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

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Basic information

Entry
Database: PDB / ID: 5xpy
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
ACETATE ION / Fermitin family homolog 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsLi, H. / Yang, H. / Sun, K. / Zhang, Z. / Yu, C. / Wei, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31500621 China
National Natural Science Foundation of China31570741 China
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4717
Polymers55,0831
Non-polymers3876
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-2 kcal/mol
Surface area23400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.069, 145.069, 59.352
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 / Kindlin-2 / Pleckstrin homology domain-containing family C member 1


Mass: 55083.320 Da / Num. of mol.: 1 / Fragment: UNP residues 15-680 / Mutation: 168-217 deletion, 367-512 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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.19 Å3/Da / Density % sol: 61.4 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 4.0 M Ammonium acetate

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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: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.099→31.408 Å / Num. obs: 42158 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.043 / Net I/σ(I): 19.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.761 / Rsym value: 0.761 / % possible all: 100

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Processing

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

5xpz


Resolution: 2.099→31.408 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.22 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.1959 3650 4.78 %
Rwork0.164 --
obs0.1655 76295 93.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.099→31.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3687 0 26 156 3869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073835
X-RAY DIFFRACTIONf_angle_d0.9665190
X-RAY DIFFRACTIONf_dihedral_angle_d14.3441441
X-RAY DIFFRACTIONf_chiral_restr0.041580
X-RAY DIFFRACTIONf_plane_restr0.004658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0989-2.12650.2726860.19471859X-RAY DIFFRACTION61
2.1265-2.15560.2136950.18541934X-RAY DIFFRACTION66
2.1556-2.18640.21511080.18622115X-RAY DIFFRACTION71
2.1864-2.2190.19611080.18672246X-RAY DIFFRACTION75
2.219-2.25370.23921250.19232394X-RAY DIFFRACTION80
2.2537-2.29060.26711330.20142587X-RAY DIFFRACTION87
2.2906-2.33010.22191320.18332787X-RAY DIFFRACTION93
2.3301-2.37240.23211570.19562951X-RAY DIFFRACTION97
2.3724-2.41810.22531510.19882923X-RAY DIFFRACTION99
2.4181-2.46740.22991520.18763011X-RAY DIFFRACTION100
2.4674-2.5210.21631500.18252960X-RAY DIFFRACTION100
2.521-2.57960.1961520.17853032X-RAY DIFFRACTION100
2.5796-2.64410.19071480.18372956X-RAY DIFFRACTION100
2.6441-2.71560.22491460.17962993X-RAY DIFFRACTION100
2.7156-2.79540.23831520.18773000X-RAY DIFFRACTION100
2.7954-2.88560.22551500.18022964X-RAY DIFFRACTION100
2.8856-2.98870.19251600.17743009X-RAY DIFFRACTION100
2.9887-3.10820.19651510.17892966X-RAY DIFFRACTION100
3.1082-3.24950.17261530.17112983X-RAY DIFFRACTION100
3.2495-3.42070.20871520.16492991X-RAY DIFFRACTION100
3.4207-3.63470.19951440.1533010X-RAY DIFFRACTION100
3.6347-3.91490.16991460.13853016X-RAY DIFFRACTION100
3.9149-4.30790.18221440.13592968X-RAY DIFFRACTION100
4.3079-4.92920.13841520.12373014X-RAY DIFFRACTION100
4.9292-6.20250.21051540.15892978X-RAY DIFFRACTION100
6.2025-31.41190.15321490.14462998X-RAY DIFFRACTION100
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)
12.1592-0.1542-0.5292.3561.44012.4671-0.0540.0786-0.1211-0.16670.2194-0.39260.03810.4052-0.13130.22720.01140.07660.1844-0.04930.2857-40.908-49.4887-16.8952
21.4148-0.6133-0.9921.37850.15731.9792-0.087-0.0982-0.12070.124-0.0114-0.08760.17020.12850.08120.2087-0.00540.00180.1243-0.00320.1894-53.3689-34.7838.2344
31.05470.0676-0.4731.0312-0.41871.0679-0.1416-0.12870.1903-0.00350.0304-0.0181-0.29450.40850.03970.2159-0.0014-0.02020.2016-0.0220.222-46.3334-19.54336.0222
40.5623-0.2942-0.40611.38421.06852.07140.0073-0.020.04520.0640.0553-0.08380.06950.0337-0.05740.14270.00150.00590.1089-0.00070.1416-57.2875-23.720713.3601
52.49330.9422-0.73751.1864-1.73943.3773-0.69640.12320.0127-0.2680.22050.00710.6304-0.15530.14240.441-0.11020.00530.4830.050.4156-70.2885-30.58435.4369
62.20340.56070.2412.66950.09132.3751-0.0919-0.1674-0.1031-0.20730.0251-0.1820.2332-0.33060.07180.2723-0.0402-0.05790.196-0.02940.1655-55.7611-14.138631.7595
70.2817-0.0223-0.09030.5197-0.19751.22820.0080.00120.03020.033-0.0243-0.003-0.1046-0.07380.00250.1973-0.01540.02210.0928-0.00990.1449-59.4774-12.719814.8051
81.42880.0751-0.51952.8817-0.36762.7127-0.04880.10890.07620.12220.21060.4145-0.1851-0.4509-0.14360.20760.05080.03690.18690.07750.2018-58.9097-10.1567-10.3213
91.8754-0.6695-0.56261.2987-0.45171.68010.03730.2858-0.4689-0.3584-0.1030.03230.1632-0.27650.05030.27040.0186-0.0250.217-0.04960.1888-63.6421-26.5825-7.9598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 95 )
2X-RAY DIFFRACTION2chain 'A' and (resid 96 through 229 )
3X-RAY DIFFRACTION3chain 'A' and (resid 230 through 258 )
4X-RAY DIFFRACTION4chain 'A' and (resid 259 through 329 )
5X-RAY DIFFRACTION5chain 'A' and (resid 330 through 358 )
6X-RAY DIFFRACTION6chain 'A' and (resid 359 through 531 )
7X-RAY DIFFRACTION7chain 'A' and (resid 532 through 583 )
8X-RAY DIFFRACTION8chain 'A' and (resid 584 through 639 )
9X-RAY DIFFRACTION9chain 'A' and (resid 640 through 679 )

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