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- PDB-8tee: Crystal structure of Kindlin2 in complex with K794Q mutated beta1... -

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Basic information

Entry
Database: PDB / ID: 8tee
TitleCrystal structure of Kindlin2 in complex with K794Q mutated beta1 integrin
Components
  • Fermitin family homolog 2
  • Integrin beta-1
KeywordsCELL ADHESION / kindlin / integrin / acylation
Function / homology
Function and homology information


protein transport within lipid bilayer / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Elastic fibre formation / MET interacts with TNS proteins / Syndecan interactions / Cell-extracellular matrix interactions / Laminin interactions / Fibronectin matrix formation / Molecules associated with elastic fibres / Signal transduction by L1 ...protein transport within lipid bilayer / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Elastic fibre formation / MET interacts with TNS proteins / Syndecan interactions / Cell-extracellular matrix interactions / Laminin interactions / Fibronectin matrix formation / Molecules associated with elastic fibres / Signal transduction by L1 / negative regulation of cell projection organization / TGF-beta receptor signaling activates SMADs / MET activates PTK2 signaling / RAC3 GTPase cycle / integrin alpha3-beta1 complex / integrin alpha5-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 / regulation of inward rectifier potassium channel activity / Basigin interactions / regulation of collagen catabolic process / integrin alpha9-beta1 complex / RAC2 GTPase cycle / cell-cell adhesion mediated by integrin / C-X3-C chemokine binding / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / ECM proteoglycans / integrin alpha1-beta1 complex / adherens junction maintenance / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / regulation of synapse pruning / hemidesmosome / reactive gliosis / RAC1 GTPase cycle / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / RHOG GTPase cycle / protein localization to cell junction / CD40 signaling pathway / positive regulation of wound healing, spreading of epidermal cells / positive regulation of mesenchymal stem cell proliferation / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / positive regulation of fibroblast growth factor receptor signaling pathway / Integrin cell surface interactions / basement membrane organization / Cell surface interactions at the vascular wall / GPER1 signaling / myelin sheath abaxonal region / regulation of postsynaptic neurotransmitter receptor diffusion trapping / cardiac muscle cell myoblast differentiation / positive regulation of integrin activation / tissue homeostasis / bicellular tight junction assembly / germ cell migration / maintenance of postsynaptic specialization structure / leukocyte tethering or rolling / type I transforming growth factor beta receptor binding / cardiac muscle cell differentiation / cell projection organization / integrin activation / regulation of G protein-coupled receptor signaling pathway / glycinergic synapse / myoblast fusion / protein localization to membrane / mesodermal cell differentiation / focal adhesion assembly / negative regulation of vascular permeability / axon extension / positive regulation of fibroblast migration / I band / cell migration involved in sprouting angiogenesis / regulation of spontaneous synaptic transmission / heterotypic cell-cell adhesion / myoblast differentiation / integrin complex / positive regulation of cell-substrate adhesion / dendrite morphogenesis / limb development / muscle organ development / negative regulation of Rho protein signal transduction / lamellipodium assembly / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell adhesion mediated by integrin / negative regulation of vasoconstriction / positive regulation of wound healing / sarcomere organization / positive regulation of neuroblast proliferation / negative regulation of fat cell differentiation / SMAD binding / alpha-actinin binding / establishment of mitotic spindle orientation / positive regulation of endocytosis / positive regulation of focal adhesion assembly
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 subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain ...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 subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / EGF-like domain, extracellular / EGF-like domain / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain / von Willebrand factor A-like domain superfamily / PH domain profile. / Pleckstrin homology domain. / EGF-like domain signature 1. / Pleckstrin homology domain / 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: 2.49 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)119,4354
Polymers119,4354
Non-polymers00
Water1,76598
1
A: Fermitin family homolog 2
C: Integrin beta-1

B: Fermitin family homolog 2
D: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)119,4354
Polymers119,4354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area6680 Å2
ΔGint-56 kcal/mol
Surface area40660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.971, 98.291, 76.003
Angle α, β, γ (deg.)90.00, 96.42, 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: 58094.777 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: 1622.816 Da / Num. of mol.: 2 / Mutation: K794Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itgb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09055
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / 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: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.91975 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2020
RadiationMonochromator: double crystal Si(111) monochromator with horizontal axis
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91975 Å / Relative weight: 1
ReflectionResolution: 2.49→29.94 Å / Num. obs: 36657 / % possible obs: 97.4 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.6
Reflection shellResolution: 2.49→2.55 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2159 / CC1/2: 0.875 / % possible all: 77.5

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Processing

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

5xpy


Resolution: 2.49→29.94 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 32.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2747 1853 5.07 %
Rwork0.2274 --
obs0.2298 36564 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6729 0 0 98 6827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036881
X-RAY DIFFRACTIONf_angle_d0.5699370
X-RAY DIFFRACTIONf_dihedral_angle_d15.279921
X-RAY DIFFRACTIONf_chiral_restr0.041078
X-RAY DIFFRACTIONf_plane_restr0.0041184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.560.40221200.3482438X-RAY DIFFRACTION90
2.56-2.640.43451370.32852685X-RAY DIFFRACTION98
2.64-2.720.37851360.3122683X-RAY DIFFRACTION99
2.72-2.820.28271430.29532645X-RAY DIFFRACTION98
2.82-2.930.29131550.27242671X-RAY DIFFRACTION99
2.93-3.070.34021420.26932656X-RAY DIFFRACTION99
3.07-3.230.32371310.26512696X-RAY DIFFRACTION99
3.23-3.430.27331510.23932679X-RAY DIFFRACTION99
3.43-3.690.29771410.21972693X-RAY DIFFRACTION99
3.69-4.060.26421430.21722694X-RAY DIFFRACTION99
4.06-4.650.21571570.18942693X-RAY DIFFRACTION99
4.65-5.850.2661470.20852727X-RAY DIFFRACTION99
5.85-29.940.24211500.18912751X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.5949 Å / Origin y: -14.766 Å / Origin z: 25.6037 Å
111213212223313233
T0.4806 Å20.0195 Å20.0172 Å2-0.6192 Å2-0.0006 Å2--0.4523 Å2
L0.7888 °2-0.0688 °20.4691 °2-0.0522 °20.004 °2--0.0588 °2
S-0.0201 Å °-0.0509 Å °-0.051 Å °-0.0294 Å °0.0507 Å °-0.0051 Å °-0.0134 Å °-0.0226 Å °-0.0334 Å °
Refinement TLS groupSelection details: all

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