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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL SH3 DOMAIN OF THE ADAPTOR PROTEIN GADS IN COMPLEX WITH SLP-76 MOTIF PEPTIDE REVEALS A UNIQUE SH3-SH3 INTERACTION
 
Authors :  N. Dimasi
Date :  04 Aug 05  (Deposition) - 23 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sh3 Domain/Complex, Mona/Gads Sh3C Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Dimasi
Crystal Structure Of The C-Terminal Sh3 Domain Of The Adaptor Protein Gads In Complex With Slp-76 Motif Peptide Reveals A Unique Sh3-Sh3 Interaction
Int. J. Biochem. Cell Biol. V. 39 109 2007
PubMed-ID: 17010654  |  Reference-DOI: 10.1016/J.BIOCEL.2006.07.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GRB2-RELATED ADAPTOR PROTEIN 2
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PT7-GADS-CSH3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL SH3 DOMAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: GADS PROTEIN, GROWTH FACTOR RECEPTOR BINDING PROTEIN, GRBLG, GRB-2-LIKE PROTEIN, GRB2L, HEMATOPOIETIC CELL-ASSOCIATED ADAPTOR PROTEIN GRPL, GRB-2-RELATED MONOCYTIC ADAPTER PROTEIN, MONOCYTIC ADAPTER, MONA, ADAPTER PROTEIN GRID
 
Molecule 2 - SLP-76 BINDING PEPTIDE
    Chains: B, D
    Engineered: YES
    Other Details: THE SLP-76 PEPTIDE WAS SYNTHESIZED SYNTHETICALLY WITH THE F-MOC CHEMISTRY
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2D0N)

(-) Sites  (0, 0)

(no "Site" information available for 2D0N)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D0N)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala C:318 -Pro C:319

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D0N)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.GRAP2_MOUSE1-56
263-322		  1-
A:267-322

(-) Exons   (0, 0)

(no "Exon" information available for 2D0N)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:59
 aligned with GRAP2_MOUSE | O89100 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:152
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  
          GRAP2_MOUSE   171 GTVGEEIRPSVNRKLSDHLPLGPQQFHPHQQPSPQFTPGPQPPQQQRYLQHFHQDRRGGSLDINDGHCGLGSEVNATLMHRRHTDPVQLQAAGRVRWARALYDFEALEEDELGFRSGEVVEVLDSSNPSWWTGRLHNKLGLFPANYVAPMMR 322
               SCOP domains d                               2d                                                              0na_ A: automated matches                                SCOP domains
               CATH domains 2                               d0                                                              nA00 A:264-322 SH3 Domains                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-------------------------------..--------------------------------------------------------------eeee..................eeeeee.....eeeeee..eeeeee...eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------SH3  PDB: A:267-322 UniProt: 263-322                         PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d0n A 264 G-------------------------------SP--------------------------------------------------------------WARALYDFEALEEDELGFRSGEVVEVLDSSNPSWWTGRLHNKLGLFPANYVAPMMR 322
                            |        -         -         -  ||     -         -         -         -         -         -      |270       280       290       300       310       320  
                            |                             265|                                                            267                                                       
                          264                              266                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ...hhhhh. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 2d0n B 233 PSIDRSTKP 241


Chain C from PDB  Type:PROTEIN  Length:56
 aligned with GRAP2_MOUSE | O89100 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:56
                                   275       285       295       305       315      
          GRAP2_MOUSE   266 RWARALYDFEALEEDELGFRSGEVVEVLDSSNPSWWTGRLHNKLGLFPANYVAPMM 321
               SCOP domains d2d0nc_ C: automated matches                             SCOP domains
               CATH domains 2d0nC00 C:266-321 SH3 Domains                            CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...................eeeeee.....eeeeee..eeeeee.hhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE SH3  PDB: - UniProt: 263-322                             PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 2d0n C 266 PWARALYDFEALEEDELGFRSGEVVEVLDSSNPSWWTGRLHNKLGLFPANYVAPMM 321
                                   275       285       295       305       315      


Chain D from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ...hhhhh. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 2d0n D 233 PSIDRSTKP 241
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D0N)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (GRAP2_MOUSE | O89100)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  Cis Peptide Bonds
    Ala C:318 - Pro C:319   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GRAP2_MOUSE | O89100: 1h3h 1oeb 1r1p 1r1q 1r1s 1uti 2w10

(-) Related Entries Specified in the PDB File

1h3h THE SAME PROTEIN COMPLEXED WITH A LONGER PEPTIDE DETERMINED BY NMR SPECTROSCOPY
1oeb THE SAME PROTEIN COMPLEXED WITH A LONGER PEPTIDE DETERMINED BY X-RAY CRYSTALLOGRAPHY
1uj0 A SIMILAR PROTEIN/PEPTIDE COMPLEX DETERMINED BY X-RAY CRYSTALLOGRAPHY
1uti THE SAME PROTEIN COMPLEXED WITH A HEMATOPOIETIC PROGENITOR KINASE 1 PEPTIDE DETERMINED BY X-RAY CRYSTALLOGRAPHY