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

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Basic information

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


Cell-extracellular matrix interactions / RAC3 GTPase cycle / adherens junction maintenance / RAC1 GTPase cycle / protein localization to cell junction / positive regulation of mesenchymal stem cell proliferation / positive regulation of wound healing, spreading of epidermal cells / positive regulation of integrin activation / type I transforming growth factor beta receptor binding / integrin activation ...Cell-extracellular matrix interactions / RAC3 GTPase cycle / adherens junction maintenance / RAC1 GTPase cycle / protein localization to cell junction / positive regulation of mesenchymal stem cell proliferation / positive regulation of wound healing, spreading of epidermal cells / positive regulation of integrin activation / type I transforming growth factor beta receptor binding / integrin activation / focal adhesion assembly / protein localization to membrane / negative regulation of vascular permeability / regulation of cell morphogenesis / I band / limb development / negative regulation of fat cell differentiation / SMAD binding / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of focal adhesion assembly / lamellipodium membrane / positive regulation of epithelial to mesenchymal transition / positive regulation of osteoblast differentiation / positive regulation of substrate adhesion-dependent cell spreading / stress fiber / positive regulation of stress fiber assembly / extrinsic component of cytoplasmic side of plasma membrane / substrate adhesion-dependent cell spreading / cell-matrix adhesion / transforming growth factor beta receptor signaling pathway / integrin-mediated signaling pathway / adherens junction / cytoplasmic side of plasma membrane / Wnt signaling pathway / positive regulation of protein localization to nucleus / actin filament binding / integrin binding / cell junction / actin binding / cell cortex / regulation of cell shape / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of cell migration / focal adhesion / protein kinase binding / cell surface / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain ...Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Fermitin family homolog 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.601 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 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Fermitin family homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9283
Polymers106,8352
Non-polymers921
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-38 kcal/mol
Surface area38210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.427, 75.427, 383.871
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 / Kindlin-2 / Pleckstrin homology domain-containing family C member 1


Mass: 53417.719 Da / Num. of mol.: 2 / Mutation: 168-217 deletion, 337-512 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fermt2, Plekhc1 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q8CIB5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.95 Å3/Da / Density % sol: 58.31 %
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: Oct 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 37581 / % possible obs: 93 % / Redundancy: 6.2 % / Biso Wilson estimate: 70.48 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.033 / Rrim(I) all: 0.084 / Χ2: 2.284 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.646.80.8540.6390.3330.921.40194.2
2.64-2.696.50.7940.6670.3110.8561.42193
2.69-2.746.80.7140.7880.2780.7691.35693.9
2.74-2.86.60.5660.8150.2220.611.39193.8
2.8-2.866.70.4550.8920.1790.4911.43793.6
2.86-2.936.50.3670.9140.1460.3971.49194.2
2.93-36.50.3150.9370.1260.3411.59294
3-3.086.60.2380.9530.0950.2581.71293.3
3.08-3.176.40.1940.9770.0780.211.80193.3
3.17-3.286.30.1510.990.0610.1642.03493.3
3.28-3.396.50.1270.9860.0520.1382.34692.2
3.39-3.536.20.1030.990.0420.1122.58292.2
3.53-3.696.20.0830.9920.0350.0912.80292.2
3.69-3.8860.0740.9950.0310.0813.03391.8
3.88-4.135.80.0650.9950.0280.0713.20590.9
4.13-4.455.40.060.9950.0270.0663.60289.1
4.45-4.895.30.0580.9940.0270.0653.62790.1
4.89-5.65.40.060.9950.0280.0673.64993.1
5.6-7.055.70.0560.9960.0250.0623.2598
7.05-505.80.0460.9970.020.053.1593.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.601→42.652 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.68
RfactorNum. reflection% reflection
Rfree0.2833 1881 5.02 %
Rwork0.2406 --
obs0.2427 37480 92.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 179.85 Å2 / Biso mean: 83.3551 Å2 / Biso min: 36.85 Å2
Refinement stepCycle: final / Resolution: 2.601→42.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6328 0 6 6 6340
Biso mean--85.44 73.2 -
Num. residues----795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026474
X-RAY DIFFRACTIONf_angle_d0.5598779
X-RAY DIFFRACTIONf_chiral_restr0.0221004
X-RAY DIFFRACTIONf_plane_restr0.0021093
X-RAY DIFFRACTIONf_dihedral_angle_d12.8932320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6013-2.67160.35861350.33492669280493
2.6716-2.75020.37391380.31972686282494
2.7502-2.83890.36931450.30082726287194
2.8389-2.94040.34431440.29882724286894
2.9404-3.05810.30951400.29282707284793
3.0581-3.19720.31731360.28162723285993
3.1972-3.36570.29751350.26542711284693
3.3657-3.57650.28361560.25172703285992
3.5765-3.85250.28471410.2342694283592
3.8525-4.23990.2761560.2192676283291
4.2399-4.85260.2611680.20972647281590
4.8526-6.11090.28421390.23882858299794
6.1109-42.6580.25521480.22013075322395
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)
12.7462-0.36731.3920.95121.11212.8039-0.13191.2156-0.0349-0.2117-0.0624-0.41160.2290.6828-00.61020.06950.01470.82580.06480.68924.38144.3242-80.0712
23.6085-0.0298-2.36452.03240.21814.6454-0.03830.2441-0.1120.07280.01180.04550.1724-0.154600.51020.0464-0.17440.3366-0.00130.485910.93954.9052-49.6991
32.8812-2.8365-0.91874.07760.7991.35740.0173-0.07220.12140.0403-0.0028-0.1634-0.05350.221800.5990.038-0.14590.5414-0.03380.584418.10188.4274-41.6979
42.2632-0.34070.39951.6067-0.49372.99360.1214-0.96920.07440.7105-0.23120.2747-0.1126-0.7739-00.9673-0.06960.09881.09180.02620.7485-3.693736.79870.8531
5-0.44790.7409-0.25871.64171.60940.65460.1715-0.0718-0.0831-0.1695-0.45790.64230.0736-0.5521-00.68010.1239-0.01980.6866-0.020.7131-6.582118.7216-30.8534
61.12780.8486-0.05410.06780.3141.2439-0.0453-0.0229-0.0604-0.12240.009-0.66660.00890.084600.53020.1231-0.00470.5947-0.02940.69690.164628.2026-26.4293
71.67892.2107-0.71631.44811.06551.4587-0.0959-0.04090.25020.2056-0.1362-0.5153-0.60010.490700.85780.0224-0.09880.73690.11710.74213.114350.1612-17.9051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 107 )A18 - 107
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 332 )A108 - 332
3X-RAY DIFFRACTION3chain 'A' and (resid 333 through 677 )A333 - 677
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 287 )B20 - 287
5X-RAY DIFFRACTION5chain 'B' and (resid 288 through 531 )B288 - 531
6X-RAY DIFFRACTION6chain 'B' and (resid 532 through 583 )B532 - 583
7X-RAY DIFFRACTION7chain 'B' and (resid 584 through 660 )B584 - 660

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