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- PDB-2qdq: Crystal structure of the talin dimerisation domain -

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Basic information

Entry
Database: PDB / ID: 2qdq
TitleCrystal structure of the talin dimerisation domain
ComponentsTalin-1
KeywordsSTRUCTURAL PROTEIN / Talin / dimerisation domain / C-terminal actin binding site / ABS3 / LATCH domain
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 / Smooth Muscle Contraction / MAP2K and MAPK activation / Platelet degranulation / LIM domain binding / cortical microtubule organization / vinculin binding ...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 / Smooth Muscle Contraction / MAP2K and MAPK activation / Platelet degranulation / LIM domain binding / cortical microtubule organization / 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
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 ...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 IBS2B domain / Talin, N-terminal F0 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 / IRS-type PTB domain / PTB domain (IRS-1 type) / 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 / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsGingras, A.R. / Putz, N.S.M. / Bate, N. / Barsukov, I.L. / Critchley, D.R.C.
CitationJournal: Embo J. / Year: 2008
Title: The structure of the C-terminal actin-binding domain of talin.
Authors: Gingras, A.R. / Bate, N. / Goult, B.T. / Hazelwood, L. / Canestrelli, I. / Grossmann, J.G. / Liu, H. / Putz, N.S. / Roberts, G.C. / Volkmann, N. / Hanein, D. / Barsukov, I.L. / Critchley, D.R.
History
DepositionJun 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 27, 2017Group: Data collection / Category: pdbx_diffrn_reflns_shell / reflns_shell
Item: _pdbx_diffrn_reflns_shell.percent_possible_obs / _reflns_shell.percent_possible_all
Revision 1.3Feb 21, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,6952
Polymers11,6952
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.820, 98.820, 98.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
DetailsThe biological assembly is a dimer

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Components

#1: Protein/peptide Talin-1


Mass: 5847.726 Da / Num. of mol.: 2 / Fragment: Reidues 2494-2541, dimerization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Plasmid: pET151 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26039
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100 mM Citrate buffer (pH 4.2), 11% (w/v) PEG 3000, 200 mM Sodium Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-111.07225
SYNCHROTRONESRF ID14-320.931
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 6, 2006
ADSC QUANTUM 3152CCDSep 23, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.072251
20.9311
ReflectionAv σ(I) over netI: 32.15 / Number: 157577 / Rmerge(I) obs: 0.047 / D res high: 2.3 Å / Num. obs: 13705 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obs
4.863010010.028
3.984.8610010.027
3.453.9899.210.032
3.093.4599.710.056
2.823.0910010.099
2.612.8210010.186
2.442.6199.610.288
2.32.4499.910.443
ReflectionResolution: 2.2→30 Å / Num. all: 8844 / Num. obs: 8844 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 39.9 % / Biso Wilson estimate: 50.658 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 51.71
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 41.7 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 9.2 / Num. measured obs: 57339 / Num. unique all: 1373 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.7650.2410.030.123
2Se50.9710.7760.4770.0610.084

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT2data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.8 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.843 / SU B: 3.935 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.315 442 5 %RANDOM
Rwork0.257 ---
all0.257 8396 --
obs0.257 8396 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.298 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms548 0 0 25 573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022546
X-RAY DIFFRACTIONr_angle_refined_deg1.0921.984719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.859565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7722532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02715130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.492158
X-RAY DIFFRACTIONr_chiral_restr0.0670.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02396
X-RAY DIFFRACTIONr_nbd_refined0.1940.2249
X-RAY DIFFRACTIONr_nbtor_refined0.2880.2371
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3070.27
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 31 -
Rwork0.242 596 -
obs-596 100 %

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