
Item: _pdbx_database_related.content_type / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin heavy chain isoform 5C
B: Kinesin heavy chain isoform 5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3664
Polymers76,5112
Non-polymers8542
Water905
1
A: Kinesin heavy chain isoform 5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6832
Polymers38,2561
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kinesin heavy chain isoform 5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6832
Polymers38,2561
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.858, 71.827, 176.891
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kinesin heavy chain isoform 5C / Kinesin heavy chain neuron-specific 2


Mass: 38255.551 Da / Num. of mol.: 2 / Fragment: Motor domain, RESIDUES 1-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif5c, Nkhc2 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P28738
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.77 % / Mosaicity: 0.597 ° / Mosaicity esd: 0.007 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ammonium sulfate, Sodium citrate, Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 21, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 25884 / Num. obs: 25753 / % possible obs: 99.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.049 / Χ2: 0.683 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.86.30.79825090.69198.4
2.8-2.916.50.51425400.56999.3
2.91-3.046.60.3225020.59799.7
3.04-3.26.70.19125610.64999.7
3.2-3.46.70.12625610.74599.8
3.4-3.666.80.07525510.82699.8
3.66-4.036.90.05625630.76699.9
4.03-4.627.10.0425990.649100
4.62-5.817.20.03526330.656100
5.81-506.70.02327340.67598.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.8.0049refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2KIN

2kin


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.303 / WRfactor Rwork: 0.228 / SU B: 15.697 / SU ML: 0.323 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.685 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2978 1299 5.1 %RANDOM
Rwork0.2244 ---
obs0.228 25646 99.11 %-
all-25878 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 200.98 Å2 / Biso mean: 84.422 Å2 / Biso min: 38.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å2-0 Å20 Å2
2--2.22 Å20 Å2
3----3.33 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4996 0 54 5 5055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195141
X-RAY DIFFRACTIONr_bond_other_d0.0060.024931
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.9716940
X-RAY DIFFRACTIONr_angle_other_deg0.886311384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9915631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6924.585229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.06415936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.471528
X-RAY DIFFRACTIONr_chiral_restr0.0920.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021135
X-RAY DIFFRACTIONr_mcbond_it6.058.1342542
X-RAY DIFFRACTIONr_mcbond_other6.0378.1342541
X-RAY DIFFRACTIONr_mcangle_it8.99412.1773167
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.702-2.7710.439930.3811725188896.292
2.771-2.8450.3271090.3091665178899.217
2.845-2.9260.324920.2841624172899.306
2.926-3.0140.286790.2621624170899.707
3.014-3.1110.326800.2591575166099.699
3.111-3.2170.347570.2641524158399.874
3.217-3.3350.314750.2711492156999.873
3.335-3.4670.347930.2331398149599.732
3.467-3.6170.29700.2211382145399.931
3.617-3.7870.272820.2151314139799.928
3.787-3.9840.325740.2141236131199.924
3.984-4.2150.273730.2121194126899.921
4.215-4.4920.222580.17811191177100
4.492-4.8320.192530.16710611114100
4.832-5.2620.26530.1929681021100
5.262-5.8330.347370.243925962100
5.833-6.6420.361450.272814859100
6.642-7.9190.378430.241703746100
7.919-10.4130.307210.18559461999.354
10.413-200.308120.2441044095.909

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