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- PDB-5ybu: Structure of the KANK1 ankyrin domain in complex with KIF21A peptide -

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Basic information

Entry
Database: PDB / ID: 5ybu
TitleStructure of the KANK1 ankyrin domain in complex with KIF21A peptide
Components
  • KN motif and ankyrin repeat domain-containing protein 1
  • Kinesin-like protein KIF21A
KeywordsCELL ADHESION
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 / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / negative regulation of actin filament polymerization / regulation of Rho protein signal transduction / ankyrin repeat binding / Kinesins / regulation of establishment of cell polarity ...negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / podocyte cell migration / negative regulation of substrate adhesion-dependent cell spreading / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / negative regulation of actin filament polymerization / regulation of Rho protein signal transduction / ankyrin repeat binding / Kinesins / regulation of establishment of cell polarity / negative regulation of Rho protein signal transduction / COPI-dependent Golgi-to-ER retrograde traffic / 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 / beta-catenin binding / ruffle membrane / positive regulation of canonical Wnt signaling pathway / negative regulation of neuron projection development / actin cytoskeleton organization / microtubule binding / Estrogen-dependent gene expression / microtubule / cell population proliferation / cytoskeleton / axon / dendrite / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / 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 repeat / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / Ankyrin repeat 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 domain-containing protein 1 / Kinesin-like protein KIF21A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsGuo, Q. / Liao, S. / Min, J. / Xu, C. / Structural Genomics Consortium (SGC)
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for the recognition of kinesin family member 21A (KIF21A) by the ankyrin domains of KANK1 and KANK2 proteins.
Authors: Guo, Q. / Liao, S. / Zhu, Z. / Li, Y. / Li, F. / Xu, C.
History
DepositionSep 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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 domain-containing protein 1
B: Kinesin-like protein KIF21A


Theoretical massNumber of molelcules
Total (without water)29,9652
Polymers29,9652
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-6 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.648, 51.624, 137.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein KN motif and ankyrin repeat domain-containing protein 1 / Ankyrin repeat domain-containing protein 15 / Kidney ankyrin repeat-containing protein


Mass: 27310.148 Da / Num. of mol.: 1 / Fragment: UNP residues 1080-1329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KANK1, ANKRD15, KANK, KIAA0172
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: Q14678
#2: Protein/peptide Kinesin-like protein KIF21A / Kinesin-like protein KIF2 / Renal carcinoma antigen NY-REN-62


Mass: 2655.081 Da / Num. of mol.: 1 / Fragment: UNP residues 1146-1167
Source method: isolated from a genetically manipulated source
Details: KIF21A (1146-1167) / Source: (gene. exp.) Homo sapiens (human) / Gene: KIF21A, KIAA1708, KIF2
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: Q7Z4S6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.05M magnesium formate, 21% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.89→48.335 Å / Num. obs: 22149 / % possible obs: 99.5 % / Redundancy: 13.9 % / Net I/σ(I): 29.3

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Processing

Software
NameVersionClassification
PHENIXdev_2722refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HBD

4hbd


Resolution: 1.89→48.335 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35
RfactorNum. reflection% reflection
Rfree0.2529 1996 9.01 %
Rwork0.2221 --
obs0.2249 22149 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.89→48.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 0 95 2047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011995
X-RAY DIFFRACTIONf_angle_d1.2272705
X-RAY DIFFRACTIONf_dihedral_angle_d19.452714
X-RAY DIFFRACTIONf_chiral_restr0.074322
X-RAY DIFFRACTIONf_plane_restr0.006350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.93730.41721390.34651405X-RAY DIFFRACTION99
1.9373-1.98970.38331410.32241424X-RAY DIFFRACTION99
1.9897-2.04820.33911380.29631376X-RAY DIFFRACTION100
2.0482-2.11430.36891390.27721419X-RAY DIFFRACTION99
2.1143-2.18990.3241420.27711416X-RAY DIFFRACTION99
2.1899-2.27760.30291390.26851416X-RAY DIFFRACTION100
2.2776-2.38120.3151430.25641436X-RAY DIFFRACTION100
2.3812-2.50680.32231410.25981433X-RAY DIFFRACTION100
2.5068-2.66380.25341430.25771442X-RAY DIFFRACTION100
2.6638-2.86940.27421430.25271442X-RAY DIFFRACTION100
2.8694-3.15820.27311430.24061443X-RAY DIFFRACTION100
3.1582-3.6150.26461440.22281464X-RAY DIFFRACTION100
3.615-4.5540.20181480.17731493X-RAY DIFFRACTION100
4.554-100.19491530.18051541X-RAY DIFFRACTION97
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)
10.9421-0.3857-0.37642.6844-1.58913.07420.09120.46870.0521-0.1377-0.1039-0.0098-0.06210.3458-0.01460.15960.0244-0.00040.3668-0.03340.3937-6.21493.7855-53.9464
20.20920.2146-0.4680.2457-0.5381.15070.1408-0.34150.0788-0.2523-0.17180.07110.8374-0.59260.00080.3892-0.0215-0.0530.3644-0.05820.4601-15.8584-5.8241-52.0755
31.831.5917-1.30271.4821-0.51045.66410.121-0.0309-0.16040.137-0.3639-0.1164-0.10480.9889-0.02260.1762-0.01630.00680.38310.03420.3125-3.36870.8587-41.4666
40.331-0.6981-0.0021.5646-0.63213.8581-0.1760.05320.15380.509-0.06360.1273-1.25640.85050.00830.5335-0.2709-0.09350.45920.01770.3467-3.64665.2442-28.9492
50.08460.31691.26541.25841.58169.1132-0.1126-0.2475-0.02510.4109-0.1219-0.0756-1.4712-0.3521-0.04220.62050-0.0140.32710.00770.2906-7.57373.0749-7.6541
63.78231.58980.91131.01170.92431.06520.4458-0.2305-0.9495-0.11410.0385-0.11430.8996-0.33770.13871.1119-0.2542-0.08850.46120.0370.421-10.9043-7.5917-8.1854
70.26360.1786-0.3921.2053-0.14720.60751.31880.1280.20320.3005-0.5714-0.89730.27812.0660.08720.62510.05750.02590.60750.05810.3932-3.9456-9.2728-19.9055
80.21850.00740.02770.00310.02220.17130.1967-0.2415-0.89030.506-0.63510.11910.7747-0.3874-0.00050.5586-0.0203-0.01960.23580.00320.4418-7.3084-9.4224-26.8486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1079 through 1105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1106 through 1119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1120 through 1177 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1178 through 1222 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1223 through 1326 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1152 through 1155 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1156 through 1161 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1162 through 1166 )

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