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- PDB-1miz: Crystal structure of an integrin beta3-talin chimera -

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Basic information

Entry
Database: PDB / ID: 1miz
TitleCrystal structure of an integrin beta3-talin chimera
Components
  • TALIN
  • integrin beta3
KeywordsSTRUCTURAL PROTEIN / FOCAL ADHESION / INTEGRIN BINDING / CYTOSKELETON / NPXY MOTIF / PTB DOMAIN
Function / homology
Function and homology information


regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization ...regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / cell-substrate junction assembly / mesodermal cell differentiation / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of bone resorption / platelet-derived growth factor receptor binding / regulation of release of sequestered calcium ion into cytosol / glycinergic synapse / filopodium membrane / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / negative regulation of low-density lipoprotein particle clearance / regulation of bone resorption / angiogenesis involved in wound healing / wound healing, spreading of epidermal cells / apoptotic cell clearance / integrin complex / positive regulation of fibroblast migration / heterotypic cell-cell adhesion / smooth muscle cell migration / Molecules associated with elastic fibres / positive regulation of smooth muscle cell migration / cell adhesion mediated by integrin / negative chemotaxis / positive regulation of cell-matrix adhesion / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / protein disulfide isomerase activity / regulation of postsynaptic neurotransmitter receptor internalization / cellular response to insulin-like growth factor stimulus / positive regulation of osteoblast proliferation / microvillus membrane / cell-substrate adhesion / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / TGF-beta receptor signaling activates SMADs / fibronectin binding / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / blood coagulation, fibrin clot formation / ECM proteoglycans / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / positive regulation of T cell migration / coreceptor activity / ruffle / cellular response to platelet-derived growth factor stimulus / Integrin signaling / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / cell adhesion molecule binding / embryo implantation / positive regulation of smooth muscle cell proliferation / positive regulation of endothelial cell migration / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / protein kinase C binding / cell-matrix adhesion / response to activity / integrin-mediated signaling pathway / Signal transduction by L1 / regulation of actin cytoskeleton organization / wound healing / cellular response to mechanical stimulus / cell-cell adhesion / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / structural constituent of cytoskeleton / VEGFA-VEGFR2 Pathway / platelet aggregation / cellular response to xenobiotic stimulus / integrin binding / ruffle membrane / positive regulation of fibroblast proliferation
Similarity search - Function
Talin VBS2 domain / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain ...Talin VBS2 domain / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain / Talin 1-like, rod segment domain / Talin, N-terminal F0 domain / : / N-terminal or F0 domain of Talin-head FERM / Talin IBS2B domain / Acyl-CoA Binding Protein - #10 / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Acyl-CoA Binding Protein / Alpha-catenin/vinculin-like superfamily / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / : / : / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta tail 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. / FERM domain signature 2. / 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 / FERM/acyl-CoA-binding protein superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 1. / EGF-like domain signature 2. / PH-like domain superfamily / Roll / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Integrin beta-3 / Talin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGarcia-Alvarez, B. / de Pereda, J.M. / Calderwood, D.A. / Ulmer, T.S. / Critchley, D. / Campbell, I.D. / Ginsberg, M.H. / Liddington, R.C.
CitationJournal: Mol.Cell / Year: 2003
Title: Structural determinants of integrin recognition by talin
Authors: Garcia-Alvarez, B. / de Pereda, J.M. / Calderwood, D.A. / Ulmer, T.S. / Critchley, D. / Campbell, I.D. / Ginsberg, M.H. / Liddington, R.C.
History
DepositionAug 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999SEQUENCE AUTHORS INFORMED THAT THE SEQUENCE OF CHICKEN TALIN IS NOT AVAILABLE IN ANY REFERENCE ...SEQUENCE AUTHORS INFORMED THAT THE SEQUENCE OF CHICKEN TALIN IS NOT AVAILABLE IN ANY REFERENCE DATABASE. THE SEQUENCE HAS BEEN DESCRIBED IN THE PUBLICATION: HEMMINGS, L., REES, D.J.G., OHANIAN, V., BOLTON, S.J., GILMORE, A.P., PATEL, N., PRIDDLE, H., TREVITHICK, J.E., HYNES, R.O., & CRITCHLEY, D.R. (1996). TALIN CONTAINS THREE ACTIN-BINDING SITES EACH OF WHICH IS ADJACENT TO A VINCULIN-BINDING SITE. J. CELL SCI., 109, 2715-2726.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: integrin beta3
B: TALIN


Theoretical massNumber of molelcules
Total (without water)24,1282
Polymers24,1282
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.533, 55.198, 46.751
Angle α, β, γ (deg.)90.00, 97.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide integrin beta3


Mass: 958.951 Da / Num. of mol.: 1 / Fragment: Residues 739-743
Source method: isolated from a genetically manipulated source
Details: Forms chimera with Talin at the C-terminus / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05106
#2: Protein TALIN


Mass: 23168.635 Da / Num. of mol.: 1 / Fragment: Residues 200-400
Source method: isolated from a genetically manipulated source
Details: Forms chimera with integrin beta3 at the N-terminus
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54939
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MTris-HCl1reservoirpH7.0
220 %(w/v)PEG2000 MME1reservoir
310 mg/mlprotein1drop
420 mMTris-HCl1droppH7.0
5150 mM1dropNaCl
62 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Mar 16, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→19.59 Å / Num. all: 15025 / Num. obs: 13705 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.6 Å2
Reflection shellResolution: 1.9→2.02 Å / % possible all: 63.5
Reflection
*PLUS
Highest resolution: 1.9 Å / % possible obs: 91.5 % / Num. measured all: 36282 / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
% possible obs: 63.7 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPCCP4phasing
CNS1.1refinement
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MIX

1mix


Resolution: 1.9→19.59 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 581928.86 / Data cutoff high rms absF: 581928.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 823 6 %RANDOM
Rwork0.204 ---
obs0.204 13688 91.1 %-
all-15025 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.3661 Å2 / ksol: 0.334104 e/Å3
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1--3 Å20 Å28.64 Å2
2---8.61 Å20 Å2
3---11.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 0 178 1874
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.412.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 96 6.1 %
Rwork0.27 1479 -
obs--63.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69
LS refinement shell
*PLUS
Rfactor Rwork: 0.27

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