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- PDB-8iw0: Crystal structure of the KANK1/liprin-beta1 complex -

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Basic information

Entry
Database: PDB / ID: 8iw0
TitleCrystal structure of the KANK1/liprin-beta1 complex
ComponentsLiprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1
KeywordsPROTEIN BINDING / Focal adhesion / Cortical microtubule stabilizing complex
Function / homology
Function and homology information


negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / Receptor-type tyrosine-protein phosphatases / 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 ...negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / Receptor-type tyrosine-protein phosphatases / 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 / neuromuscular junction development / positive regulation of wound healing / presynaptic active zone / 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
Liprin-beta, SAM domain repeat 1 / Liprin-beta, SAM domain repeat 2 / Liprin-beta, SAM domain repeat 3 / : / Kank N-terminal motif / KN motif / LAR-interacting protein, Liprin / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / SAM domain profile. ...Liprin-beta, SAM domain repeat 1 / Liprin-beta, SAM domain repeat 2 / Liprin-beta, SAM domain repeat 3 / : / Kank N-terminal motif / KN motif / LAR-interacting protein, Liprin / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
KN motif and ankyrin repeat domain-containing protein 1 / Liprin-beta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, J. / Chen, S. / Wei, Z. / Yu, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971131 China
National Natural Science Foundation of China (NSFC)32170697 China
CitationJournal: Cell Rep / Year: 2023
Title: KANK1 shapes focal adhesions by orchestrating protein binding, mechanical force sensing, and phase separation.
Authors: Guo, K. / Zhang, J. / Huang, P. / Xu, Y. / Pan, W. / Li, K. / Chen, L. / Luo, L. / Yu, W. / Chen, S. / He, S. / Wei, Z. / Yu, C.
History
DepositionMar 29, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Liprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1
B: Liprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1
D: Liprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1
C: Liprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)43,0664
Polymers43,0664
Non-polymers00
Water1,802100
1
A: Liprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1
B: Liprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)21,5332
Polymers21,5332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-44 kcal/mol
Surface area10000 Å2
MethodPISA
2
D: Liprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1
C: Liprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)21,5332
Polymers21,5332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-42 kcal/mol
Surface area9670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.151, 36.882, 93.011
Angle α, β, γ (deg.)90.00, 95.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Liprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1 / Protein tyrosine phosphatase receptor type f polypeptide-interacting protein-binding protein 1 / ...Protein tyrosine phosphatase receptor type f polypeptide-interacting protein-binding protein 1 / PTPRF-interacting protein-binding protein 1 / Ankyrin repeat domain-containing protein 15 / Kidney ankyrin repeat-containing protein


Mass: 10766.383 Da / Num. of mol.: 4 / Fragment: N-terminal,N-terminal
Source method: isolated from a genetically manipulated source
Details: The liprin-beta1 N-terminal sequence "MMSDASDMLAAALEQMDGIIAGS" is fused to The KANK1 sequence "SPMHLQHIREQMAIALKRLKELEEQVRTIPVLQVKISVLQEEKRQLVSQLKNQRAASQIN" with 2-GS linker in between.,The ...Details: The liprin-beta1 N-terminal sequence "MMSDASDMLAAALEQMDGIIAGS" is fused to The KANK1 sequence "SPMHLQHIREQMAIALKRLKELEEQVRTIPVLQVKISVLQEEKRQLVSQLKNQRAASQIN" with 2-GS linker in between.,The liprin-beta1 N-terminal sequence "MMSDASDMLAAALEQMDGIIAGS" is fused to The KANK1 sequence "SPMHLQHIREQMAIALKRLKELEEQVRTIPVLQVKISVLQEEKRQLVSQLKNQRAASQIN" with 2-GS linker in between.
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Ppfibp1, Kiaa1230, KANK1, ANKRD15, KANK, KIAA0172 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8C8U0, UniProt: Q14678
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 1.91 Å3/Da / Density % sol: 35.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 2% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.06→47.92 Å / Num. obs: 20404 / % possible obs: 99.2 % / Redundancy: 5.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.154 / Rrim(I) all: 0.169 / Χ2: 0.96 / Net I/σ(I): 8.2
Reflection shellResolution: 2.06→2.17 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2971 / CC1/2: 0.756 / Rrim(I) all: 0.914 / Χ2: 0.88 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.92 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 1911 9.99 %
Rwork0.2274 --
obs0.2306 19138 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 0 100 2572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042497
X-RAY DIFFRACTIONf_angle_d0.5413344
X-RAY DIFFRACTIONf_dihedral_angle_d12.775998
X-RAY DIFFRACTIONf_chiral_restr0.036399
X-RAY DIFFRACTIONf_plane_restr0.006434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.40891340.31021215X-RAY DIFFRACTION100
2.15-2.210.3661340.30321199X-RAY DIFFRACTION99
2.21-2.280.33561370.26991244X-RAY DIFFRACTION100
2.28-2.350.25191330.25881198X-RAY DIFFRACTION98
2.35-2.430.27221380.25441238X-RAY DIFFRACTION99
2.43-2.530.29761370.26281232X-RAY DIFFRACTION99
2.53-2.650.32511370.24361235X-RAY DIFFRACTION100
2.65-2.790.28371340.24031211X-RAY DIFFRACTION100
2.79-2.960.29111380.23361236X-RAY DIFFRACTION100
2.96-3.190.25581360.23541228X-RAY DIFFRACTION98
3.19-3.510.25241360.22361224X-RAY DIFFRACTION99
3.51-4.020.20371410.19041268X-RAY DIFFRACTION99
4.02-5.060.20551350.18321216X-RAY DIFFRACTION97
5.06-47.920.24751410.22061283X-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)
12.3049-1.05-0.22312.5610.28174.3585-0.12820.35840.5313-0.178-0.7727-0.2946-0.2856-0.53390.74870.6252-0.001-0.06110.3734-0.02260.383514.4337.9422-9.9622
20.64540.1970.49841.09490.74483.76940.1767-0.12730.03180.4626-0.0948-0.03080.7442-0.562-0.10440.3788-0.03350.01270.1658-0.00090.238420.62387.929622.1094
31.7802-1.34470.44042.30891.91634.1154-0.14740.5252-0.3785-0.1748-0.41290.95110.9544-2.44630.5860.7639-0.2635-0.00250.6256-0.11110.425112.8433-5.2831-5.4912
41.15820.42390.1471.88761.68033.2256-0.0480.05280.02750.0012-0.10190.1849-0.022-0.28180.10470.308-0.01570.04190.12860.00840.229919.333411.031819.6704
53.72510.06550.76752.26550.08982.60260.2411-0.6918-1.4480.3086-0.3499-0.30250.58210.5741-0.01590.6669-0.084-0.04780.51930.14950.393543.8852-3.643260.4515
62.7750.3732.40330.84050.77653.8014-0.3871-0.2090.244-0.2168-0.03120.124-0.6004-0.4610.32650.282-0.006-0.00570.17870.00970.22428.2052-1.861636.9636
76.07831.77222.00343.14640.39333.379-0.1261-0.59871.04480.3812-0.0130.6448-0.1972-0.83730.28780.37470.112-0.10940.4549-0.12310.471236.67889.335954.9508
82.11660.86950.81751.22631.62924.23430.1618-0.39670.09070.1424-0.0713-0.00580.05-0.22380.12160.3180.01580.01940.1362-0.02380.238928.0081-4.981739.1684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 256 )
2X-RAY DIFFRACTION2chain 'A' and (resid 257 through 314 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 256 )
4X-RAY DIFFRACTION4chain 'B' and (resid 257 through 311 )
5X-RAY DIFFRACTION5chain 'D' and (resid 3 through 256 )
6X-RAY DIFFRACTION6chain 'D' and (resid 257 through 307 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 21 )
8X-RAY DIFFRACTION8chain 'C' and (resid 22 through 309 )

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