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- PDB-5xq0: Structural basis of kindlin-mediated integrin recognition and act... -

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Basic information

Entry
Database: PDB / ID: 5xq0
TitleStructural basis of kindlin-mediated integrin recognition and activation
ComponentsFermitin family homolog 2,Integrin beta-1
KeywordsSIGNALING PROTEIN / Integrin Binding / Multi-domain containing protein
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: 2.75 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

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Assembly

Deposited unit
A: Fermitin family homolog 2,Integrin beta-1
B: Fermitin family homolog 2,Integrin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,2253
Polymers112,1332
Non-polymers921
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-39 kcal/mol
Surface area39010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.866, 75.866, 384.219
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Fermitin family homolog 2,Integrin beta-1 / Kindlin-2 / Pleckstrin homology domain-containing family C member 1 / Fibronectin receptor subunit ...Kindlin-2 / Pleckstrin homology domain-containing family C member 1 / Fibronectin receptor subunit beta / VLA-4 subunit beta


Mass: 56066.676 Da / Num. of mol.: 2 / Fragment: UNP residues 784-798 / Mutation: 168-217 deletion, 337-512 deletion
Source method: isolated from a genetically manipulated source
Details: Beta-integrin tail sequence was fused to the C-terminus of kindlin2
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fermt2, Plekhc1, Itgb1 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q8CIB5, UniProt: P09055
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.85 Å3/Da / Density % sol: 56.79 %
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: BL17U1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 34443 / % possible obs: 98.7 % / Redundancy: 4 % / Biso Wilson estimate: 67.25 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.045 / Rrim(I) all: 0.098 / Χ2: 2.621 / Net I/σ(I): 12 / Num. measured all: 139053
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.84.40.7880.5160.4130.8951.42599.8
2.8-2.854.40.6710.7010.3540.7641.479100
2.85-2.94.20.5270.7220.2820.6021.46699.9
2.9-2.964.30.4830.7570.2570.551.52699.3
2.96-3.034.10.3830.8490.2070.4391.60799.9
3.03-3.14.20.3230.8760.1720.3681.64899.6
3.1-3.174.10.2620.9290.1410.31.87999.7
3.17-3.264.20.2070.9730.110.2362.08199.4
3.26-3.3640.1770.9660.0960.2032.18199.8
3.36-3.463.90.1530.9680.0840.1762.47498.9
3.46-3.593.90.1260.980.0690.1452.77598.7
3.59-3.733.80.1130.9840.0620.133.27598.8
3.73-3.93.70.0980.9860.0550.1143.49698.2
3.9-4.113.60.0840.990.0480.0973.75897.9
4.11-4.363.50.0740.9920.0420.0853.88996.9
4.36-4.73.50.0670.9920.0380.0773.9796.3
4.7-5.173.60.0630.9940.0350.0733.7796.6
5.17-5.923.70.0630.9940.0350.0733.60197.8
5.92-7.464.40.0590.9960.030.0673.60399.3
7.46-5050.0480.9970.0220.0533.48997.5

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Processing

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

5xpz


Resolution: 2.75→45.858 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8
RfactorNum. reflection% reflection
Rfree0.2845 1733 5.05 %
Rwork0.2315 --
obs0.2341 34335 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 207.14 Å2 / Biso mean: 74.5935 Å2 / Biso min: 27.57 Å2
Refinement stepCycle: final / Resolution: 2.75→45.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6635 0 6 29 6670
Biso mean--77.23 56.69 -
Num. residues----834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026787
X-RAY DIFFRACTIONf_angle_d0.4869201
X-RAY DIFFRACTIONf_chiral_restr0.021050
X-RAY DIFFRACTIONf_plane_restr0.0021145
X-RAY DIFFRACTIONf_dihedral_angle_d12.1382433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.747-2.82780.39421320.31912680281299
2.8278-2.91910.3141270.307127352862100
2.9191-3.02340.31551680.294126502818100
3.0234-3.14440.33571470.270326992846100
3.1444-3.28750.32771370.253127092846100
3.2875-3.46080.27921510.24952709286099
3.4608-3.67750.30451300.23482670280099
3.6775-3.96130.24771490.22632690283998
3.9613-4.35960.27541540.21712672282697
4.3596-4.98980.25931540.20092657281196
4.9898-6.28410.28191450.22992784292998
6.2841-45.86450.28041390.21082947308698
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)
10.8937-0.071-0.74650.9918-0.24553.7469-0.04490.2084-0.0018-0.03750.0098-0.09840.1152-0.0130.05710.3550.0583-0.03080.3376-0.00010.3817.55924.5286-63.6227
21.6609-0.3508-0.19861.58160.24771.1479-0.0488-0.08340.20560.1365-0.0071-0.1818-0.00220.17110.04810.42490.1061-0.10150.3265-0.00160.413617.64398.4483-41.9136
30.2559-0.20180.07930.9102-0.44340.2599-0.5049-1.77680.0919-0.21810.22960.10250.9754-0.33720.14191.57250.02810.18081.797-0.14040.7558-3.302538.832819.5073
41.8552-0.04380.12342.80071.32982.25550.082-0.3043-0.0340.9397-0.42350.52680.5019-0.24920.28840.84040.02750.27020.61290.07660.5304-3.438436.1724-10.6425
50.1020.4863-0.05733.98660.5636-0.13550.0667-0.17070.2895-0.081-0.26670.46510.0037-0.47490.17770.51120.19980.00820.6149-0.07350.5185-7.400511.7361-34.2188
60.7671.06960.28624.17031.33861.00140.0417-0.1064-0.0039-0.2496-0.333-0.32470.042-0.02610.38470.40860.12350.07430.46080.00350.4550.085428.3981-26.6436
72.54030.5725-0.05582.30550.84681.5899-0.10340.00730.21780.2351-0.0456-0.2307-0.06160.44260.07760.6109-0.0009-0.0250.54270.13540.424714.399449.3367-16.4968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 310 )A18 - 310
2X-RAY DIFFRACTION2chain 'A' and (resid 311 through 797 )A311 - 797
3X-RAY DIFFRACTION3chain 'B' and (resid 20 through 79 )B20 - 79
4X-RAY DIFFRACTION4chain 'B' and (resid 80 through 310 )B80 - 310
5X-RAY DIFFRACTION5chain 'B' and (resid 311 through 531 )B311 - 531
6X-RAY DIFFRACTION6chain 'B' and (resid 532 through 583 )B532 - 583
7X-RAY DIFFRACTION7chain 'B' and (resid 584 through 797 )B584 - 797

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