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- PDB-1h3h: Structural Basis for Specific Recognition of an RxxK-containing S... -

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Basic information

Entry
Database: PDB / ID: 1h3h
TitleStructural Basis for Specific Recognition of an RxxK-containing SLP-76 peptide by the Gads C-terminal SH3 domain
Components
  • GRB2-RELATED ADAPTOR PROTEIN 2
  • LYMPHOCYTE CYTOSOLIC PROTEIN 2
KeywordsPROTEIN BINDING / PROTEIN-BINDING / COMPLEX (SH3-PEPTIDE) / T-CELL SIGNALING / SH3 DOMAIN / SH2 DOMAIN
Function / homology
Function and homology information


TCR signalosome / FLT3 Signaling / Co-stimulation by CD28 / FCERI mediated MAPK activation / Signaling by SCF-KIT / Generation of second messenger molecules / mast cell activation / FCERI mediated Ca+2 mobilization / DAP12 signaling / positive regulation of protein kinase activity ...TCR signalosome / FLT3 Signaling / Co-stimulation by CD28 / FCERI mediated MAPK activation / Signaling by SCF-KIT / Generation of second messenger molecules / mast cell activation / FCERI mediated Ca+2 mobilization / DAP12 signaling / positive regulation of protein kinase activity / Generation of second messenger molecules / plasma membrane raft / GPVI-mediated activation cascade / FCERI mediated Ca+2 mobilization / cell surface receptor protein tyrosine kinase signaling pathway / FCERI mediated MAPK activation / cell-cell junction / DAP12 signaling / T cell receptor signaling pathway / endosome / intracellular signal transduction / immune response / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
GRAP2, C-terminal SH3 domain / : / Grb2-like / SAM domain (Sterile alpha motif) / SH3 Domains / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / SH3 domain / SH2 domain ...GRAP2, C-terminal SH3 domain / : / Grb2-like / SAM domain (Sterile alpha motif) / SH3 Domains / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
GRB2-related adaptor protein 2 / Lymphocyte cytosolic protein 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodSOLUTION NMR / MDSA
AuthorsLiu, Q. / Berry, D. / Nash, P. / Pawson, T. / McGlade, C.J. / Li, S.S.
Citation
Journal: Mol.Cell / Year: 2003
Title: Structural Basis for Specific Binding of the Gads SH3 Domain to an Rxxk Motif-Containing Slp-76 Peptide: A Novel Mode of Peptide Recognition
Authors: Liu, Q. / Berry, D. / Nash, P. / Pawson, T. / Mcglade, C.J. / Li, S.S.
#1: Journal: Curr.Biol. / Year: 2002
Title: A High-Affinity Arg-X-X-Lys SH3 Binding Motif Confers Specificity for the Interaction between Gads and Slp-76 in T-Cell Signaling
Authors: Berry, D. / Nash, P. / Liu, S. / Pawson, T. / Mcglade, C.
History
DepositionSep 3, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Derived calculations / Other ...Derived calculations / Other / Source and taxonomy / Version format compliance
Revision 1.2May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GRB2-RELATED ADAPTOR PROTEIN 2
B: LYMPHOCYTE CYTOSOLIC PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)8,0932
Polymers8,0932
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein GRB2-RELATED ADAPTOR PROTEIN 2 / GADS PROTEIN / GRBLG / GRB2L


Mass: 6948.813 Da / Num. of mol.: 1 / Fragment: C-TERMINAL SH3 DOMAIN, RESIDUES 263-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell: T-LYMPHOCYTE / Plasmid: PGEX-2TK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O89100
#2: Protein/peptide LYMPHOCYTE CYTOSOLIC PROTEIN 2 / SLP-76


Mass: 1144.279 Da / Num. of mol.: 1 / Fragment: RESIDUES 226-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PAED4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13094
Compound detailsGRB2-RELATED ADAPTOR PROTEIN 2: CHAIN A REGULATES NF-AT ACTIVATION BY INTERACTING WITH SLP-76. ...GRB2-RELATED ADAPTOR PROTEIN 2: CHAIN A REGULATES NF-AT ACTIVATION BY INTERACTING WITH SLP-76. CONTAINS 1 SH2 DOMAIN AND 1 SH3 DOMAIN. LYMPHOCYTE CYTOSOLIC PROTEIN 2: CHAIN B T CELL ANTIGEN RECEPTOR MEDIATED SIGNALING. INTERACTS WITH ADAPTER PROTEINS GRB2 AND FYB.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB
121CBCA(CO)NH
131HCC(CO)NH
141CC(CO)NH
151HBCB(CRCD)HD
161HBCB(CRCDCE)HE
171(H)CCH-TOCSY
181HNHA
19115N/13C-EDITED NOESY
1101HALF-FIL 15N/13C-EDITED NOESY
11111H/13C-HSQC
11211
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY ON 13C,15N-LABLED GADS C-TERMINAL SH3 DOMAIN AND SLP-76 PEPTIDE.

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Sample preparation

Sample conditionsIonic strength: 100MM NACL, 50MM SODIUM PHOSPHATE / pH: 6 / Pressure: 1 atm / Temperature: 285 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionClassification
ARIA1refinement
ARIA1structure solution
RefinementMethod: MDSA / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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