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- PDB-5ybj: Structure of apo KANK1 ankyrin domain -

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Basic information

Entry
Database: PDB / ID: 5ybj
TitleStructure of apo KANK1 ankyrin domain
ComponentsKN motif and ankyrin repeat domain-containing protein 1
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 / regulation of establishment of cell polarity / negative regulation of Rho protein signal transduction / positive regulation of wound healing ...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 / regulation of establishment of cell polarity / negative regulation of Rho protein signal transduction / positive regulation of wound healing / 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 / Estrogen-dependent gene expression / cell population proliferation / cytoskeleton / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / Kank N-terminal motif / KN motif / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat ...: / Kank N-terminal motif / KN motif / Ankyrin repeat-containing domain / Ankyrin repeat / 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 / Mainly Alpha
Similarity search - Domain/homology
KN motif and ankyrin repeat domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.341 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 2.0Dec 13, 2017Group: Database references / Polymer sequence / Category: citation / entity_poly
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity_poly.pdbx_target_identifier
Revision 2.1Jan 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 2.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: KN motif and ankyrin repeat domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5864
Polymers27,3101
Non-polymers2763
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-0 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.903, 47.602, 137.745
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, pH 7.5, 0.2M Lithium sulfate monohydrate, 25% 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: 2.34→44.99 Å / Num. obs: 12363 / % possible obs: 99.7 % / Redundancy: 5.7 % / Net I/σ(I): 28.1

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Processing

Software
NameVersionClassification
PHENIXdev_2722refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.341→44.99 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.46
RfactorNum. reflection% reflection
Rfree0.2417 583 4.72 %
Rwork0.2125 --
obs0.214 12362 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.341→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 18 15 1857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011895
X-RAY DIFFRACTIONf_angle_d1.2292572
X-RAY DIFFRACTIONf_dihedral_angle_d18.645671
X-RAY DIFFRACTIONf_chiral_restr0.07302
X-RAY DIFFRACTIONf_plane_restr0.004336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3415-2.57710.27841400.22322828X-RAY DIFFRACTION97
2.5771-2.94990.29951310.24082921X-RAY DIFFRACTION100
2.9499-3.71630.26641490.23352953X-RAY DIFFRACTION100
3.7163-44.99950.21571630.19583077X-RAY DIFFRACTION99

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