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- PDB-3dyj: Crystal Structure of the R11R12 Domains of Talin -

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Basic information

Entry
Database: PDB / ID: 3dyj
TitleCrystal Structure of the R11R12 Domains of Talin
ComponentsTALIN-1
KeywordsSTRUCTURAL PROTEIN / TALIN / HELIX BUNDLES / CYTOSKELETAL PROTEIN / integrin-bindin site / IBS2 / Cell membrane / Cell projection / Cytoplasm / Cytoskeleton / Membrane / Phosphoprotein
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 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsGingras, A.R. / Joyce, M.G. / Critchley, D.R. / Emsley, J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural determinants of integrin binding to the talin rod
Authors: Gingras, A.R. / Ziegler, W.H. / Bobkov, A.A. / Joyce, M.G. / Fasci, D. / Himmel, M. / Rothemund, S. / Ritter, A. / Grossmann, J.G. / Patel, B. / Bate, N. / Goult, B.T. / Emsley, J. / ...Authors: Gingras, A.R. / Ziegler, W.H. / Bobkov, A.A. / Joyce, M.G. / Fasci, D. / Himmel, M. / Rothemund, S. / Ritter, A. / Grossmann, J.G. / Patel, B. / Bate, N. / Goult, B.T. / Emsley, J. / Barsukov, I.L. / Roberts, G.C. / Liddington, R.C. / Ginsberg, M.H. / Critchley, D.R.
History
DepositionJul 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 25, 2021Group: Database references / Derived calculations / Structure summary
Category: database_2 / struct ...database_2 / struct / 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.title / _struct_conn.pdbx_leaving_atom_flag / _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)70,4642
Polymers70,4642
Non-polymers00
Water5,981332
1
A: TALIN-1


Theoretical massNumber of molelcules
Total (without water)35,2321
Polymers35,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TALIN-1


Theoretical massNumber of molelcules
Total (without water)35,2321
Polymers35,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.713, 57.648, 92.547
Angle α, β, γ (deg.)90.00, 102.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TALIN-1


Mass: 35232.207 Da / Num. of mol.: 2 / Fragment: TALIN ROD (UNP RESIDUES:1974-2293)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Plasmid: PET-151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26039
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 8000, 1% PEG 3350, 100MM HEPES (PH 7.5), 10MM SODIUM THIOCYANATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 273K, pH 7.50, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9757
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2005 / Details: GE(220) CRYSTAL AND MULTILAYER
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9757 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 52439 / % possible obs: 98.1 % / Rsym value: 0.085 / Net I/σ(I): 16.8
Reflection shellResolution: 1.85→1.92 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.449 / % possible all: 87.5

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.2.0019refinement
ADSCdata collection
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.85→19.57 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.774 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25989 1300 2.6 %RANDOM
Rwork0.2138 ---
obs0.215 49457 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.897 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.27 Å2
2--0.18 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 0 332 5010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224726
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9716410
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8395632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.94525.227176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84915840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1691528
X-RAY DIFFRACTIONr_chiral_restr0.0990.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023422
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.22657
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.23425
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2322
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3040.2101
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0741.53238
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68325056
X-RAY DIFFRACTIONr_scbond_it3.2831626
X-RAY DIFFRACTIONr_scangle_it5.0684.51354
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 87 -
Rwork0.287 3184 -
obs--87.3 %
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)
11.55050.34150.861.7147-0.38744.10340.0246-0.1086-0.03010.15120.0276-0.01830.07580.1268-0.0523-0.1191-0.00540.026-0.2-0.0372-0.126234.389632.4074.4452
20.92281.04131.23.01543.31314.01510.03360.070.02030.0842-0.07620.04470.082-0.32740.0427-0.14690.00020.0153-0.05670.0233-0.106119.773620.1333-39.1872
31.4879-0.360.41451.76130.64373.46920.02750.0419-0.08140.0217-0.0219-0.01110.1253-0.254-0.0056-0.1352-0.01420.046-0.15550.0255-0.11135.05122.9583-49.7518
41.8257-0.43120.81252.1967-2.093.3783-0.07160.19480.22590.0332-0.0723-0.1284-0.09840.35980.144-0.1081-0.0338-0.00930.0038-0.0026-0.066149.3447-6.9696-5.7673
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1977 - 200116 - 40
2X-RAY DIFFRACTION1AA2012 - 203751 - 76
3X-RAY DIFFRACTION1AA2041 - 206980 - 108
4X-RAY DIFFRACTION1AA2074 - 2102113 - 141
5X-RAY DIFFRACTION1AA2109 - 2136148 - 175
6X-RAY DIFFRACTION2AA2140 - 2161179 - 200
7X-RAY DIFFRACTION2AA2172 - 2194211 - 233
8X-RAY DIFFRACTION2AA2199 - 2224238 - 263
9X-RAY DIFFRACTION2AA2230 - 2259269 - 298
10X-RAY DIFFRACTION2AA2264 - 2289303 - 328
11X-RAY DIFFRACTION3BB1977 - 200116 - 40
12X-RAY DIFFRACTION3BB2012 - 203751 - 76
13X-RAY DIFFRACTION3BB2041 - 206980 - 108
14X-RAY DIFFRACTION3BB2074 - 2102113 - 141
15X-RAY DIFFRACTION3BB2109 - 2136148 - 175
16X-RAY DIFFRACTION4BB2140 - 2161179 - 200
17X-RAY DIFFRACTION4BB2172 - 2194211 - 233
18X-RAY DIFFRACTION4BB2199 - 2224238 - 263
19X-RAY DIFFRACTION4BB2230 - 2259269 - 298
20X-RAY DIFFRACTION4BB2264 - 2289303 - 328

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