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(-) Description

Title :  CRYSTAL STRUCTURE OF ENDOPHILIN-A1 BAR DOMAIN
 
Authors :  W. Weissenhorn
Date :  06 Jun 05  (Deposition) - 02 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Coiled Coil, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Weissenhorn
Crystal Structure Of The Endophilin-A1 Bar Domain.
J. Mol. Biol. V. 351 653 2005
PubMed-ID: 16023669  |  Reference-DOI: 10.1016/J.JMB.2005.06.013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SH3-CONTAINING GRB2-LIKE PROTEIN 2
    Chains: A, B
    EC Number: 2.3.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM30
    Expression System Strain: BL21 CODON+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ENDOPHILIN BAR DOMAIN
    Gene: SH3GL2, SH3D2A
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: SH3 DOMAIN PROTEIN 2A, ENDOPHILIN 1, SH3P4

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1CD11Ligand/IonCADMIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:108 , HOH B:941BINDING SITE FOR RESIDUE CD A 900
02AC2SOFTWAREGLU B:123 , GLU B:126 , HIS B:156 , HOH B:937BINDING SITE FOR RESIDUE CD B 901
03AC3SOFTWAREGLU A:119 , GLU A:123 , GLU A:126BINDING SITE FOR RESIDUE CD A 902
04AC4SOFTWARECYS A:108BINDING SITE FOR RESIDUE CD A 903
05AC5SOFTWAREHOH A:921 , HOH A:928 , ASP B:106 , CYS B:108 , CD B:905BINDING SITE FOR RESIDUE CD B 904
06AC6SOFTWAREASP A:180 , HOH A:921 , HOH A:929 , CYS B:108 , CD B:904BINDING SITE FOR RESIDUE CD B 905
07AC7SOFTWAREHIS A:147 , HOH A:933BINDING SITE FOR RESIDUE CD A 906
08AC8SOFTWAREHIS A:157BINDING SITE FOR RESIDUE CD A 907
09AC9SOFTWAREHIS B:147 , HOH B:939BINDING SITE FOR RESIDUE CD B 909
10BC1SOFTWAREGLU B:153 , HIS B:157 , HOH B:945BINDING SITE FOR RESIDUE CD B 910
11BC2SOFTWAREASP A:191 , GLU A:198 , HOH A:918BINDING SITE FOR RESIDUE CD A 911

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZWW)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZWW)

(-) 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:199
 aligned with SH3G2_MOUSE | Q62420 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:220
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246
          SH3G2_MOUSE    27 TKLDDDFKEMERKVDVTSRAVMEIMTKTIEYLQPNPASRAKLSMINTMSKIRGQEKGPGYPQAEALLAEAMLKFGRELGDDCNFGPALGEVGEAMRELSEVKDSLDMEVKQNFIDPLQNLHDKDLREIQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFDESKEIAESSMFNLLEMDIEQVSQLSALVQAQLEYHKQAVQILQQVTVRLEERIRQ 246
               SCOP domains d1zwwa1 A:27-246 Endophilin-1                                                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......---------------------.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zww A  27 TKLDDDFKEMERKVDVTSRAVMEIMTKTIEYLQPNPASR---------------------PQAEALLAEAMLKFGRELGDDCNFGPALGEVGEAMRELSEVKDSLDMEVKQNFIDPLQNLHDKDLREIQHHLKKLEGRRLDFGYKKKRQGKIPDEELRQALEKFDESKEIAESSMFNLLEMDIEQVSQLSALVQAQLEYHKQAVQILQQVTVRLEERIRQ 246
                                    36        46        56        |-         -         -|       96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246
                                                                 65                    87                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:196
 aligned with SH3G2_MOUSE | Q62420 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:220
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247
          SH3G2_MOUSE    28 KLDDDFKEMERKVDVTSRAVMEIMTKTIEYLQPNPASRAKLSMINTMSKIRGQEKGPGYPQAEALLAEAMLKFGRELGDDCNFGPALGEVGEAMRELSEVKDSLDMEVKQNFIDPLQNLHDKDLREIQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFDESKEIAESSMFNLLEMDIEQVSQLSALVQAQLEYHKQAVQILQQVTVRLEERIRQA 247
               SCOP domains d1zwwb_ B: Endophilin-1                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) BAR-1zwwB01 B:28-242                                                                                                                                                                                                   ----- Pfam domains (1)
           Pfam domains (2) BAR-1zwwB02 B:28-242                                                                                                                                                                                                   ----- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........-------------------.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..-----..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zww B  28 KLDDDFKEMERKVDVTSRAVMEIMTKTIEYLQPNPASRAK-------------------PQAEALLAEAMLKFGRELGDDCNFGPALGEVGEAMRELSEVKDSLDMEVKQNFIDPLQNLHDKDLREIQHHLKKLEGRRLDFGYKKKR-----DEELRQALEKFDESKEIAESSMFNLLEMDIEQVSQLSALVQAQLEYHKQAVQILQQVTVRLEERIRQA 247
                                    37        47        57        67         -        87        97       107       117       127       137       147       157       167      |  -  |    187       197       207       217       227       237       247
                                                                  67                  87                                                                                    174   180
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZWW)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Golgi-transport (12)
(-)
Family: BAR (7)
(-)
Mus musculus (Mouse) (1)
1aBAR-1zwwB01B:28-242
1bBAR-1zwwB02B:28-242

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SH3G2_MOUSE | Q62420)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0002090    regulation of receptor internalization    Any process that modulates the frequency, rate or extent of receptor internalization.
    GO:0048488    synaptic vesicle endocytosis    Clathrin-mediated endocytosis of presynaptic membrane that recycles synaptic vesicle membrane and its components following synaptic vesicle exocytosis. This process starts with coating of the membrane with adaptor proteins and clathrin prior to invagination and ends when uncoating has finished.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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