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- PDB-5ybe: Structure of KANK1/KIF21A complex -

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Basic information

Entry
Database: PDB / ID: 5ybe
TitleStructure of KANK1/KIF21A complex
Components
  • KIF21A
  • Kank1 protein
KeywordsCELL ADHESION / Microtubule-cell adhesion crosstalk / KANK1-KIF21A complex / Ankyrin repeat / Scaffold protein / Structural Biology
Function / homology
Function and homology information


negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / podocyte cell migration / negative regulation of substrate adhesion-dependent cell spreading / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / negative regulation of actin filament polymerization / MHC class II antigen presentation / ankyrin repeat binding / regulation of Rho protein signal transduction ...negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / podocyte cell migration / negative regulation of substrate adhesion-dependent cell spreading / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / negative regulation of actin filament polymerization / MHC class II antigen presentation / ankyrin repeat binding / regulation of Rho protein signal transduction / regulation of establishment of cell polarity / negative regulation of Rho protein signal transduction / microtubule motor activity / kinesin complex / positive regulation of wound healing / microtubule-based movement / positive regulation of Wnt signaling pathway / negative regulation of insulin receptor signaling pathway / negative regulation of cell migration / ruffle membrane / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / negative regulation of neuron projection development / actin cytoskeleton organization / microtubule binding / cell population proliferation / microtubule / cytoskeleton / axon / dendrite / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Domain of unknown function DUF3447 / Kinesin-like protein / Ankyrin repeat-containing 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 / Kinesin motor domain superfamily ...Domain of unknown function DUF3447 / Kinesin-like protein / Ankyrin repeat-containing 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 / Kinesin motor domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular 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 / Mainly Alpha
Similarity search - Domain/homology
Kank1 protein / Kinesin-like protein KIF21A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.111 Å
AuthorsWeng, Z.F. / Shang, Y. / Yao, D.Q. / Zhu, J.W. / Zhang, R.G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470733; U1532121 China
Chinese Academy of SciencesXDB08030104 China
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural analyses of key features in the KANK1/KIF21A complex yield mechanistic insights into the cross-talk between microtubules and the cell cortex.
Authors: Weng, Z. / Shang, Y. / Yao, D. / Zhu, J. / Zhang, R.
History
DepositionSep 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kank1 protein
B: KIF21A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2473
Polymers33,1852
Non-polymers621
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-3 kcal/mol
Surface area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.513, 51.958, 136.984
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 Kank1 protein


Mass: 30887.000 Da / Num. of mol.: 1 / Fragment: UNP residues 923-1202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kank1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6AXG6
#2: Protein/peptide KIF21A


Mass: 2297.657 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9QXL2*PLUS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M sodium formate pH8.0, 14% PEG3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97538 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97538 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 14123 / % possible obs: 92.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.054 / Rrim(I) all: 0.118 / Χ2: 0.901 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.142.50.4224840.7610.2920.5170.92465.2
2.14-2.182.50.3945250.7820.2610.4761.03171
2.18-2.222.70.3585440.8470.2350.4310.82671.5
2.22-2.262.90.4085810.8680.2550.4841.00779.3
2.26-2.3130.3776160.8910.2340.4470.80981.3
2.31-2.373.20.3516790.870.2120.4130.889.6
2.37-2.423.60.3337260.930.1930.3870.92397.3
2.42-2.494.10.3837230.9140.2080.4380.91797.4
2.49-2.564.40.3247360.9280.1710.3680.85996.6
2.56-2.654.70.2897360.9560.1480.3260.8999.2
2.65-2.744.60.2657760.9640.1370.30.95798.6
2.74-2.854.80.1977330.9750.1010.2230.84599.3
2.85-2.985.30.1947620.9770.0940.2170.91699.6
2.98-3.145.30.1547630.9780.0740.1720.94799.9
3.14-3.335.20.1217560.9840.0590.1360.89199.7
3.33-3.594.90.0967700.9860.0480.1070.95299.7
3.59-3.955.10.0777920.9910.0380.0860.97999.1
3.95-4.525.30.0637660.9910.0310.070.83899
4.52-5.74.70.0627980.9930.0310.070.88398.9
5.7-504.70.068570.9960.0310.0680.84597.9

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
PHENIX1.10_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HBD

4hbd


Resolution: 2.111→41.395 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.32
RfactorNum. reflection% reflection
Rfree0.2456 601 4.94 %
Rwork0.1804 --
obs0.1836 12160 79.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.64 Å2 / Biso mean: 32.7242 Å2 / Biso min: 15.53 Å2
Refinement stepCycle: final / Resolution: 2.111→41.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 4 94 2146
Biso mean--39.08 33.2 -
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132080
X-RAY DIFFRACTIONf_angle_d1.2152817
X-RAY DIFFRACTIONf_chiral_restr0.065330
X-RAY DIFFRACTIONf_plane_restr0.007369
X-RAY DIFFRACTIONf_dihedral_angle_d15.3791268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1111-2.32360.325780.20521645172346
2.3236-2.65980.2771510.20982677282876
2.6598-3.35080.26331720.193498367097
3.3508-41.40280.22112000.16493739393999

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