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- PDB-4w8p: Crystal structure of RIAM TBS1 in complex with talin R7R8 domains -

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Basic information

Entry
Database: PDB / ID: 4w8p
TitleCrystal structure of RIAM TBS1 in complex with talin R7R8 domains
Components
  • Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
  • Talin-1
KeywordsPEPTIDE BINDING PROTEIN / Talin / rod domains / R7R8 / R8 / RIAM / TBS1
Function / homology
Function and homology information


GRB2:SOS provides linkage to MAPK signaling for Integrins / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / 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 ...GRB2:SOS provides linkage to MAPK signaling for Integrins / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / 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 / T cell receptor complex / phosphatidylserine binding / positive regulation of cell adhesion / ruffle / phosphatidylinositol binding / integrin-mediated signaling pathway / adherens junction / structural constituent of cytoskeleton / platelet aggregation / ruffle membrane / cell-cell adhesion / actin filament binding / integrin binding / lamellipodium / cytoskeleton / focal adhesion / cell surface / signal transduction / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Talin, central domain / GRB/APBB1IP / APBB1IP, PH domain / A middle domain of Talin 1 / : / Talin, R4 domain / Alpha-catenin/vinculin-like / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain ...Talin, central domain / GRB/APBB1IP / APBB1IP, PH domain / A middle domain of Talin 1 / : / Talin, R4 domain / Alpha-catenin/vinculin-like / 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 / Ras association (RalGDS/AF-6) domain / Phosphotyrosine-binding domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) 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 domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Talin-1 / Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChang, Y.C.E. / Zhang, H. / Wu, J.
CitationJournal: Structure / Year: 2014
Title: Structural and Mechanistic Insights into the Recruitment of Talin by RIAM in Integrin Signaling.
Authors: Chang, Y.C. / Zhang, H. / Franco-Barraza, J. / Brennan, M.L. / Patel, T. / Cukierman, E. / Wu, J.
History
DepositionAug 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 2.0Sep 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: atom_site_anisotrop / chem_comp_atom ...atom_site_anisotrop / chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine_hist
Item: _atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id ..._atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Talin-1
B: Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1284
Polymers34,0042
Non-polymers1242
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-6 kcal/mol
Surface area16280 Å2
MethodPISA
2
A: Talin-1
B: Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
hetero molecules

A: Talin-1
B: Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2578
Polymers68,0094
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7590 Å2
ΔGint-22 kcal/mol
Surface area29030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.722, 105.884, 49.027
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Talin-1


Mass: 31603.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26039
#2: Protein/peptide Amyloid beta A4 precursor protein-binding family B member 1-interacting protein / APBB1-interacting protein 1 / Proline-rich EVH1 ligand 1 / PREL-1 / Proline-rich protein 48


Mass: 2400.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8R5A3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM NaCl, 20% (w/v) polyethylene glycol 3350 and 20% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 285419 / Num. obs: 49933 / % possible obs: 98.6 % / Redundancy: 5.7 % / Rsym value: 0.051 / Net I/σ(I): 47.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.9 / % possible all: 96.9

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X0C

2x0c


Resolution: 1.5→24.79 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.21 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24192 2535 5.1 %RANDOM
Rwork0.22262 ---
obs0.22363 47327 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.122 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.5→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 8 305 2677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192451
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9341.9743335
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0165338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28725.882102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51615417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.4081514
X-RAY DIFFRACTIONr_chiral_restr0.0680.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211859
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.499→1.538 Å
RfactorNum. reflection% reflection
Rfree0.303 161 5 %
Rwork0.28 3113 -
obs--94.16 %
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)
10.08230.2375-0.01750.7862-0.17250.1940.0094-0.00560.01670.05150.03860.0645-0.0061-0.0462-0.0480.01660.0212-0.00590.0415-0.00640.05066.0665-7.2118-15.0829
26.5191-1.86064.23412.2857-1.2852.94610.12410.1546-0.2469-0.1602-0.01080.1460.10540.0957-0.11330.02970.01920.00590.05050.00840.03293.8259-31.9773-19.9889
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1357 - 1657
2X-RAY DIFFRACTION2B5 - 25

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