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- PDB-5yay: Crystal structure of KANK1/KIF21A complex -

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Basic information

Entry
Database: PDB / ID: 5yay
TitleCrystal structure of KANK1/KIF21A complex
Components
  • KN motif and ankyrin repeat domains 1
  • Kinesin-like protein KIF21A
KeywordsPROTEIN BINDING / Scaffold protein / ANK repeat
Function / homology
Function and homology information


regulation of microtubule depolymerization / negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / regulation of axon guidance / 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 / cortical microtubule organization ...regulation of microtubule depolymerization / negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / regulation of axon guidance / 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 / cortical microtubule organization / ankyrin repeat binding / plus-end-directed microtubule motor activity / 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 / regulation of microtubule polymerization / axonal growth cone / negative regulation of insulin receptor signaling pathway / negative regulation of cell migration / beta-catenin binding / ruffle membrane / positive regulation of canonical Wnt signaling pathway / negative regulation of neuron projection development / cell cortex / protein-macromolecule adaptor activity / actin cytoskeleton organization / microtubule binding / microtubule / cell population proliferation / cytoskeleton / dendrite / ATP hydrolysis activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Kank N-terminal motif / KN motif / : / Kinesin-like protein / Ankyrin repeat-containing domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain ...Kank N-terminal motif / KN motif / : / Kinesin-like protein / Ankyrin repeat-containing domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain / Kinesin motor domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / 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
KN motif and ankyrin repeat domains 1 / Kinesin-like protein KIF21A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsWei, Z. / Pan, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770791 China
National Natural Science Foundation of China31570741 China
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural insights into ankyrin repeat-mediated recognition of the kinesin motor protein KIF21A by KANK1, a scaffold protein in focal adhesion.
Authors: Pan, W. / Sun, K. / Tang, K. / Xiao, Q. / Ma, C. / Yu, C. / Wei, Z.
History
DepositionSep 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Mar 7, 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

Downloads & links

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Assembly

Deposited unit
A: KN motif and ankyrin repeat domains 1
B: Kinesin-like protein KIF21A


Theoretical massNumber of molelcules
Total (without water)31,0082
Polymers31,0082
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-5 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.043, 52.080, 136.095
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 KN motif and ankyrin repeat domains 1


Mass: 27705.535 Da / Num. of mol.: 1 / Fragment: UNP residues 1088-1338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kank1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(C plus) / References: UniProt: E9Q238
#2: Protein/peptide Kinesin-like protein KIF21A


Mass: 3301.966 Da / Num. of mol.: 1 / Fragment: UNP residues 1142-1169 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9QXL2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium formate and 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 39577 / % possible obs: 98.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 22.36 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.028 / Rrim(I) all: 0.064 / Χ2: 1.957 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.585.50.83520050.6880.3970.9291.439100
1.58-1.615.50.67419610.7380.3220.7511.438100
1.61-1.645.50.55119570.8190.2630.6131.432100
1.64-1.675.50.44319840.8510.2110.4931.451100
1.67-1.715.50.40519790.890.1920.451.44999.9
1.71-1.755.50.32219980.9120.1540.3591.49399.9
1.75-1.795.60.26319860.9480.1250.2931.48100
1.79-1.845.50.21419790.9670.1010.2381.537100
1.84-1.895.50.17319970.9770.0820.1921.63899.9
1.89-1.955.50.13819880.9850.0650.1531.80799.9
1.95-2.025.50.11419930.9880.0540.1272.06499.6
2.02-2.15.40.09319870.9910.0450.1042.28699.8
2.1-2.25.30.07719920.9930.0370.0862.42199.6
2.2-2.325.30.06920140.9950.0330.0772.61899.4
2.32-2.465.30.06519770.9940.0310.0732.81999.1
2.46-2.655.40.05320010.9970.0250.0592.48998.8
2.65-2.925.30.04320150.9980.020.0472.23497.9
2.92-3.345.50.03919930.9980.0180.0432.37898.1
3.34-4.215.10.03819730.9960.0190.0432.55394.1
4.21-504.50.03917980.9960.0210.0442.43181

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HBD

4hbd


Resolution: 1.55→28.484 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 1976 5 %
Rwork0.1833 37542 -
obs0.1841 39518 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.49 Å2 / Biso mean: 35.4218 Å2 / Biso min: 14.42 Å2
Refinement stepCycle: final / Resolution: 1.55→28.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 0 121 2081
Biso mean---35.8 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122022
X-RAY DIFFRACTIONf_angle_d1.3532742
X-RAY DIFFRACTIONf_chiral_restr0.06321
X-RAY DIFFRACTIONf_plane_restr0.006357
X-RAY DIFFRACTIONf_dihedral_angle_d13.481748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5498-1.58860.29791410.24582691283299
1.5886-1.63150.25061400.229626612801100
1.6315-1.67950.27441420.213326882830100
1.6795-1.73370.22581430.205227012844100
1.7337-1.79570.21071410.193326932834100
1.7957-1.86760.20091400.194626662806100
1.8676-1.95250.21181430.187727142857100
1.9525-2.05550.2031420.179226932835100
2.0555-2.18420.18841420.168826982840100
2.1842-2.35280.1961430.17952729287299
2.3528-2.58940.20551430.18122694283799
2.5894-2.96370.20251420.1882713285598
2.9637-3.73270.19311430.17452712285597
3.7327-28.48880.18161310.17882489262085
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.04892.00320.64315.09040.51314.5822-0.332-0.87670.19091.22420.28270.2312-0.6551-0.62730.03340.78030.15120.03890.4808-0.04730.2586-2.01331.463759.7579
20.5929-0.5747-0.37270.5418-0.19760.72850.0311-0.38480.34780.7235-0.1331-0.2404-0.14370.37080.1750.6021-0.0142-0.1020.3674-0.03710.30998.2468-0.113255.8785
33.47530.527-0.22492.56620.13783.7562-0.1807-0.35640.32410.61080.14490.1459-0.3374-0.11640.0290.34480.0718-0.02720.18880.00510.1803-0.54390.312248.1089
43.53-0.7148-0.90963.62860.16943.6859-0.0175-0.06870.24820.32260.0714-0.1521-0.3655-0.0468-0.06230.18190.0185-0.0320.1380.03390.15472.0987-0.163137.7063
56.3887-0.7428-0.78836.2563-0.2224.41840.07030.44380.0809-0.18040.10410.731-0.1319-0.7099-0.13530.11770.0072-0.00490.24510.04660.2065-2.82980.206328.7897
62.12760.5299-0.52834.4843-1.26434.6077-0.05440.27-0.0705-0.7376-0.162-0.60470.3450.36670.17050.23840.05020.09130.22760.04040.231510.4547-0.06615.548
73.330.5284-1.62323.9005-2.25175.5371-0.22320.05230.1114-0.36010.25210.82360.0960.12640.11140.93930.01280.19170.39860.0180.30949.6476-0.01350.4063
86.89434.5372-8.25443.0394-5.63062.0557-0.25450.5735-0.5952-1.0967-0.45-1.2490.62890.44120.57040.45120.05260.21030.48990.0270.493615.5144-9.53819.8682
92.05541.642-0.62237.7692-1.7469.1172-0.15690.3333-0.49460.33960.2886-0.63970.6341-0.0139-0.15120.24590.04120.01560.2035-0.02190.29159.345-11.065733.6898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1090 through 1107 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1108 through 1134 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1135 through 1172 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1173 through 1206 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1207 through 1231 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1232 through 1321 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1322 through 1333 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 1154 through 1161 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1162 through 1168 )B0

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