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- PDB-7x4n: Crystal Structure of C. elegans kinesin-4 KLP-12 complexed with t... -

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Basic information

Entry
Database: PDB / ID: 7x4n
TitleCrystal Structure of C. elegans kinesin-4 KLP-12 complexed with tubulin and DARPin
Components
  • DARPin
  • Kinesin-like protein
  • Tubulin alpha-1A chain
  • Tubulin beta chain
KeywordsMOTOR PROTEIN / kinesin-4 / KLP-12 / KIF21A / KIF21B / microtubule / tubulin / axon / CFEOM1 / DARPin
Function / homology
Function and homology information


COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / microtubule motor activity / kinesin complex / microtubule-based movement / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule binding ...COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / microtubule motor activity / kinesin complex / microtubule-based movement / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / GTPase activity / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm
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 / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin ...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 / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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 / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Kinesin-like protein / Tubulin alpha-1A chain / Tubulin beta chain
Similarity search - Component
Biological speciessynthetic construct (others)
Caenorhabditis elegans (invertebrata)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsTaguchi, S. / Imasaki, T. / Saijo-Hamano, Y. / Sakai, N. / Nitta, R.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101070 Japan
Japan Society for the Promotion of Science (JSPS)19K07246 Japan
Japan Society for the Promotion of Science (JSPS)19H03396 Japan
Japan Agency for Medical Research and Development (AMED)JP21gm0810013 Japan
Japan Science and TechnologyJPMJMS2024 Japan
CitationJournal: Elife / Year: 2022
Title: Structural model of microtubule dynamics inhibition by kinesin-4 from the crystal structure of KLP-12 -tubulin complex.
Authors: Taguchi, S. / Nakano, J. / Imasaki, T. / Kita, T. / Saijo-Hamano, Y. / Sakai, N. / Shigematsu, H. / Okuma, H. / Shimizu, T. / Nitta, E. / Kikkawa, S. / Mizobuchi, S. / Niwa, S. / Nitta, R.
History
DepositionMar 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1A chain
B: Tubulin beta chain
C: DARPin
E: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,3559
Polymers156,8344
Non-polymers1,5215
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-63 kcal/mol
Surface area51020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.330, 80.980, 117.750
Angle α, β, γ (deg.)90.00, 93.51, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 4 types, 4 molecules ABCE

#1: Protein Tubulin alpha-1A chain / Alpha-tubulin 1 / Tubulin alpha-1 chain


Mass: 50121.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02550
#2: Protein Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554
#3: Protein DARPin


Mass: 16792.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Protein Kinesin-like protein


Mass: 40013.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: klp-12, CELE_T01G1.1, T01G1.1 / Production host: Escherichia coli (E. coli) / References: UniProt: G5EGS3

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Non-polymers , 4 types, 5 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#8: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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Details

Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: ammonium acetate, HEPES, polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 34669 / % possible obs: 98.2 % / Redundancy: 87.1 % / CC1/2: 0.977 / Rrim(I) all: 0.355 / Net I/σ(I): 19.28
Reflection shellResolution: 2.88→3.05 Å / Mean I/σ(I) obs: 3.39 / Num. unique obs: 5455 / CC1/2: 0.513 / Rrim(I) all: 1.97

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MIO

5mio


Resolution: 2.88→49.25 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2958 1707 5.05 %
Rwork0.2105 --
obs0.2149 33796 95.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.88→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10295 0 93 0 10388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110595
X-RAY DIFFRACTIONf_angle_d1.39914369
X-RAY DIFFRACTIONf_dihedral_angle_d23.1221465
X-RAY DIFFRACTIONf_chiral_restr0.0771611
X-RAY DIFFRACTIONf_plane_restr0.0081866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.960.38151200.29172350X-RAY DIFFRACTION84
2.96-3.060.37511330.28052510X-RAY DIFFRACTION91
3.06-3.170.36451400.28542646X-RAY DIFFRACTION95
3.17-3.30.37311490.27642684X-RAY DIFFRACTION97
3.3-3.450.37581410.26572722X-RAY DIFFRACTION99
3.45-3.630.3531450.25382721X-RAY DIFFRACTION99
3.63-3.860.32551370.21472764X-RAY DIFFRACTION98
3.86-4.150.28821470.19372708X-RAY DIFFRACTION98
4.15-4.570.26641380.17432736X-RAY DIFFRACTION97
4.57-5.230.23461460.16822700X-RAY DIFFRACTION97
5.23-6.590.29241520.1982747X-RAY DIFFRACTION98
6.59-49.250.2151590.16322801X-RAY DIFFRACTION97

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