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- PDB-9qn7: Structure of talin in complex with a peptide fragment -

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Basic information

Entry
Database: PDB / ID: 9qn7
TitleStructure of talin in complex with a peptide fragment
Components
  • Talin-1
  • Tensin-3
KeywordsCELL ADHESION / talin / tensin3 / phase seperation / adhesion
Function / homology
Function and homology information


GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / LIM domain binding / Smooth Muscle Contraction / Platelet degranulation / MET interacts with TNS proteins / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases ...GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / LIM domain binding / Smooth Muscle Contraction / Platelet degranulation / MET interacts with TNS proteins / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / cortical microtubule organization / vinculin binding / integrin activation / cell-substrate junction assembly / cortical actin cytoskeleton organization / podosome / phosphatidylserine binding / positive regulation of Rac protein signal transduction / phosphoprotein phosphatase activity / ruffle / phosphatidylinositol binding / integrin-mediated signaling pathway / cell projection / adherens junction / structural constituent of cytoskeleton / ruffle membrane / integrin binding / actin filament binding / cytoskeleton / cell adhesion / focal adhesion / cell surface / cytosol
Similarity search - Function
Tensin, phosphotyrosine-binding domain / Tensin-like, SH2 domain / : / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. ...Tensin, phosphotyrosine-binding domain / Tensin-like, SH2 domain / : / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / 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 / 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) / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / 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 / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / C2 domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsZacharchenko, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of the talin R11R12-tensin3 complex
Authors: Zacharchenko, T.
History
DepositionMar 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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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
C: Tensin-3
D: Tensin-3


Theoretical massNumber of molelcules
Total (without water)75,7044
Polymers75,7044
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-27 kcal/mol
Surface area32910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.940, 84.940, 346.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Talin-1


Mass: 34726.590 Da / Num. of mol.: 2
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/peptide Tensin-3 / Tensin-like SH2 domain-containing protein 1 / Tumor endothelial marker 6


Mass: 3125.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q68CZ2, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion / pH: 7.4
Details: 0.9M sodium potassium tartrate tetrathydrate, 20% w/v glycerol, 0.05M HEPES pH 7.4
Temp details: 21 degrees celsius.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo stream synchrotron / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.76→86.58 Å / Num. obs: 33905 / % possible obs: 99.9 % / Redundancy: 26.2 % / Biso Wilson estimate: 64.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.441 / Rpim(I) all: 0.087 / Net I/σ(I): 10.6
Reflection shellResolution: 2.76→2.89 Å / Redundancy: 27.7 % / Rmerge(I) obs: 3.087 / Num. unique obs: 4373 / CC1/2: 0.483 / Rpim(I) all: 0.59 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→76.26 Å / SU ML: 0.5591 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.0211
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2958 1689 5.01 %
Rwork0.257 32012 -
obs0.2589 33701 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.05 Å2
Refinement stepCycle: LAST / Resolution: 2.76→76.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5076 0 0 21 5097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00475135
X-RAY DIFFRACTIONf_angle_d0.94956966
X-RAY DIFFRACTIONf_chiral_restr0.051868
X-RAY DIFFRACTIONf_plane_restr0.0064901
X-RAY DIFFRACTIONf_dihedral_angle_d14.86411898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.840.49511430.44082621X-RAY DIFFRACTION99.93
2.84-2.930.42261460.41692591X-RAY DIFFRACTION99.67
2.93-3.040.39681540.39272585X-RAY DIFFRACTION99.56
3.04-3.160.3631240.36172652X-RAY DIFFRACTION99.75
3.16-3.30.36181400.35392599X-RAY DIFFRACTION99.82
3.3-3.480.39231610.33842589X-RAY DIFFRACTION99.78
3.48-3.70.39731370.31552675X-RAY DIFFRACTION99.68
3.7-3.980.31811330.27782654X-RAY DIFFRACTION99.54
3.98-4.380.25231240.21082674X-RAY DIFFRACTION99.47
4.38-5.010.23651510.20112695X-RAY DIFFRACTION99.06
5.02-6.320.27391300.23962733X-RAY DIFFRACTION99.38
6.32-76.260.20951460.17332944X-RAY DIFFRACTION99.68
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)
13.420962767030.232971769378-0.4382445960022.71642659860.9343367326321.080166299490.08040655802770.1719627657530.721920922622-0.329645731378-0.0609429199570.06799395305360.0255412239947-0.51417597202-0.04466231834810.974609250496-0.06797510218170.05166392476310.7908152495590.1671479583770.31355868307815.084280814337.540356351944.1971794574
22.11067492711.49460884424-1.319881546731.94829385468-0.3928594871011.49143894061-0.6366259262580.5965887869080.03194040855-0.1219125034730.146461462616-0.4508289139720.444996953351-0.6936573192410.1311870182041.018695798430.201659188161-0.00831541924770.6400926194310.1753462200320.15719432174321.411121239636.371828188235.3801761072
34.675409056641.35134812491-0.4111996850443.42615369453-1.30545891656.69784691671-0.414850533499-0.406544046145-0.38354484033-0.144733501425-0.20210324946-0.2450335621650.2606121228030.06942447977220.4463611020221.16771123481-0.08359997148960.05987536684950.7265557781940.08388423790720.32991645988120.85264135551.8047671509-4.77911460908
45.89525059457-0.2295837562750.8251518033444.11623899006-0.04884366859624.302614894030.077812648932-0.340418827251-0.0677980536743-0.102922544954-0.1157090382870.682322963476-0.2798119604240.4341703973010.2833583420220.836564519867-0.13084840284-0.1068602939080.683958479814-0.1088907661270.42725923438631.97972570894.496796150862.21633415049
50.269341598173-0.1638535371950.9893921405161.103699505370.1774339593845.43743812972-0.219444805083-0.199290690469-0.2433411226960.3466010183440.1507139684840.2333382226270.128236525173-0.6515243669540.1317912720130.8445308229160.1914106739810.1726394194731.22868231660.04585480710880.45614003367732.3539614582.4950957421944.2709004346
69.26523437293-4.138901010435.050991166149.60003692708-2.894041042644.451862770240.540847821302-0.1850580012831.292793403651.02882208821-1.85726803138-0.7980557946010.5923433841541.239857045930.749461928040.8661247160480.2880916273470.2763481114291.406908466530.1135723249590.56015297254434.82659673734.266266076740.8567440403
74.77476903531-1.60604014701-0.7262876549170.7598419810920.8198052965871.518907864280.444929027533-2.04252069343-0.6706605880280.866901302950.01282620560130.6214741700540.149925105971-0.508989735155-0.5387417990171.79478266215-0.849955796814-0.1021757347491.370110904470.0540847615821.0083033531820.602579356-5.4147618778513.8634962828
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1967 through 2040 )AA1967 - 20401 - 74
22chain 'A' and (resid 2041 through 2161 )AA2041 - 216175 - 195
33chain 'A' and (resid 2162 through 2291 )AA2162 - 2291196 - 325
44chain 'B' and (resid 1971 through 2108 )BB1971 - 21081 - 138
55chain 'B' and (resid 2109 through 2291 )BB2109 - 2291139 - 321
66chain 'C' and (resid 692 through 715 )CC692 - 7151 - 24
77chain 'D' and (resid 694 through 707 )DD694 - 7071 - 14

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