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- PDB-2x0c: Crystal Structure of the R7R8 domains of Talin -

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Basic information

Entry
Database: PDB / ID: 2x0c
TitleCrystal Structure of the R7R8 domains of Talin
ComponentsTALIN-1
KeywordsCELL ADHESION / CYTOSKELETON / CELL MEMBRANE / ACTIN / SYNEMIN / INTEGRIN / VINCULIN / CELL PROJECTION
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 / LIM domain binding / Platelet degranulation / 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 / LIM domain binding / Platelet degranulation / 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 / ruffle membrane / platelet aggregation / cell-cell adhesion / 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 / Alpha-catenin/vinculin-like / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / MAD / Resolution: 2 Å
AuthorsGingras, A.R. / Goult, B.T. / Bate, N. / Barsukov, I.L. / Emsley, J. / Critchely, D.R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Central Region of Talin Has a Unique Fold that Binds Vinculin and Actin.
Authors: Gingras, A.R. / Bate, N. / Goult, B.T. / Patel, B. / Kopp, P.M. / Emsley, J. / Barsukov, I.L. / Roberts, G.C.K. / Critchley, D.R.
History
DepositionDec 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 1, 2023Group: Database references / Other / Structure summary / Category: database_2 / pdbx_database_status / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct.title
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TALIN-1


Theoretical massNumber of molelcules
Total (without water)32,5751
Polymers32,5751
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.000, 66.810, 185.710
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: 32574.725 Da / Num. of mol.: 1 / Fragment: RESIDUES 1359-1659
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Variant: TALIN1 / Plasmid: PET-151 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26039
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 8 AMINO ACIDS ARE FROM THE VECTOR AFTER TAG CLEAVAGE

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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

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.78 % / Description: NONE
Crystal growpH: 8.5
Details: 18% PEG 8K, 100MM TRIS, 180MM SODIUM PHOSPHATE DIBASIC, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97905
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 24, 2008 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 33121 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.863 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.26367 1641 5 %RANDOM
Rwork0.21156 ---
obs0.21419 31178 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.717 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å20 Å20 Å2
2--2.6 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 0 185 2455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222302
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1711.9643123
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6165307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2225.52196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16515386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9461514
X-RAY DIFFRACTIONr_chiral_restr0.1770.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211741
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3571.51538
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.28622461
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8133764
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.2714.5662
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 117 -
Rwork0.243 2236 -
obs--100 %
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)
11.64580.13621.20140.289-0.13221.072-0.08330.05720.14970.0324-0.0020.0347-0.09330.0560.08530.0102-0.0051-0.00380.0463-0.01870.0279-2.035858.324311.5147
20.9156-0.061.26270.1978-0.22532.02230.0566-0.0769-0.11640.02380.06610.02660.0741-0.0875-0.12260.00930.00780.00150.07260.02620.0331-6.457344.849620.6561
31.7914-0.06281.5670.29370.04291.4043-0.0324-0.05640.00970.03030.0291-0.0174-0.02-0.04710.00340.00610.0014-0.00070.0719-0.00190.0016-0.610351.300421.6175
40.7224-1.59930.0725.404-0.85550.28590.02750.0469-0.0012-0.0674-0.0283-0.01350.0293-0.0020.00080.04670.0159-0.01720.0371-0.00230.00727.672484.963330.6181
55.8201-6.54773.35698.0066-4.29372.3774-0.07490.1104-0.26440.12910.20660.284-0.0634-0.1917-0.13170.0906-0.0127-0.05710.18750.0190.06433.696881.791438.6754
65.6909-5.58652.48476.9893-2.09571.18330.0310.0774-0.32280.08060.21730.02810.05950.0527-0.24830.0393-0.0167-0.05380.18780.01910.126611.205984.289646.0321
70.2010.09570.30872.8174-1.07831.0253-0.01140.0399-0.071-0.22660.0393-0.2990.12510.012-0.0280.1048-0.0206-0.00770.11620.03440.079711.020490.754837.9267
81.6234-0.4181.51820.2677-0.27351.5084-0.01340.05490.0001-0.00120.0429-0.0407-0.01750.0833-0.02950.0010.00110.00020.0581-0.01340.01377.300346.982314.9998
90.6074-0.08551.03870.1132-0.38992.38410.0449-0.0062-0.08690.00060.0017-0.02980.0731-0.018-0.04660.0120.0004-0.0080.02710.00510.03082.150539.532115.9481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1354 - 1378
2X-RAY DIFFRACTION2A1389 - 1416
3X-RAY DIFFRACTION3A1419 - 1450
4X-RAY DIFFRACTION4A1465 - 1482
5X-RAY DIFFRACTION5A1488 - 1513
6X-RAY DIFFRACTION6A1519 - 1546
7X-RAY DIFFRACTION7A1552 - 1577
8X-RAY DIFFRACTION8A1590 - 1622
9X-RAY DIFFRACTION9A1627 - 1658

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