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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 1ST SH3 DOMAIN FROM HUMAN CD2AP (CMS) IN COMPLEX WITH A PROLINE-RICH PEPTIDE (AA 378-393) FROM HUMAN RIN3
 
Authors :  E. Rouka, P. C. Simister, M. Janning, K. H. Kirsch, T. Krojer, S. Knapp, F Delft, C. H. Arrowsmith, A. M. Edwards, C. Bountra, S. M. Feller, Struc Genomics Consortium (Sgc)
Date :  04 Sep 14  (Deposition) - 19 Aug 15  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Endocytosis Adaptor Protein Protein-Peptide Binary Complex Kidney, Signaling Protein, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Rouka, P. C. Simister, M. Janning, J. Kumbrink, T. Konstantinou, J. R. Muniz, D. Joshi, N. O'Reilly, R. Volkmer, B. Ritter, S. Knapp, F. Von Delft, K. H. Kirsch, S. M. Feller
Differential Recognition Preferences Of The Three Src Homology 3 (Sh3) Domains From The Adaptor Cd2-Associated Protein (Cd2Ap) And Direct Association With Ras And Rab Interactor 3 (Rin3).
J. Biol. Chem. V. 290 25275 2015
PubMed-ID: 26296892  |  Reference-DOI: 10.1074/JBC.M115.637207

(-) Compounds

Molecule 1 - CD2-ASSOCIATED PROTEIN
    Chains: A, C, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-6P-1
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-60
    Gene: CD2AP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ADAPTER PROTEIN CMS,CAS LIGAND WITH MULTIPLE SH3 DOMAINS
 
Molecule 2 - RAS AND RAB INTERACTOR 3
    Chains: B, D, F
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAS INTERACTION/INTERFERENCE PROTEIN 3
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:27 , HOH A:232 , HOH A:234 , HOH A:237 , ARG C:27 , HOH C:236 , HOH C:248 , ARG E:27 , HOH E:130binding site for residue SO4 A 101
2AC2SOFTWAREARG A:27 , ARG C:27 , ARG E:27binding site for residue SO4 C 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WCI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WCI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WCI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WCI)

(-) Exons   (0, 0)

(no "Exon" information available for 4WCI)

(-) Sequences/Alignments

Asymmetric 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
                                                                                           
               SCOP domains ----------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..................eeeeee......eeeeee..eeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 4wci A   0 SMVDYIVEYDYDAVHDDELTIRVGEIIRNVKKLQEEGWLEGELNGRRGMFPDNFVKEIK  58
                                     9        19        29        39        49         


Chain B from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4wci B 381 NLPTAPPRRR 390
                                   390


Chain C from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..................eeeeee......eeeeee..eeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 4wci C  -4 GPLGSMVDYIVEYDYDAVHDDELTIRVGEIIRNVKKLQEEGWLEGELNGRRGMFPDNFVKEIK  58
                                     5        15        25        35        45        55   


Chain D from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4wci D 380 KNLPTAPPRR 389
                                   389


Chain E from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..................eeeeee......eeeeee..eeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 4wci E  -4 GPLGSMVDYIVEYDYDAVHDDELTIRVGEIIRNVKKLQEEGWLEGELNGRRGMFPDNFVKEIK  58
                                     5        15        25        35        45        55   


Chain F from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4wci F 380 KNLPTAPPRRR 390
                                   389
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 4WCI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WCI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WCI)

(-) Gene Ontology  (43, 46)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CD2AP_HUMAN | Q9Y5K6: 2fei 2j6f 2j6k 2j6o 2j7i 3aa6 3lk4 3u23 4x1v
        RIN3_HUMAN | Q8TB24: 3u23

(-) Related Entries Specified in the PDB File

3u23