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- PDB-6mfs: Mouse talin1 residues 1-138 fused to residues 169-400 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6mfs
TitleMouse talin1 residues 1-138 fused to residues 169-400 in complex with phosphatidylinositol 4,5-bisphosphate (PIP2)
ComponentsTalin-1 fusion
KeywordsCELL ADHESION / angiogenesis / integrin activation / phospholipids / phosphoinositides / talin activation
Function / homology
Function and homology information


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 / Platelet degranulation / LIM domain binding / vinculin binding / integrin activation ...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 / Platelet degranulation / LIM domain binding / vinculin binding / integrin activation / cell-substrate junction assembly / cortical actin cytoskeleton organization / phosphatidylserine binding / ruffle / phosphatidylinositol binding / integrin-mediated signaling pathway / adherens junction / structural constituent of cytoskeleton / cell-cell adhesion / ruffle membrane / actin filament binding / integrin binding / cytoskeleton / focal adhesion / cell surface / plasma membrane / cytoplasm
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 / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / Alpha-catenin/vinculin-like superfamily / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-PIO / PHOSPHATE ION / Talin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsIzard, T. / Chinthalapudi, K. / Rangarajan, E.S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: The interaction of talin with the cell membrane is essential for integrin activation and focal adhesion formation.
Authors: Chinthalapudi, K. / Rangarajan, E.S. / Izard, T.
History
DepositionSep 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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: Talin-1 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0025
Polymers42,9711
Non-polymers1,0314
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.686, 73.055, 162.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Talin-1 fusion


Mass: 42970.520 Da / Num. of mol.: 1 / Fragment: FERM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21, BL21 / Variant (production host): RIL / References: UniProt: P26039
#2: Chemical ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H49O19P3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.75 Å3/Da / Density % sol: 55.24 % / Description: Plates
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 18-25% PEG 3350, 200 mM Ammonium citrate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→40.59 Å / Num. obs: 11685 / % possible obs: 93.9 % / Redundancy: 6 % / Biso Wilson estimate: 69.28 Å2 / Net I/σ(I): 11
Reflection shellResolution: 2.85→3 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSNov 1 2016data reduction
PDB_EXTRACT3.24data extraction
Aimlessdata scaling
PHASER0.5.32phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IVF

3ivf


Resolution: 2.85→22.41 Å / Cor.coef. Fo:Fc: 0.821 / Cor.coef. Fo:Fc free: 0.769 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.441
RfactorNum. reflection% reflectionSelection details
Rfree0.29 562 4.88 %RANDOM
Rwork0.237 ---
obs0.239 11527 99.3 %-
Displacement parametersBiso mean: 74.22 Å2
Baniso -1Baniso -2Baniso -3
1--55.6808 Å20 Å20 Å2
2--29.3704 Å20 Å2
3---26.3104 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 2.85→22.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 50 122 3172
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013103HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.114178HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1500SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes517HARMONIC5
X-RAY DIFFRACTIONt_it3103HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion3.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion394SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3417SEMIHARMONIC4
LS refinement shellResolution: 2.85→2.89 Å / Total num. of bins used: 28
RfactorNum. reflection% reflection
Rfree0.3128 -4.37 %
Rwork0.309 394 -
all0.3092 412 -
obs--99.76 %

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