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- PDB-7v1a: Stapled TBS peptide from RIAM bound to talin R7R8 domains -

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Basic information

Entry
Database: PDB / ID: 7v1a
TitleStapled TBS peptide from RIAM bound to talin R7R8 domains
Components
  • ASP-ILE-ASP-GLN-MET-PHE-SER-THR-LEU-LEU-GLY-GLU-MK8-ASP-LEU-LEU-MK8-GLN-SER
  • Talin-1
KeywordsCELL ADHESION / RIAM / Talin / integrin / MRL / stapled / helix
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 / LIM domain binding / 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 / Smooth Muscle Contraction / MAP2K and MAPK activation / LIM domain binding / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.845 Å
AuthorsZhang, P. / Gao, T. / Wu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)119560 United States
CitationJournal: Structure / Year: 2023
Title: Inhibition of talin-induced integrin activation by a double-hit stapled peptide.
Authors: Gao, T. / Cho, E.A. / Zhang, P. / Wu, J.
History
DepositionMay 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 16, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Talin-1
B: ASP-ILE-ASP-GLN-MET-PHE-SER-THR-LEU-LEU-GLY-GLU-MK8-ASP-LEU-LEU-MK8-GLN-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8453
Polymers33,7832
Non-polymers621
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-11 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.864, 104.334, 48.233
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Fragment: R7R8 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Production host: Escherichia coli (E. coli) / References: UniProt: P26039
#2: Protein/peptide ASP-ILE-ASP-GLN-MET-PHE-SER-THR-LEU-LEU-GLY-GLU-MK8-ASP-LEU-LEU-MK8-GLN-SER


Mass: 2179.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 293 K / Method: evaporation
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.845→104.33 Å / Num. obs: 27043 / % possible obs: 99.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 48.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Net I/σ(I): 22.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.886.11.546922615120.4750.6721.689191.9
9.04-104.335.20.02215072880.9990.0110.02459.698.3

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4w8p

4w8p


Resolution: 1.845→52.572 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 1361 5.05 %
Rwork0.2154 25612 -
obs0.2175 26973 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.22 Å2 / Biso mean: 60.7747 Å2 / Biso min: 33.72 Å2
Refinement stepCycle: final / Resolution: 1.845→52.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 4 144 2465
Biso mean--56.28 63.26 -
Num. residues----319
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8452-1.91120.31781260.3225238194
1.9112-1.98770.34961120.31652545100
1.9877-2.07820.34741350.29172534100
2.0782-2.18770.27811200.26792560100
2.1877-2.32480.29111540.26472541100
2.3248-2.50430.33511250.25682567100
2.5043-2.75630.25711460.24762558100
2.7563-3.15510.31391560.23452558100
3.1551-3.97490.27991420.20592623100
3.9749-520.1931450.18262745100
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)
10.5802-0.66190.25833.1809-0.54910.9970.04930.04410.00310.06250.0364-0.0801-0.0932-0.0028-0.08860.2995-0.1126-0.01910.3916-0.03370.32946.82776.5453-9.4724
21.07970.39750.18881.7683-0.34980.2174-0.0692-0.34150.12080.06150.1759-0.0383-0.41390.0494-0.11250.8659-0.2765-0.22951.40790.32360.86366.057328.7149-3.3864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1357:1656)A1357 - 1656
2X-RAY DIFFRACTION2(chain B and resseq 8:25)B8 - 25

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