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- PDB-1sj7: Crystal Structure of Talin Rod 482-655 -

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Basic information

Entry
Database: PDB / ID: 1sj7
TitleCrystal Structure of Talin Rod 482-655
ComponentsTalin 1
KeywordsSTRUCTURAL PROTEIN
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 / 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 / MAP2K and MAPK activation / LIM domain binding / Smooth Muscle Contraction / Platelet degranulation / 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 / ruffle membrane / integrin binding / actin filament binding / cytoskeleton / cell adhesion / focal adhesion / cell surface / cytosol
Similarity search - Function
Talin, central domain / A middle domain of Talin 1 / Talin VBS2 domain / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site ...Talin, central domain / A middle domain of Talin 1 / 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) / 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: 2.5 Å
AuthorsPapagrigoriou, E. / Gingras, A.R. / Barsukov, I.L. / Critchley, D.R. / Emsley, J.
CitationJournal: EMBO J. / Year: 2004
Title: Activation of a vinculin-binding site in the talin rod involves rearrangement of a five-helix bundle
Authors: Papagrigoriou, E. / Gingras, A.R. / Barsukov, I.L. / Bate, N. / Fillingham, I.J. / Patel, B. / Frank, R. / Ziegler, W.H. / Roberts, G.C. / Critchley, D.R. / Emsley, J.
History
DepositionMar 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Talin 1
B: Talin 1
C: Talin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,23710
Polymers53,8713
Non-polymers1,3667
Water2,342130
1
A: Talin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3473
Polymers17,9571
Non-polymers3902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Talin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5424
Polymers17,9571
Non-polymers5853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Talin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3473
Polymers17,9571
Non-polymers3902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Talin 1
hetero molecules

C: Talin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6946
Polymers35,9142
Non-polymers7804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+4/31
Buried area2100 Å2
ΔGint-71 kcal/mol
Surface area15920 Å2
MethodPISA
5
A: Talin 1
B: Talin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8897
Polymers35,9142
Non-polymers9755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-90 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.662, 95.662, 115.215
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Talin 1


Mass: 17956.994 Da / Num. of mol.: 3 / Fragment: Residues 482-655
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: TLN1, TLN / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P26039
#2: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Pt
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG 2000 MME, 0.1M Ammonium Acetate, 0.2M Ammonium Sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: 0.9 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 21554 / Num. obs: 21513 / % possible obs: 99.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 28.05
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 3.576 / Num. unique all: 2120 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→28.163 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.699 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.514 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28619 1122 5.2 %RANDOM
Rwork0.24113 ---
all0.24336 21561 --
obs-20414 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.414 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20.95 Å20 Å2
2--1.9 Å20 Å2
3----2.85 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 7 142 3743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0213647
X-RAY DIFFRACTIONr_angle_refined_deg2.5521.9654962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7593503
X-RAY DIFFRACTIONr_dihedral_angle_3_deg27.03915617
X-RAY DIFFRACTIONr_chiral_restr0.1620.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022758
X-RAY DIFFRACTIONr_nbd_refined0.3360.32084
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2460.5271
X-RAY DIFFRACTIONr_metal_ion_refined0.5270.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.365
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3640.57
X-RAY DIFFRACTIONr_mcbond_it1.0151.52508
X-RAY DIFFRACTIONr_mcangle_it1.84723961
X-RAY DIFFRACTIONr_scbond_it3.47731139
X-RAY DIFFRACTIONr_scangle_it5.3274.51001
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.427 93
Rwork0.321 1457

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