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- PDB-6vgu: Crystal structure of FERM-folded talin head domain bound to the N... -

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Basic information

Entry
Database: PDB / ID: 6vgu
TitleCrystal structure of FERM-folded talin head domain bound to the NPLY motif of beta3-integrin
ComponentsIntegrin beta-3,Talin-1
KeywordsSIGNALING PROTEIN / talin / FERM-fold / NPLY motif / integrin
Function / homology
Function and homology information


Elastic fibre formation / Syndecan interactions / Molecules associated with elastic fibres / C-X3-C chemokine binding / regulation of protein tyrosine kinase activity / Signal transduction by L1 / cell projection morphogenesis / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / integrin alpha9-beta1 complex ...Elastic fibre formation / Syndecan interactions / Molecules associated with elastic fibres / C-X3-C chemokine binding / regulation of protein tyrosine kinase activity / Signal transduction by L1 / cell projection morphogenesis / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / integrin alpha9-beta1 complex / neuregulin binding / ECM proteoglycans / : / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / Smooth Muscle Contraction / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / Integrin cell surface interactions / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / Platelet degranulation / LIM domain binding / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / vinculin binding / positive regulation of glomerular mesangial cell proliferation / regulation of extracellular matrix organization / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / glycinergic synapse / integrin activation / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / regulation of G protein-coupled receptor signaling pathway / insulin-like growth factor I binding / negative regulation of low-density lipoprotein receptor activity / cell-substrate junction assembly / regulation of release of sequestered calcium ion into cytosol / mesodermal cell differentiation / alphav-beta3 integrin-IGF-1-IGF1R complex / VEGFA-VEGFR2 Pathway / positive regulation of osteoclast differentiation / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / regulation of postsynaptic neurotransmitter receptor internalization / apolipoprotein A-I-mediated signaling pathway / apoptotic cell clearance / heterotypic cell-cell adhesion / integrin complex / positive regulation of cell adhesion mediated by integrin / cellular response to insulin-like growth factor stimulus / positive regulation of leukocyte migration / positive regulation of cell-matrix adhesion / cell adhesion mediated by integrin / smooth muscle cell migration / microvillus membrane / cortical actin cytoskeleton organization / negative chemotaxis / phosphatidylserine binding / fibroblast growth factor binding / cellular response to platelet-derived growth factor stimulus / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of smooth muscle cell migration / activation of protein kinase activity / positive regulation of osteoblast proliferation / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / platelet-derived growth factor receptor signaling pathway / fibronectin binding / positive regulation of T cell migration / positive regulation of bone resorption / positive regulation of substrate adhesion-dependent cell spreading / embryo implantation / ruffle / positive regulation of endothelial cell proliferation / phosphatidylinositol binding / cell adhesion molecule binding / substrate adhesion-dependent cell spreading / cell-matrix adhesion / protein kinase C binding / positive regulation of endothelial cell migration / response to activity / synaptic membrane / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / adherens junction / positive regulation of smooth muscle cell proliferation / response to radiation / structural constituent of cytoskeleton / cell-cell adhesion
Similarity search - Function
: / Talin, R4 domain / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment / Vinculin Binding Site / Talin, middle domain / N-terminal or F0 domain of Talin-head FERM ...: / Talin, R4 domain / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment / Vinculin Binding Site / Talin, middle domain / N-terminal or F0 domain of Talin-head FERM / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / Alpha-catenin/vinculin-like superfamily / 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 / FERM domain signature 1. / FERM conserved site / 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 / FERM domain signature 2. / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Integrin beta-3 / Talin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsZhang, P. / Sun, Y. / Wu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119560 United States
American Cancer SocietyRSG-15-167-01-DMC United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Crystal structure of the FERM-folded talin head reveals the determinants for integrin binding.
Authors: Zhang, P. / Azizi, L. / Kukkurainen, S. / Gao, T. / Baikoghli, M. / Jacquier, M.C. / Sun, Y. / Maatta, J.A.E. / Cheng, R.H. / Wehrle-Haller, B. / Hytonen, V.P. / Wu, J.
History
DepositionJan 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Integrin beta-3,Talin-1


Theoretical massNumber of molelcules
Total (without water)50,3831
Polymers50,3831
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.071, 66.825, 114.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Integrin beta-3,Talin-1 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 50382.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itgb3, Tln1, Tln / Plasmid: pET28a
Details (production host): modified to include a TEV cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O54890, UniProt: P26039
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 50.77 % / Description: rod, 20um*10um*300um
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium chloride 0.1 M MES pH6.5 10 % w/v PEG 4000

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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: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 13, 2019
RadiationMonochromator: double crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.779→29.62 Å / Num. obs: 12141 / % possible obs: 92.4 % / Redundancy: 2.4 % / Biso Wilson estimate: 63.85 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.1
Reflection shellResolution: 2.78→2.85 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 1.9 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IVF

3ivf


Resolution: 2.78→29.62 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.51
RfactorNum. reflection% reflection
Rfree0.263 611 5.04 %
Rwork0.215 --
obs0.217 12117 91.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 69.71 Å2
Refinement stepCycle: LAST / Resolution: 2.78→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 0 0 34 3084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.779-3.05840.35741410.27762878X-RAY DIFFRACTION93
3.0584-3.50030.30261530.24322868X-RAY DIFFRACTION92
3.5003-4.40770.24771720.19552874X-RAY DIFFRACTION92
4.4077-29.620.2421450.20292886X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: -25.8421 Å / Origin y: -2.3246 Å / Origin z: 11.0096 Å
111213212223313233
T0.3529 Å2-0.0162 Å2-0.0782 Å2-0.3081 Å2-0.0346 Å2--0.4349 Å2
L2.5198 °20.4972 °2-0.7689 °2-1.0064 °2-0.5155 °2--0.876 °2
S-0.0703 Å °-0.2085 Å °-0.0998 Å °0.0386 Å °0.047 Å °-0.053 Å °0.0428 Å °-0.026 Å °0.0391 Å °
Refinement TLS groupSelection details: ALL

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