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Title :   STRUCTURAL DETERMINANTS OF PEPTIDE-BINDING ORIENTATION AND OF SEQUENCE SPECIFICITY IN SH3 DOMAINS

Authors :   W. A. Lim, F. M. Richards, R. O. Fox

Date :   28 Mar 95 (Deposition) - 10 Jul 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Src-Homology 3 (Sh3) Domain, Peptide-Binding Protein, Guanine Nucleotide Exchange Factor, Signal Transduction Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. A. Lim, F. M. Richards, R. O. Fox
Structural Determinants Of Peptide-Binding Orientation And Of Sequence Specificity In Sh3 Domains.
Nature V. 372 375 1994
PubMed-ID: 7802869 | Reference-DOI: 10.1038/372375A0
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (1, 1)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:58
 aligned with SEM5_CAEEL | P29355 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:58
                                   164       174       184       194       204        
           SEM5_CAEEL   155 ETKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVCPYN 212
               SCOP domains d1sema_ A:                                                 SCOP domains
               CATH domains 1semA00 A:155-212 SH3 Domains                              CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..................eeeeee.....eeeeee..eeeeeehhheeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 1sem A 155 ETKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVCPYN 212
                                   164       174       184       194       204

Chain B from PDB  Type:PROTEIN  Length:57
 aligned with SEM5_CAEEL | P29355 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:57
                                   165       175       185       195       205       
           SEM5_CAEEL   156 TKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVCPYN 212
               SCOP domains d1semb_ B:                                                SCOP domains
               CATH domains 1semB00 B:156-212 SH3 Domains                             CATH domains
           Pfam domains (1) ----SH3_1-1semB01 B:160-205                       ------- Pfam domains (1)
           Pfam domains (2) ----SH3_1-1semB02 B:160-205                       ------- Pfam domains (2)
         Sec.struct. author ..eeee..................eeeeee.....eeeeee..eeeeeehhheee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 1sem B 156 TKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVCPYN 212
                                   165       175       185       195       205

Chain C from PDB  Type:PROTEIN  Length:8
                                        
               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
                 1sem C   1 xPPPVPPR   8
                            |       
                            1-ACE

Chain D from PDB  Type:PROTEIN  Length:8
                                        
               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
                 1sem D   1 xPPPVPPR   8
                            |       
                            1-ACE

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 (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SEM5_CAEEL | P29355)

molecular function
	GO:0005070	SH3/SH2 adaptor activity	Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
	GO:0005154	epidermal growth factor receptor binding	Interacting selectively and non-covalently with the epidermal growth factor receptor.
	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).
biological process
	GO:0016477	cell migration	The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
	GO:0030539	male genitalia development	The process whose specific outcome is the progression of the male genitalia over time, from its formation to the mature structure.
	GO:0007517	muscle organ development	The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
	GO:0002119	nematode larval development	The process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
	GO:0009967	positive regulation of signal transduction	Any process that activates or increases the frequency, rate or extent of signal transduction.
	GO:0031344	regulation of cell projection organization	Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.
	GO:0040028	regulation of vulval development	Any process that modulates the frequency, rate or extent of development of the vulva. Vulval development is the process whose specific outcome is the progression of the egg-laying organ of female and hermaphrodite nematodes over time, from its formation to the mature structure. In nematodes, the vulva is formed from ventral epidermal cells during larval stages to give rise to a fully formed vulva in the adult.

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