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- PDB-5xq1: Structural basis of kindlin-mediated integrin recognition and act... -

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Basic information

Entry
Database: PDB / ID: 5xq1
TitleStructural basis of kindlin-mediated integrin recognition and activation
ComponentsFermitin family homolog 2,Integrin beta-3
KeywordsSIGNALING PROTEIN / Integrin Binding / Multi-domain containing protein
Function / homology
Function and homology information


Elastic fibre formation / Cell-extracellular matrix interactions / Syndecan interactions / C-X3-C chemokine binding / Signal transduction by L1 / Molecules associated with elastic fibres / PECAM1 interactions / cell projection morphogenesis / RAC3 GTPase cycle / neuregulin binding ...Elastic fibre formation / Cell-extracellular matrix interactions / Syndecan interactions / C-X3-C chemokine binding / Signal transduction by L1 / Molecules associated with elastic fibres / PECAM1 interactions / cell projection morphogenesis / RAC3 GTPase cycle / neuregulin binding / TGF-beta receptor signaling activates SMADs / ECM proteoglycans / adherens junction maintenance / integrin alpha9-beta1 complex / RAC1 GTPase cycle / protein localization to cell junction / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / MAP2K and MAPK activation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / positive regulation of wound healing, spreading of epidermal cells / Integrin cell surface interactions / positive regulation of mesenchymal stem cell proliferation / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / Platelet degranulation / integrin alphaIIb-beta3 complex / positive regulation of integrin activation / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / type I transforming growth factor beta receptor binding / alphav-beta3 integrin-PKCalpha complex / integrin activation / fibrinogen binding / focal adhesion assembly / blood coagulation, fibrin clot formation / alphav-beta3 integrin-HMGB1 complex / insulin-like growth factor I binding / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / VEGFA-VEGFR2 Pathway / positive regulation of vascular endothelial growth factor signaling pathway / regulation of release of sequestered calcium ion into cytosol / negative regulation of vascular permeability / positive regulation of osteoclast differentiation / mesodermal cell differentiation / glycinergic synapse / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of bone resorption / filopodium membrane / extracellular matrix binding / negative regulation of low-density lipoprotein particle clearance / protein localization to membrane / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / I band / limb development / apoptotic cell clearance / positive regulation of fibroblast migration / heterotypic cell-cell adhesion / positive regulation of smooth muscle cell migration / smooth muscle cell migration / positive regulation of cell-matrix adhesion / negative chemotaxis / cell adhesion mediated by integrin / positive regulation of osteoblast proliferation / cellular response to insulin-like growth factor stimulus / protein disulfide isomerase activity / negative regulation of fat cell differentiation / regulation of postsynaptic neurotransmitter receptor internalization / microvillus membrane / positive regulation of Rho protein signal transduction / SMAD binding / platelet-derived growth factor receptor signaling pathway / fibroblast growth factor binding / phosphatidylinositol-3,4,5-trisphosphate binding / fibronectin binding / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / positive regulation of focal adhesion assembly / positive regulation of osteoblast differentiation / positive regulation of T cell migration / negative regulation of endothelial cell apoptotic process / positive regulation of epithelial to mesenchymal transition / stress fiber / positive regulation of stress fiber assembly / cellular response to platelet-derived growth factor stimulus / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / embryo implantation / positive regulation of smooth muscle cell 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. / EGF-like domain signature 2. / PH-like domain superfamily
Similarity search - Domain/homology
Integrin beta-3 / Fermitin family homolog 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.954 Å
AuthorsLi, H. / Yang, H. / Sun, K. / Zhang, Z. / Yu, C. / Wei, Z.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of kindlin-mediated integrin recognition and activation
Authors: Li, H. / Deng, Y. / Sun, K. / Yang, H. / Liu, J. / Wang, M. / Zhang, Z. / Lin, J. / Wu, C. / Wei, Z. / Yu, C.
History
DepositionJun 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fermitin family homolog 2,Integrin beta-3
B: Fermitin family homolog 2,Integrin beta-3


Theoretical massNumber of molelcules
Total (without water)112,2692
Polymers112,2692
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-39 kcal/mol
Surface area39170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.973, 75.973, 387.042
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Fermitin family homolog 2,Integrin beta-3 / Kindlin-2 / Pleckstrin homology domain-containing family C member 1 / Platelet membrane ...Kindlin-2 / Pleckstrin homology domain-containing family C member 1 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 56134.645 Da / Num. of mol.: 2 / Fragment: UNP residues 773-787 / Mutation: 168-217 deletion, 337-512 deletion
Source method: isolated from a genetically manipulated source
Details: Beta3-integrin tail was fused to the C-terminus of kindlin2
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fermt2, Plekhc1, Itgb3 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q8CIB5, UniProt: O54890
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v pentaerythritol propoxylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 28446 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 86.93 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Χ2: 0.621 / Net I/σ(I): 5.6 / Num. measured all: 186136
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-36.80.9870.7010.4021.0680.51199.9
3-3.0670.810.7990.3250.8740.51299.9
3.06-3.116.80.6510.9030.2650.7040.51699.9
3.11-3.186.90.5480.9180.2230.5920.51199.9
3.18-3.256.80.3820.9820.1570.4130.523100
3.25-3.326.70.3250.9630.1340.3520.548100
3.32-3.416.70.2560.9730.1060.2780.545100
3.41-3.56.50.2120.9770.090.2310.581100
3.5-3.660.1510.9870.0670.1660.573100
3.6-3.726.20.1260.9920.0550.1380.619100
3.72-3.856.90.1070.9950.0440.1160.59999.9
3.85-470.090.9960.0370.0980.6799.9
4-4.196.90.0750.9970.0310.0810.69999.7
4.19-4.416.70.0630.9980.0260.0680.74599.7
4.41-4.686.70.0570.9970.0230.0620.74599.9
4.68-5.046.30.0530.9980.0230.0580.72699.9
5.04-5.555.80.0520.9970.0230.0570.67299.9
5.55-6.356.60.0520.9980.0210.0560.63399.8
6.35-86.30.0440.9990.0180.0480.67399.4
8-505.60.0380.9980.0170.0420.83297.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XPZ

5xpz


Resolution: 2.954→37.986 Å / SU ML: 0.41 / σ(F): 1.35 / Phase error: 26.53
RfactorNum. reflection% reflection
Rfree0.26 1415 5 %
Rwork0.2196 --
obs0.2216 28295 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 221.58 Å2 / Biso mean: 94.3501 Å2 / Biso min: 33.74 Å2
Refinement stepCycle: LAST / Resolution: 2.954→37.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6707 0 0 5 6712
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)
11.8991-0.3209-0.8821.53860.35196.19760.14050.1156-0.1387-0.3109-0.1088-0.0056-0.028-0.0052-0.0460.4766-0.0703-0.02460.36110.06730.496-24.232753.6124385.1062
21.6109-0.38080.9061.72580.88221.52090.0033-0.28660.51340.1836-0.2012-0.2686-0.4313-0.09670.20580.6368-0.208-0.04920.515-0.00340.6863-24.614977.9171412.1794
33.03210.3933-1.10334.2548-0.60312.6032-0.1643-0.2695-0.50630.136-0.1172-0.17010.88350.47190.27250.6626-0.0177-0.09140.54030.21830.7002-20.319739.2895407.2622
42.1214-0.1550.69881.59910.02471.9088-0.3425-1.02980.01930.27390.0667-0.1294-0.2644-0.56270.21170.96390.06010.18771.1704-0.10460.7729-6.406288.9275453.7532
53.56990.95911.40430.32680.56690.6233-0.1912-0.56340.2945-0.1646-0.0350.0882-0.1713-0.39990.16090.7767-0.13740.10210.5743-0.11550.6572-20.413881.3172425.2876
65.0028-1.74451.29233.1732.50543.6886-0.1456-0.2201-0.23250.51980.1106-0.29340.64990.55240.04810.8207-0.08560.07470.76040.09660.598112.536980.8625433.7729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 287 )A18 - 287
2X-RAY DIFFRACTION2chain 'A' and (resid 288 through 564 )A288 - 564
3X-RAY DIFFRACTION3chain 'A' and (resid 565 through 786 )A565 - 786
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 259 )B20 - 259
5X-RAY DIFFRACTION5chain 'B' and (resid 260 through 564 )B260 - 564
6X-RAY DIFFRACTION6chain 'B' and (resid 565 through 786 )B565 - 786

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