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- PDB-3wrd: Crystal Structure of the KIF5C Motor Domain Without Any Nucleotide -

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Basic information

Entry
Database: PDB / ID: 3wrd
TitleCrystal Structure of the KIF5C Motor Domain Without Any Nucleotide
ComponentsKinesin heavy chain isoform 5C
KeywordsMOTOR PROTEIN / kinesin / motor domain / nucleotide-free / ATPase / nucleotide binding / microtubule / transport protein
Function / homology
Function and homology information


distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / anterograde axonal protein transport / apolipoprotein receptor binding / intracellular mRNA localization / ciliary rootlet / motor neuron axon guidance / kinesin complex / microtubule motor activity / mRNA transport ...distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / anterograde axonal protein transport / apolipoprotein receptor binding / intracellular mRNA localization / ciliary rootlet / motor neuron axon guidance / kinesin complex / microtubule motor activity / mRNA transport / postsynaptic cytosol / axonal growth cone / axon cytoplasm / dendrite cytoplasm / GABA-ergic synapse / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / microtubule binding / microtubule / neuron projection / neuronal cell body / 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
Kinesin heavy chain isoform 5C
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.86 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
DepositionFeb 21, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Structure summary
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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)76,7034
Polymers76,5112
Non-polymers1922
Water905
1
A: Kinesin heavy chain isoform 5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3522
Polymers38,2561
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin heavy chain isoform 5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3522
Polymers38,2561
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.585, 71.322, 176.163
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 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P28738
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / 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: 2.94 Å3/Da / Density % sol: 58.15 % / Mosaicity: 0.686 ° / Mosaicity esd: 0.008 °
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: 2.86→50 Å / Num. all: 21497 / Num. obs: 21432 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.079 / Χ2: 0.889 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.86-2.916.90.94210150.876100
2.91-2.967.30.83910730.919100
2.96-3.027.30.66710480.903100
3.02-3.087.40.55710570.927100
3.08-3.157.40.41910540.982100
3.15-3.227.40.35310600.986100
3.22-3.37.40.29510460.992100
3.3-3.397.40.21410970.986100
3.39-3.497.40.16410350.956100
3.49-3.67.30.12910720.927100
3.6-3.737.40.10610550.914100
3.73-3.887.30.09410640.887100
3.88-4.067.30.08610630.859100
4.06-4.277.20.07310760.852100
4.27-4.547.10.06610860.87599.8
4.54-4.897.10.06410650.839100
4.89-5.387.20.06411030.79699.7
5.38-6.167.10.06610900.778100
6.16-7.756.90.0611300.766100
7.75-506.10.05511430.73195

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.7.0032refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KIN

2kin


Resolution: 2.86→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.324 / WRfactor Rwork: 0.254 / SU B: 0 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.845 / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2993 1096 5.1 %RANDOM
Rwork0.2373 ---
obs0.2405 21376 99.57 %-
all-21469 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 228.46 Å2 / Biso mean: 102.294 Å2 / Biso min: 45.92 Å2
Baniso -1Baniso -2Baniso -3
1--2.16 Å2-0 Å20 Å2
2--0.94 Å2-0 Å2
3---1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.86→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 10 5 4995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195072
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9616834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9235628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.69524.649228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.68815942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6911528
X-RAY DIFFRACTIONr_chiral_restr0.1040.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213740
X-RAY DIFFRACTIONr_mcbond_it8.0659.9252530
X-RAY DIFFRACTIONr_mcangle_it12.02814.853152
X-RAY DIFFRACTIONr_scbond_it9.16610.3872542
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 (%)
2.863-2.9360.436610.3541425149399.531
2.936-3.0150.432810.32114241505100
3.015-3.10.388710.3413751446100
3.1-3.1930.386790.311319139999.929
3.193-3.2950.46720.30912981370100
3.295-3.4070.332790.2751276135699.926
3.407-3.5320.356670.28411971264100
3.532-3.6720.318620.2721180124399.92
3.672-3.8290.279660.23711351201100
3.829-4.0080.271540.2361090114599.913
4.008-4.2160.287570.22710711128100
4.216-4.4590.291430.204984102999.806
4.459-4.750.275550.19192998599.898
4.75-5.1070.252510.20287692899.892
5.107-5.5580.338500.23380285499.766
5.558-6.1550.345410.251752793100
6.155-6.9980.324320.232686718100
6.998-8.320.268270.211591618100
8.32-10.8630.191290.19547551997.11
10.863-200.289180.24634038293.717

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