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- PDB-2mwn: Talin-F3 / RIAM N-terminal Peptide complex -

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Basic information

Entry
Database: PDB / ID: 2mwn
TitleTalin-F3 / RIAM N-terminal Peptide complex
Components
  • Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
  • Talin-1
KeywordsSTRUCTURAL PROTEIN/SIGNALING PROTEIN / RIAM / Talin / Integrin / STRUCTURAL PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / LIM domain binding / vinculin binding / XBP1(S) activates chaperone genes / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / integrin activation / cell-substrate junction assembly / cell-cell junction assembly / cortical actin cytoskeleton organization / T cell receptor complex ...T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / LIM domain binding / vinculin binding / XBP1(S) activates chaperone genes / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / integrin activation / cell-substrate junction assembly / cell-cell junction assembly / cortical actin cytoskeleton organization / T cell receptor complex / regulation of focal adhesion assembly / p130Cas linkage to MAPK signaling for integrins / phosphatidylserine binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of cell adhesion / Smooth Muscle Contraction / ruffle / Integrin signaling / phosphatidylinositol binding / integrin-mediated signaling pathway / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / structural constituent of cytoskeleton / platelet aggregation / ruffle membrane / cell-cell adhesion / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / actin filament binding / integrin binding / Platelet degranulation / lamellipodium / cytoskeleton / cadherin binding / focal adhesion / cell surface / signal transduction / extracellular exosome / extracellular region / plasma membrane / cytosol
Similarity search - Function
GRB/APBB1IP / APBB1IP, PH domain / : / 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 ...GRB/APBB1IP / APBB1IP, PH domain / : / 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 / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Amyloid beta A4 precursor protein-binding family B member 1-interacting protein / Talin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsYang, J. / Zhu, L. / Zhang, H. / Hirbawi, J. / Fukuda, K. / Dwivedi, P. / Liu, J. / Byzova, T. / Plow, E.F. / Wu, J. / Qin, J.
CitationJournal: Nat Commun / Year: 2014
Title: Conformational activation of talin by RIAM triggers integrin-mediated cell adhesion.
Authors: Yang, J. / Zhu, L. / Zhang, H. / Hirbawi, J. / Fukuda, K. / Dwivedi, P. / Liu, J. / Byzova, T. / Plow, E.F. / Wu, J. / Qin, J.
History
DepositionNov 13, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,3392
Polymers13,3392
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 99structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: 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 73 / Rap1- ...APBB1-interacting protein 1 / Proline-rich EVH1 ligand 1 / PREL-1 / Proline-rich protein 73 / Rap1-GTP-interacting adapter molecule / RIAM / Retinoic acid-responsive proline-rich protein 1 / RARP-1


Mass: 2642.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q7Z5R6
#2: Protein Talin-1


Mass: 10696.351 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLN1, KIAA1027, TLN / Plasmid: pET30Xa/LIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y490

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-15N NOESY
1322D 1H-1H TOCSY (N/C-filtered)
1422D 1H-1H NOESY (N/C-filtered)

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-15N] Talin-F3, 50 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 1 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
21.5 mM RIAM-N peptide, 0.5 mM [U-15N; U-2H] Talin-F3, 50 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 1 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTalin-F3-1[U-15N]1
50 mMsodium phosphate-21
50 mMsodium chloride-31
2 mMsodium azide-41
1 mMDSS-51
1.5 mMRIAM-N peptide-62
0.5 mMTalin-F3-7[U-15N; U-2H]2
50 mMsodium phosphate-82
50 mMsodium chloride-92
2 mMsodium azide-102
1 mMDSS-112
Sample conditionsIonic strength: 50 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettdata analysis
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntonevaluation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1593 / NOE intraresidue total count: 374 / NOE long range total count: 408 / NOE medium range total count: 266 / NOE sequential total count: 545 / Protein phi angle constraints total count: 80 / Protein psi angle constraints total count: 80
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 99 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.1 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å
NMR ensemble rmsDistance rms dev: 0.104 Å / Distance rms dev error: 0.001 Å

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