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(-) Description

Title :  CRYSTAL STRUCTURE OF ENDOPHILIN BAR DOMAIN
 
Authors :  M. Masuda, S. Takeda, M. Sone, Y. Kamioka, H. Mori, N. Mochizuki
Date :  14 Mar 05  (Deposition) - 02 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Bar Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Masuda, S. Takeda, M. Sone, T. Ohki, H. Mori, Y. Kamioka, N. Mochizuk
Endophilin Bar Domain Drives Membrane Curvature By Two Newl Identified Structure-Based Mechanisms
Embo J. V. 25 2889 2006
PubMed-ID: 16763557  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601176

(-) Compounds

Molecule 1 - SH3-CONTAINING GRB2-LIKE PROTEIN 2
    ChainsA
    EC Number2.3.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P3
    Expression System StrainB834(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentENDOPHILIN BAR DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymENDOPHILIN A1, SH3 DOMAIN PROTEIN 2A, ENDOPHILIN 1, EEN-B1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1X03)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X03)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X03)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X03)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X03)

(-) Exons   (7, 7)

Asymmetric Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003806071cENSE00001868540chr9:17579121-17579285165SH3G2_HUMAN1-15150--
1.3ENST000003806073ENSE00000691736chr9:17747064-1774713269SH3G2_HUMAN16-38231A:26-3813
1.4bENST000003806074bENSE00001782561chr9:17761435-1776150773SH3G2_HUMAN39-63251A:39-6325
1.7aENST000003806077aENSE00000691743chr9:17786379-17786522144SH3G2_HUMAN63-111491A:63-111 (gaps)49
1.8ENST000003806078ENSE00000691749chr9:17787378-17787511134SH3G2_HUMAN111-155451A:111-15545
1.9ENST000003806079ENSE00000691752chr9:17789390-17789548159SH3G2_HUMAN156-208531A:156-20853
1.10ENST0000038060710ENSE00000691755chr9:17791229-17791332104SH3G2_HUMAN209-243351A:209-24335
1.11ENST0000038060711ENSE00002161882chr9:17793365-17793495131SH3G2_HUMAN243-287451A:243-2475
1.12bENST0000038060712bENSE00001676590chr9:17795542-177971271586SH3G2_HUMAN287-352660--

(-) 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:210
 aligned with SH3G2_HUMAN | Q99962 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:222
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245  
          SH3G2_HUMAN    26 GTKLDDDFKEMERKVDVTSRAVMEIMTKTIEYLQPNPASRAKLSMINTMSKIRGQEKGPGYPQAEALLAEAMLKFGRELGDDCNFGPALGEVGEAMRELSEVKDSLDIEVKQNFIDPLQNLHDKDLREIQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFDESKEIAESSMFNLLEMDIEQVSQLSALVQAQLEYHKQAVQILQQVTVRLEERIRQA 247
               SCOP domains d1x03a1 A:26-247 Endophilin-1                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains BAR-1x03A01 A:26-242                                                                                                                                                                                                     ----- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh..------------....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3     Exon 1.4b  PDB: A:39-63  -----------------------------------------------Exon 1.8  PDB: A:111-155 UniProt: 111-155    Exon 1.9  PDB: A:156-208 UniProt: 156-208            Exon 1.10  PDB: A:209-243          ---- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.7a  PDB: A:63-111 (gaps) UniProt: 63-111  -----------------------------------------------------------------------------------------------------------------------------------1.11  Transcript 1 (2)
                 1x03 A  26 GTKLDDDFKEmERKVDVTSRAVmEImTKTIEYLQPNPASRAKLSmI------------PGYPQAEALLAEAmLKFGRELGDDCNFGPALGEVGEAmRELSEVKDSLDIEVKQNFIDPLQNLHDKDLREIQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFDESKEIAESSmFNLLEmDIEQVSQLSALVQAQLEYHKQAVQILQQVTVRLEERIRQA 247
                                    35|       45  |  |  55        65    ||   -        85        95 |     105       115     | 125       135       145       155       165       175       185       195     | 205 |     215       225       235       245  
                                     36-MSE      48-MSE                70-MSE        84           97-MSE                 121-MSE                                                                         201-MSE |                                        
                                                    51-MSE              71                                                                                                                                     207-MSE                                    

   Legend:   → Mismatch (orange background)
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  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, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X03)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (SH3G2_HUMAN | Q99962)
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:0019886    antigen processing and presentation of exogenous peptide antigen via MHC class II    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    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:0007018    microtubule-based movement    A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
    GO:0042059    negative regulation of epidermal growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:0002090    regulation of receptor internalization    Any process that modulates the frequency, rate or extent of receptor internalization.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0030669    clathrin-coated endocytic vesicle membrane    The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SH3G2_HUMAN | Q999621x04 2d4c 2dbm

(-) Related Entries Specified in the PDB File

1x04 ENDOPHILIN BAR DOMAIN (APPENDAGE-LESS MUTANT)