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- PDB-6ba6: Solution structure of Rap1b/talin complex -

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Basic information

Entry
Database: PDB / ID: 6ba6
TitleSolution structure of Rap1b/talin complex
Components
  • Ras-related protein Rap-1b
  • Talin-1
KeywordsCELL ADHESION / Complex / Small GTPase / ubiquitin-like fold
Function / homology
Function and homology information


Rap protein signal transduction / 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 / modification of postsynaptic structure / regulation of cell junction assembly / Platelet degranulation ...Rap protein signal transduction / 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 / modification of postsynaptic structure / regulation of cell junction assembly / Platelet degranulation / LIM domain binding / negative regulation of calcium ion-dependent exocytosis / vinculin binding / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / integrin activation / cell-substrate junction assembly / Rap1 signalling / establishment of endothelial barrier / regulation of establishment of cell polarity / MET activates RAP1 and RAC1 / azurophil granule membrane / cortical actin cytoskeleton organization / phosphatidylserine binding / p130Cas linkage to MAPK signaling for integrins / GRB2:SOS provides linkage to MAPK signaling for Integrins / cellular response to cAMP / ruffle / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / phosphatidylinositol binding / lipid droplet / Integrin signaling / small monomeric GTPase / G protein activity / integrin-mediated signaling pathway / establishment of localization in cell / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / structural constituent of cytoskeleton / cell-cell adhesion / ruffle membrane / GDP binding / 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 / actin filament binding / cell-cell junction / Signaling by BRAF and RAF1 fusions / integrin binding / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / focal adhesion / GTPase activity / glutamatergic synapse / Neutrophil degranulation / protein-containing complex binding / GTP binding / cell surface / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ras-related protein Rap1 / : / 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 ...Ras-related protein Rap1 / : / 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 / 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 / Small GTPase, Ras-type / FERM superfamily, second domain / small GTPase Ras family profile. / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Talin-1 / Ras-related protein Rap-1b
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsZhu, L. / Yang, J. / Qin, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01HL073311 United States
CitationJournal: Nat Commun / Year: 2017
Title: Structure of Rap1b bound to talin reveals a pathway for triggering integrin activation.
Authors: Zhu, L. / Yang, J. / Bromberger, T. / Holly, A. / Lu, F. / Liu, H. / Sun, K. / Klapproth, S. / Hirbawi, J. / Byzova, T.V. / Plow, E.F. / Moser, M. / Qin, J.
History
DepositionOct 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Talin-1
B: Ras-related protein Rap-1b


Theoretical massNumber of molelcules
Total (without water)29,8082
Polymers29,8082
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1680 Å2
ΔGint-3 kcal/mol
Surface area12500 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 5020 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Talin-1


Mass: 10607.293 Da / Num. of mol.: 1 / Fragment: F0 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26039
#2: Protein Ras-related protein Rap-1b / GTP-binding protein smg p21B


Mass: 19200.734 Da / Num. of mol.: 1 / Mutation: G12V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1B, OK/SW-cl.11 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61224

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 15N/13C-edited NOESY
132isotropic13D 15N/13C-edited NOESY
143isotropic13D 15N-edited NOESY
254isotropic13D 15N/13C-filtered NOESY
165isotropic3Standard triple-resonance experiments

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.6 mM [U-13C; U-15N] Rap1b, 0.9 mM talin-F0, 95% H2O/5% D2O15N/13C-labeled Rap1b in the presence of unlabeled talin-F015N 13C95% H2O/5% D2O
solution20.5 mM [U-13C; U-15N] talin-F0, 0.7 mM Rap1b, 95% H20, 5% D2O15N/13C- labeled talin-F0 in the presence of unlabeled Rap1b15N 13C95% H20, 5% D2O
solution30.5 mM [U-15N; U-2H] talin-F0, 0.7 mM Rap1b, 95% H20, 5% D2O15N/100% 2H-labeled talin-F0 in the presence of unlabeled Rap1b15N 2H95% H20, 5% D2O
solution40.5 mM [U-13C; U-15N] talin-F0, 0.7 mM Rap1b, 0.2% H20, 99.8% D2015N/13C-labeled talin-F0 in the presence of unlabeled Rap1b prepared in 99.8% D2O15N 13C0.2% H20, 99.8% D20
solution50.6 mM [U-13C; U-15N] Rap1b, 95% H2O/5% D2O15N/13C-labeled Rap1b15N 13C95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMRap1b[U-13C; U-15N]1
0.9 mMtalin-F0natural abundance1
0.5 mMtalin-F0[U-13C; U-15N]2
0.7 mMRap1bnatural abundance2
0.5 mMtalin-F0[U-15N; U-2H]3
0.7 mMRap1bnatural abundance3
0.5 mMtalin-F0[U-13C; U-15N]4
0.7 mMRap1bnatural abundance4
0.6 mMRap1b[U-13C; U-15N]5
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
120 mM NaH2PO4/Na2HPO4 (pH 6.6), 50 mM NaCl, 5 mM MgCl2, 2 mM d-DTT, and 5% D2O50mM NaCl, 5mM MgCl2 mMconditions_16.6 101325 Pa301 K
220 mM NaH2PO4/Na2HPO4 (pH 6.6), 50 mM NaCl, 5 mM MgCl2, 2 mM d-DTT, and 99.8% D2O50mM NaCl, 5mM MgCl2 mMconditions_26.6 101325 Pa301 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCE IIIBrukerAVANCE III8502
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
PASAXu, Wang, Yang, Vaynberg, Qinchemical shift assignment
PIPPGarrettpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: X-PLOR
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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