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- PDB-4f7g: Crystal structure of talin autoinhibition complex -

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Basic information

Entry
Database: PDB / ID: 4f7g
TitleCrystal structure of talin autoinhibition complex
Components(Talin-1) x 2
KeywordsCELL ADHESION / alpha-helix bundle / integrin 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, central domain / A middle domain of Talin 1 / : / 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, central domain / A middle domain of Talin 1 / : / 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 / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSong, X. / Qin, J. / Ye, S. / Zhang, R.
CitationJournal: Cell Res. / Year: 2012
Title: A novel membrane-dependent on/off switch mechanism of talin FERM domain at sites of cell adhesion.
Authors: Song, X. / Yang, J. / Hirbawi, J. / Ye, S. / Perera, H.D. / Goksoy, E. / Dwivedi, P. / Plow, E.F. / Zhang, R. / Qin, J.
History
DepositionMay 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Talin-1
B: Talin-1


Theoretical massNumber of molelcules
Total (without water)48,4732
Polymers48,4732
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.665, 86.876, 113.629
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 Talin-1


Mass: 25613.430 Da / Num. of mol.: 1 / Fragment: F2F3 subdomain, UNP residues 206-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Production host: Escherichia coli (E. coli) / References: UniProt: P26039
#2: Protein Talin-1


Mass: 22859.459 Da / Num. of mol.: 1 / Fragment: RS subdomain, UNP residues 1654-1847
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Production host: Escherichia coli (E. coli) / References: UniProt: P26039
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.8734.11
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2891vapor diffusion, hanging drop6.518.5% (w/v) PEG 1500, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
2892vapor diffusion, hanging drop6.518.5% (w/v) PEG 1500, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.97915
SYNCHROTRONSSRF BL17U20.97915
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJan 4, 2011
ADSC QUANTUM 3152CCDJan 28, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.05→69.02 Å / Num. all: 23478 / Num. obs: 20930 / % possible obs: 89.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Biso Wilson estimate: 56.37 Å2
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2.5 % / Num. unique all: 778 / % possible all: 51.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→69.02 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 14.917 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1046 5.1 %RANDOM
Rwork0.21041 ---
all0.215 23478 --
obs0.21245 19565 87.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.913 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---1.68 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.05→69.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 0 0 109 2906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222842
X-RAY DIFFRACTIONr_bond_other_d0.0010.021908
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9643837
X-RAY DIFFRACTIONr_angle_other_deg0.96834703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69125.794126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.55715518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2651510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023151
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02517
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2071.51800
X-RAY DIFFRACTIONr_mcbond_other0.3731.5733
X-RAY DIFFRACTIONr_mcangle_it4.09622877
X-RAY DIFFRACTIONr_scbond_it3.98231042
X-RAY DIFFRACTIONr_scangle_it6.7424.5960
X-RAY DIFFRACTIONr_rigid_bond_restr1.85134750
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.052→2.106 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 45 -
Rwork0.349 795 -
obs--49.91 %

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