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- PDB-5yaz: Crystal structure of the ANKRD domain of KANK1 -

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Basic information

Entry
Database: PDB / ID: 5yaz
TitleCrystal structure of the ANKRD domain of KANK1
ComponentsKN motif and ankyrin repeat domains 1
KeywordsPROTEIN BINDING / Scaffold protein / ANK repeat
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 / negative regulation of actin filament polymerization / regulation of establishment of cell polarity / negative regulation of Rho protein signal transduction / positive regulation of wound healing / negative regulation of insulin receptor signaling pathway / negative regulation of cell migration ...negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / podocyte cell migration / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of actin filament polymerization / regulation of establishment of cell polarity / negative regulation of Rho protein signal transduction / positive regulation of wound healing / 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 / cell population proliferation / cytoskeleton / cytoplasm
Similarity search - Function
: / Kank N-terminal motif / KN motif / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...: / Kank N-terminal motif / KN motif / Ankyrin repeat-containing domain / 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
ACETATE ION / KN motif and ankyrin repeat domains 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsWei, Z. / Pan, W.
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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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 domains 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7652
Polymers27,7061
Non-polymers591
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-1 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.102, 70.207, 60.655
Angle α, β, γ (deg.)90.000, 96.910, 90.000
Int Tables number4
Space group name H-MP1211

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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: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M calcium acetate, 0.1 M Sodium acetate, 10% w/v polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 19134 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 30.54 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.047 / Rrim(I) all: 0.09 / Χ2: 1.736 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.933.51.1999490.5450.7411.4131.30699.9
1.93-1.973.60.8659390.7460.5271.0151.297100
1.97-2.013.70.7239550.7310.4350.8451.35899.8
2.01-2.053.70.5759340.8070.3460.6721.3399.8
2.05-2.093.70.4359830.8440.2610.5081.37799.9
2.09-2.143.70.3549320.9220.2130.4141.4499.9
2.14-2.193.70.3219560.9310.1940.3761.49699.9
2.19-2.253.70.2689640.9580.1610.3131.42199.9
2.25-2.323.80.2349410.9680.1390.2721.54799.7
2.32-2.393.70.1899690.9740.1140.2211.699.7
2.39-2.483.70.1559420.9830.0930.1811.58699.9
2.48-2.583.80.1319530.9850.0780.1531.618100
2.58-2.73.80.1089720.9910.0650.1271.66599.9
2.7-2.843.80.099370.990.0540.1051.80799.7
2.84-3.023.70.0779590.9940.0460.091.933100
3.02-3.253.70.0679780.9940.0410.0782.43799.8
3.25-3.583.60.069650.9940.0360.072.73599.8
3.58-4.093.60.0529520.9950.0320.0623.12299.7
4.09-5.163.60.0379660.9970.0230.0432.00899.8
5.16-503.70.0339880.9980.020.0391.68398.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YAY

5yay


Resolution: 1.9→30.107 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.56
RfactorNum. reflection% reflection
Rfree0.2346 956 5.01 %
Rwork0.1934 --
obs0.1956 19099 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.73 Å2 / Biso mean: 38.9071 Å2 / Biso min: 19.16 Å2
Refinement stepCycle: final / Resolution: 1.9→30.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 4 66 1844
Biso mean--48.66 38.16 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141804
X-RAY DIFFRACTIONf_angle_d1.4092448
X-RAY DIFFRACTIONf_chiral_restr0.066290
X-RAY DIFFRACTIONf_plane_restr0.007319
X-RAY DIFFRACTIONf_dihedral_angle_d14.28630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8964-1.99630.3951300.31862476260696
1.9963-2.12140.26881380.244526022740100
2.1214-2.28510.27291360.210625842720100
2.2851-2.5150.2791380.203326112749100
2.515-2.87870.24531370.204726142751100
2.8787-3.62580.24121370.194326102747100
3.6258-30.11090.18621400.16122646278699
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)
13.6648-0.4149-0.3872.9196-0.71454.203-0.0380.2262-0.2293-0.29530.2831-0.75630.03890.2626-0.17070.3068-0.00240.10410.3314-0.00930.29724.813-5.209862.9802
26.1831-2.4144-1.84532.899-1.16564.93670.14940.1359-0.18850.23340.3472-1.31060.5791.7334-0.37880.24860.0297-0.06480.6278-0.11160.47577.717-6.380373.1039
31.95970.4662-1.44732.3261-0.175.65120.069-0.0063-0.0461-0.16340.1034-0.23780.01020.1892-0.17720.12950.0060.00690.25650.00960.2653-0.3871-4.164972.1775
43.13161.9347-3.4787.6071-0.55527.38030.19450.08090.19170.1299-0.0398-0.1469-0.0157-0.0849-0.13940.11590.01390.00930.29920.01810.2529-5.7661-4.583981.7591
56.08891.1049-2.87813.2861-2.91558.15120.00890.1570.32890.4188-0.04720.1757-0.3824-0.2550.00760.21110.0067-0.01860.3280.02250.2628-12.4871-3.722888.5218
64.69572.0938-1.32265.1315-3.33256.61680.21470.55620.20440.165-0.0954-0.0217-0.3751-0.2331-0.09140.22930.0640.06010.29820.00070.202-16.5777-7.773597.2069
73.1139-0.1675-1.51583.61240.7944.8817-0.0024-0.01180.01230.1298-0.0795-0.2334-0.043-0.11120.07870.30490.04610.0080.28430.01710.214-21.4489-9.7503105.4098
82.8498-3.0744-2.38966.02561.25022.6756-0.3656-0.3395-0.28050.42080.2990.2351-0.1495-0.72390.04710.30970.06850.03260.33710.02570.2483-23.5509-8.166113.9503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1087 through 1120 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1121 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 1244 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1245 through 1277 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1278 through 1311 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1312 through 1332 )A0

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