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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BAR DOMAIN OF HUMAN AMPHIPHYSIN, ISOFORM 1 AT 1.8 ANGSTROM RESOLUTION FEATURING INCREASED ORDER AT THE N-TERMINUS.
 
Authors :  C. K. Allerston, T. Krojer, C. H. Arrowsmith, J. Weigelt, A. Edwards, C. F. Von Delft, O. Gileadi
Date :  08 May 12  (Deposition) - 30 May 12  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Invagination, Knobs-In-Holes, Structural Genomics Consortium, Sgc, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. K. Allerston, T. Krojer, O. Gileadi
Crystal Structure Of The Bar Domain Of Human Amphiphysin, Isoform 1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMPHIPHYSIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-242
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2GOL4Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:42 , ASN A:45 , PRO A:192 , TRP A:195 , HOH A:2038 , HOH A:2189 , HOH A:2219 , HOH A:2227BINDING SITE FOR RESIDUE EDO A1240
2AC2SOFTWAREASP A:32 , TYR A:145 , ASP A:146 , ARG A:149BINDING SITE FOR RESIDUE EDO A1241
3AC3SOFTWAREGLU A:72 , HIS A:151 , LEU A:155 , ARG A:165 , LYS A:168 , ALA A:169 , GLU A:172 , EDO A:1245 , HOH A:2228BINDING SITE FOR RESIDUE GOL A1242
4AC4SOFTWARELEU A:28 , ASP A:32 , TYR A:145 , GLN A:177 , GLU A:181BINDING SITE FOR RESIDUE EDO A1243
5AC5SOFTWAREILE A:135 , ALA A:136 , SER A:139 , HOH A:2148 , HOH A:2230BINDING SITE FOR RESIDUE EDO A1244
6AC6SOFTWAREGLU A:72 , LYS A:168 , GOL A:1242 , HOH A:2231 , HOH A:2232BINDING SITE FOR RESIDUE EDO A1245
7AC7SOFTWARETHR A:78 , VAL A:98 , CYS A:102 , SER A:210 , GLU A:213 , CYS A:224 , LEU A:227 , HOH A:2205 , HOH A:2206 , HOH A:2233BINDING SITE FOR RESIDUE GOL A1246

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_053004K218EAMPH_HUMANPolymorphism35166354AK218E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_053004K218EAMPH_HUMANPolymorphism35166354AK218E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BARPS51021 BAR domain profile.AMPH_HUMAN24-240  1A:24-239
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BARPS51021 BAR domain profile.AMPH_HUMAN24-240  2A:24-239

(-) Exons   (9, 9)

Asymmetric Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003562641aENSE00001865805chr7:38671167-38670883285AMPH_HUMAN1-23231A:19-235
1.2ENST000003562642ENSE00001646088chr7:38574611-3857453181AMPH_HUMAN24-50271A:24-5027
1.3ENST000003562643ENSE00001611965chr7:38543304-3854325055AMPH_HUMAN51-69191A:51-6919
1.4ENST000003562644ENSE00001792437chr7:38534127-3853403395AMPH_HUMAN69-100321A:69-10032
1.5ENST000003562645ENSE00001770901chr7:38530745-3853065096AMPH_HUMAN101-132321A:101-13232
1.6ENST000003562646ENSE00001607557chr7:38516569-38516462108AMPH_HUMAN133-168361A:133-16836
1.7ENST000003562647ENSE00001792678chr7:38515016-3851493186AMPH_HUMAN169-197291A:169-19729
1.8ENST000003562648ENSE00001727100chr7:38505848-3850577376AMPH_HUMAN197-222261A:197-22226
1.9ENST000003562649ENSE00001723487chr7:38505149-3850506783AMPH_HUMAN223-250281A:223-23917
1.10ENST0000035626410ENSE00001772878chr7:38502713-38502575139AMPH_HUMAN250-296470--
1.11ENST0000035626411ENSE00001605286chr7:38501011-38500883129AMPH_HUMAN297-339430--
1.12ENST0000035626412ENSE00001784795chr7:38475988-38475872117AMPH_HUMAN340-378390--
1.13ENST0000035626413ENSE00001023141chr7:38471812-3847178924AMPH_HUMAN379-38680--
1.14bENST0000035626414bENSE00001363931chr7:38469465-3846944224AMPH_HUMAN387-39480--
1.16ENST0000035626416ENSE00001228876chr7:38466586-3846655433AMPH_HUMAN395-405110--
1.17ENST0000035626417ENSE00000832438chr7:38462077-3846202157AMPH_HUMAN406-424190--
1.19bENST0000035626419bENSE00000678924chr7:38457550-38457425126AMPH_HUMAN425-466420--
1.20bENST0000035626420bENSE00001656509chr7:38433814-38433605210AMPH_HUMAN467-536700--
1.22cENST0000035626422cENSE00002201938chr7:38431618-38431349270AMPH_HUMAN537-626900--
1.23bENST0000035626423bENSE00001730994chr7:38429506-38429405102AMPH_HUMAN627-660340--
1.24cENST0000035626424cENSE00001602804chr7:38424526-384233051222AMPH_HUMAN661-695350--

(-) 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:221
 aligned with AMPH_HUMAN | P49418 from UniProtKB/Swiss-Prot  Length:695

    Alignment length:221
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238 
           AMPH_HUMAN    19 RAQEKVLQKLGKADETKDEQFEEYVQNFKRQEAEGTRLQRELRGYLAAIKGMQEASMKLTESLHEVYEPDWYGREDVKMVGEKCDVLWEDFHQKLVDGSLLTLDTYLGQFPDIKNRIAKRSRKLVDYDSARHHLEALQSSKRKDESRISKAEEEFQKAQKVFEEFNVDLQEELPSLWSRRVGFYVNTFKNVSSLEAKFHKEIAVLCHKLYEVMTKLGDQHA 239
               SCOP domains d4atma_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------E--------------------- SAPs(SNPs)
                    PROSITE -----BAR  PDB: A:24-239 UniProt: 24-240                                                                                                                                                                                       PROSITE
           Transcript 1 (1) 1.1a Exon 1.2  PDB: A:24-50     Exon 1.3           -------------------------------Exon 1.5  PDB: A:101-132        Exon 1.6  PDB: A:133-168            Exon 1.7  PDB: A:169-197     -------------------------Exon 1.9          Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.4  PDB: A:69-100         ------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:197-222  ----------------- Transcript 1 (2)
                 4atm A  19 RAQEKVLQKLGKADETKDEQFEEYVQNFKRQEAEGTRLQRELRGYLAAIKGMQEASMKLTESLHEVYEPDWYGREDVKMVGEKCDVLWEDFHQKLVDESLLTLDTYLGQFPDIKNRIAKRSRKLVDYDSARHHLEALQSSKRKDESRISKAEEEFQKAQKVFEEFNVDLQEELPSLWSRRVGFYVNTFKNVSSLEAKFHKEIAVLCHKLYEVMTKLGDQHA 239
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238 

   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, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A   (AMPH_HUMAN | P49418)
molecular function
    GO:0005086    ARF guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with the GTPase ARF. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    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:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0031256    leading edge membrane    The portion of the plasma membrane surrounding the leading edge of a motile cell.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
    GO:0030672    synaptic vesicle membrane    The lipid bilayer surrounding a synaptic vesicle.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMPH_HUMAN | P494181ky7 1utc 3sog 5m5s 5m61

(-) Related Entries Specified in the PDB File

1ky7 THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITHAMPHIPHYSIN FXDXF
1utc CLATHRIN TERMINAL DOMAIN COMPLEXED WITH TLPWDLWTT
4a3a CRYSTAL STRUCTURE OF THE BAR DOMAIN OF HUMAN AMPHIPHYSIN, ISOFORM 1 AT 1.8 ANGSTROM RESOLUTION FEATURING INCREASED ORDER AT THE N-TERMINUS.