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(-) Description

Title :  CRYSTAL STRUCTURE OF PEX13P(301-386) SH3 DOMAIN
 
Authors :  A. Douangamath, O. Mayans, P. Barnett, B. Distel, M. Wilmanns
Date :  08 Aug 01  (Deposition) - 06 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Compact Beta-Barrel Of Five Anti-Parrallel Beta-Strands, Protein Transport, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Douangamath, F. V. Filipp, A. T. J. Klein, P. Barnett, P. Zou, T. Voorn-Brouwer, M. C. Vega, O. Mayans, M. Sattler, B. Distel, M. Wilmanns
Topography For Independent Binding Of Alpha-Helical And Ppii-Helical Ligands To A Peroxisomal Sh3 Domain
Mol. Cell V. 10 1007 2002
PubMed-ID: 12453410  |  Reference-DOI: 10.1016/S1097-2765(02)00749-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXISOMAL MEMBRANE PROTEIN PAS20
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMALC2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SH3 DOMAIN
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: PEX13P

 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 1JQQ)

(-) Sites  (0, 0)

(no "Site" information available for 1JQQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JQQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JQQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JQQ)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.PEX13_YEAST306-372
 
 
 		  4A:12-78
B:12-78
C:12-77
D:12-78

(-) Exons   (1, 4)

Asymmetric/Biological Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR191W1YLR191W.1XII:537274-5384341161PEX13_YEAST1-3863864A:1-79 (gaps)
B:1-82 (gaps)
C:6-77 (gaps)
D:6-78		95
98
72
73

(-) 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:79
 aligned with PEX13_YEAST | P80667 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:95
                                   288       298       308       318       328       338       348       358       368     
          PEX13_YEAST   279 LNKFITKLQTSGTIRASQGNGSEPIDPSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIKRR 373
               SCOP domains d1jq                qa_ A: Peroxisomal membrane protein Pex13p                                  SCOP domains
               CATH domains 1jqq                A00 A:1-79 SH3 Domains                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....----------------..........eeeee...................eeeeeeee.....eeeeeeeee....eeeee...eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------SH3  PDB: A:12-78 UniProt: 306-372                                 - PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-79 (gaps) UniProt: 1-386 [INCOMPLETE]                                        Transcript 1
                 1jqq A   1 ISEF----------------GSEPIDPSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIKRR  79
                               |     -         -|       14        24        34        44        54        64        74     
                               4                5                                                                          


Chain B from PDB  Type:PROTEIN  Length:82
 aligned with PEX13_YEAST | P80667 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:98
                                   288       298       308       318       328       338       348       358       368        
          PEX13_YEAST   279 LNKFITKLQTSGTIRASQGNGSEPIDPSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIKRRKKI 376
               SCOP domains d1jq                qb_ B: Peroxisomal membrane protein Pex13p                                     SCOP domains
               CATH domains 1jqq                B00 B:1-82 SH3 Domains                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....----------------.....hhhhheeeee...................eeeeeeee.....eeeeeeeee....eeeee...eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------SH3  PDB: B:12-78 UniProt: 306-372                                 ---- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-82 (gaps) UniProt: 1-386 [INCOMPLETE]                                           Transcript 1
                 1jqq B   1 ISEF----------------GSEPIDPSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIKRRKKI  82
                               |     -         -|       14        24        34        44        54        64        74        
                               4                5                                                                             


Chain C from PDB  Type:PROTEIN  Length:70
 aligned with PEX13_YEAST | P80667 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:72
                                   309       319       329       339       349       359       369  
          PEX13_YEAST   300 SEPIDPSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIK 371
               SCOP domains d1jqqc_ C: Peroxisoma  l membrane protein Pex13p                         SCOP domains
               CATH domains 1jqqC00 C:6-77 SH3 Do  mains                                             CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeee.......--..........eeeeeeee.....eeeeeeeee....eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------SH3  PDB: C:12-77 UniProt: 306-372                                 PROSITE
               Transcript 1 Exon 1.1  PDB: C:6-77 (gaps) UniProt: 1-386 [INCOMPLETE]                 Transcript 1
                 1jqq C   6 SEPIDPSKLEFARALYDFVPE--EMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIK  77
                                    15        25|  |    35        45        55        65        75  
                                               26 29                                                


Chain D from PDB  Type:PROTEIN  Length:73
 aligned with PEX13_YEAST | P80667 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:73
                                   309       319       329       339       349       359       369   
          PEX13_YEAST   300 SEPIDPSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIKR 372
               SCOP domains d1jqqd_ D: Peroxisomal membrane protein Pex13p                            SCOP domains
               CATH domains 1jqqD00 D:6-78 SH3 Domains                                                CATH domains
           Pfam domains (1) ------------SH3_1-1jqqD01 D:18-70                                -------- Pfam domains (1)
           Pfam domains (2) ------------SH3_1-1jqqD02 D:18-70                                -------- Pfam domains (2)
           Pfam domains (3) ------------SH3_1-1jqqD03 D:18-70                                -------- Pfam domains (3)
           Pfam domains (4) ------------SH3_1-1jqqD04 D:18-70                                -------- Pfam domains (4)
         Sec.struct. author ..........eeee...................eeeeeeee.....eeeeeeeee....eeeee...eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------SH3  PDB: D:12-78 UniProt: 306-372                                  PROSITE
               Transcript 1 Exon 1.1  PDB: D:6-78 UniProt: 1-386 [INCOMPLETE]                         Transcript 1
                 1jqq D   6 SEPIDPSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIKR  78
                                    15        25        35        45        55        65        75
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: SH3 (175)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PEX13_YEAST | P80667)
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).
    GO:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
biological process
    GO:0016560    protein import into peroxisome matrix, docking    The process in which a complex formed of a peroxisome targeting sequence (PTS) receptor bound to a PTS-bearing protein docks with translocation machinery in the peroxisomal membrane.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:1990415    Pex17p-Pex14p docking complex    A protein complex involved in the peroxisomal import machinery. In S. cerevisiae, this complex contains the proteins Pex17p, Pex14p, Pex19, and Pex13p.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:1990429    peroxisomal importomer complex    A protein complex responsible for transporting proteins into the peroxisomal matrix. An example of this complex is Pex14 found in S. cerevisae which has 9 core components and 12 transient interaction partners.
    GO:0005778    peroxisomal membrane    The lipid bilayer surrounding a peroxisome.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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  1jqq
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 Related Entries

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

UniProtKB/Swiss-Prot
        PEX13_YEAST | P80667: 1n5z 1nm7 2v1r

(-) Related Entries Specified in the PDB File

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