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- PDB-8tec: Crystal structure of Kindlin2 in complex with acylated beta1 inte... -

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Basic information

Entry
Database: PDB / ID: 8tec
TitleCrystal structure of Kindlin2 in complex with acylated beta1 integrin peptide
Components
  • Fermitin family homolog 2
  • Integrin beta-1
KeywordsCELL ADHESION / kindlin / integrin / acylation
Function / homology
Function and homology information


Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Laminin interactions / MET interacts with TNS proteins / Elastic fibre formation / Cell-extracellular matrix interactions / Fibronectin matrix formation / Syndecan interactions / C-X3-C chemokine binding / Signal transduction by L1 / Molecules associated with elastic fibres ...Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Laminin interactions / MET interacts with TNS proteins / Elastic fibre formation / Cell-extracellular matrix interactions / Fibronectin matrix formation / Syndecan interactions / C-X3-C chemokine binding / Signal transduction by L1 / Molecules associated with elastic fibres / MET activates PTK2 signaling / Basigin interactions / RAC3 GTPase cycle / TGF-beta receptor signaling activates SMADs / ECM proteoglycans / RAC2 GTPase cycle / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / integrin alpha9-beta1 complex / adherens junction maintenance / regulation of collagen catabolic process / cardiac cell fate specification / integrin alpha1-beta1 complex / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / reactive gliosis / RAC1 GTPase cycle / protein localization to cell junction / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / myelin sheath abaxonal region / positive regulation of wound healing, spreading of epidermal cells / Integrin cell surface interactions / positive regulation of mesenchymal stem cell proliferation / Cell surface interactions at the vascular wall / CD40 signaling pathway / calcium-independent cell-matrix adhesion / positive regulation of fibroblast growth factor receptor signaling pathway / GPER1 signaling / RHOG GTPase cycle / regulation of synapse pruning / integrin alphav-beta1 complex / basement membrane organization / cardiac muscle cell myoblast differentiation / positive regulation of integrin activation / fibroblast migration / cardiac muscle cell differentiation / type I transforming growth factor beta receptor binding / integrin activation / germ cell migration / leukocyte tethering or rolling / focal adhesion assembly / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / negative regulation of vascular permeability / mesodermal cell differentiation / myoblast differentiation / axon extension / cell migration involved in sprouting angiogenesis / protein localization to membrane / I band / limb development / cardiac muscle tissue development / central nervous system neuron differentiation / regulation of spontaneous synaptic transmission / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of fibroblast migration / sarcomere organization / heterotypic cell-cell adhesion / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / muscle organ development / cell adhesion mediated by integrin / positive regulation of wound healing / dendrite morphogenesis / negative regulation of neuron differentiation / positive regulation of neuroblast proliferation / negative regulation of Rho protein signal transduction / negative regulation of fat cell differentiation / positive regulation of Rho protein signal transduction / response to muscle activity / SMAD binding / phosphatidylinositol-3,4,5-trisphosphate binding / establishment of mitotic spindle orientation / fibronectin binding / lamellipodium membrane / negative regulation of anoikis / intercalated disc / cellular response to low-density lipoprotein particle stimulus / neuroblast proliferation
Similarity search - Function
Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt ...Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin domain superfamily / FERM central domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain / PH domain profile. / von Willebrand factor A-like domain superfamily / Pleckstrin homology domain. / Pleckstrin homology domain / EGF-like domain signature 1. / PH-like domain superfamily
Similarity search - Domain/homology
Integrin beta-1 / Fermitin family homolog 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsZhang, P.F. / Wu, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Iscience / Year: 2024
Title: Acetyl-NPKY of integrin-beta 1 binds KINDLIN2 to control endothelial cell proliferation and junctional integrity.
Authors: Sidibe, A. / Mykuliak, V.V. / Zhang, P. / Hytonen, V.P. / Wu, J. / Wehrle-Haller, B.
History
DepositionJul 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fermitin family homolog 2
B: Fermitin family homolog 2
C: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)124,2173
Polymers124,2173
Non-polymers00
Water4,396244
1
A: Fermitin family homolog 2
C: Integrin beta-1

B: Fermitin family homolog 2


Theoretical massNumber of molelcules
Total (without water)124,2173
Polymers124,2173
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area5470 Å2
ΔGint-45 kcal/mol
Surface area40970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.487, 102.093, 76.029
Angle α, β, γ (deg.)90.00, 96.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fermitin family homolog 2 / Kindlin-2 / Pleckstrin homology domain-containing family C member 1


Mass: 61276.211 Da / Num. of mol.: 2 / Fragment: UNP residues 1-336,513-680
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fermt2, Plekhc1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CIB5
#2: Protein/peptide Integrin beta-1 / Fibronectin receptor subunit beta / VLA-4 subunit beta


Mass: 1664.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P09055
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 10% isopropanal

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2020
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.04→102.09 Å / Num. obs: 69860 / % possible obs: 98.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.028 / Rrim(I) all: 0.075 / Net I/σ(I): 12.8
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.728 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3942 / CC1/2: 0.394 / % possible all: 87.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
ADSCdata collection
Cootmodel building
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5XPY

5xpy


Resolution: 2.04→75.49 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 3350 4.83 %
Rwork0.1938 --
obs0.1955 69366 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→75.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6797 0 0 244 7041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076972
X-RAY DIFFRACTIONf_angle_d0.8129484
X-RAY DIFFRACTIONf_dihedral_angle_d21.5462445
X-RAY DIFFRACTIONf_chiral_restr0.0491089
X-RAY DIFFRACTIONf_plane_restr0.0071191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.070.46691200.45082167X-RAY DIFFRACTION79
2.07-2.10.46081340.40552766X-RAY DIFFRACTION98
2.1-2.140.37311350.40062671X-RAY DIFFRACTION97
2.14-2.170.40191360.36162726X-RAY DIFFRACTION97
2.17-2.210.43371340.33722765X-RAY DIFFRACTION100
2.21-2.250.40431380.36972785X-RAY DIFFRACTION99
2.25-2.290.36541490.34912759X-RAY DIFFRACTION99
2.29-2.340.3731380.31872747X-RAY DIFFRACTION100
2.34-2.390.32951440.29482771X-RAY DIFFRACTION100
2.39-2.450.35111610.26862789X-RAY DIFFRACTION100
2.45-2.510.33781550.23932739X-RAY DIFFRACTION100
2.51-2.580.27851450.22092752X-RAY DIFFRACTION100
2.58-2.650.23891210.20832815X-RAY DIFFRACTION100
2.65-2.740.24771470.20462800X-RAY DIFFRACTION100
2.74-2.830.2231540.20172780X-RAY DIFFRACTION100
2.83-2.950.26231250.20372793X-RAY DIFFRACTION100
2.95-3.080.26161200.20292760X-RAY DIFFRACTION98
3.08-3.240.20941540.19462774X-RAY DIFFRACTION99
3.24-3.450.22721720.18222764X-RAY DIFFRACTION100
3.45-3.710.22641320.17262804X-RAY DIFFRACTION100
3.71-4.090.19531280.16032814X-RAY DIFFRACTION99
4.09-4.680.17151370.1452802X-RAY DIFFRACTION100
4.68-5.890.21911260.18092814X-RAY DIFFRACTION99
5.9-75.490.18031450.16422859X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -8.3364 Å / Origin y: -5.0603 Å / Origin z: 13.5829 Å
111213212223313233
T0.4846 Å2-0.0161 Å20.0217 Å2-0.5313 Å2-0.0214 Å2--0.4639 Å2
L0.6976 °2-0.0624 °20.4545 °2-0.1632 °20.0317 °2--0.018 °2
S0.0028 Å °0.0728 Å °-0.1163 Å °-0.0262 Å °0.0364 Å °-0.0075 Å °0.05 Å °0.0202 Å °-0.0403 Å °
Refinement TLS groupSelection details: all

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