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(-) Description

Title :  CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF DROSOPHILA AP180
 
Authors :  Y. Mao, J. Chen, J. A. Maynard, B. Zhang, F. A. Quiocho
Date :  12 Jan 01  (Deposition) - 28 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  All Alpha, Alpha Helices Repeats, Coiled-Coil, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Mao, J. Chen, J. A. Maynard, B. Zhang, F. A. Quiocho
A Novel All Helix Fold Of The Ap180 Amino-Terminal Domain For Phosphoinositide Binding And Clathrin Assembly In Synaptic Vesicle Endocytosis.
Cell(Cambridge, Mass. ) V. 104 433 2001
PubMed-ID: 11239400  |  Reference-DOI: 10.1016/S0092-8674(01)00230-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SYNAPSE-ENRICHED CLATHRIN ADAPTOR PROTEIN LAP
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX4T-1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN (RESIDUES 1-299)
    GeneLAP
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:138 , ARG A:139 , LYS B:253 , VAL B:256 , ARG B:257 , ARG B:260BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREARG B:138 , ARG B:139 , HOH B:345BINDING SITE FOR RESIDUE SO4 B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HX8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HX8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HX8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HX8)

(-) Exons   (0, 0)

(no "Exon" information available for 1HX8)

(-) 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:270
 aligned with PICAL_DROME | Q9VI75 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:278
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        
          PICAL_DROME    22 QGLAKSVCKATTEECIGPKKKHLDYLVHCTNEPNVSIPHLANLLIERSQNANWVVVYKSLITTHHLMAYGNERFMQYLASSNSTFNLSSFLDKGTVQDGGMGVPGGRMGYDMSPFIRRYAKYLNEKSLSYRAMAFDFCKVKRGKEEGSLRSMNAEKLLKTLPVLQAQLDALLEFDCQSNDLSNGVINMSFMLLFRDLIRLFACYNDGIINLLEKYFDMNKKHARDALDLYKKFLVRMDRVGEFLKVAENVGIDKGDIPDLTKAPSSLLDALEQHLATL 299
               SCOP domains d1hx8a2 A:22-161 AP180 (Lap)                                                                                                                     d1hx8a1 A:167-299 AP180 (Lap)                                                                                                         SCOP domains
               CATH domains 1hx8A01 A:22-142  [code=1.25.40.90, no name defined]                                                                     -----------------1h     x8A02 A:160-281  [code=1.20.58.150, no name defined]                                                               ------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............---........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh-----.......hhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hx8 A  22 QGLAKSVCKATTEECIGPKKKHLDYLVHCANEPNVSIPHLANLLIERSQNANWVVVYKSLITTHHLMAYGNERFMQYLASSNSTFNLSSFLDKGT---GGMGVPGGRMGYDMSPFIRRYAKYLNEKSLSYRAMAFDFCKV-----EGSLRSMNAEKLLKTLPVLQAQLDALLEFDCQSNDLSNGVINMSFMLLFRDLIRLFACYNDGIINLLEKYFDMNKKHARDALDLYKKFLVRMDRVGEFLKVAENVGIDKGDIPDLTKAPSSLLDALEQHLATL 299
                                    31        41        51        61        71        81        91       101       111    |  121       131       141       151       161     | 171       181       191       201       211       221       231       241       251       261       271       281       291        
                                                                                                                        116 120                                      161   167                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:269
 aligned with PICAL_DROME | Q9VI75 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:278
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        
          PICAL_DROME    22 QGLAKSVCKATTEECIGPKKKHLDYLVHCTNEPNVSIPHLANLLIERSQNANWVVVYKSLITTHHLMAYGNERFMQYLASSNSTFNLSSFLDKGTVQDGGMGVPGGRMGYDMSPFIRRYAKYLNEKSLSYRAMAFDFCKVKRGKEEGSLRSMNAEKLLKTLPVLQAQLDALLEFDCQSNDLSNGVINMSFMLLFRDLIRLFACYNDGIINLLEKYFDMNKKHARDALDLYKKFLVRMDRVGEFLKVAENVGIDKGDIPDLTKAPSSLLDALEQHLATL 299
               SCOP domains d1hx8b2 B:22-162 AP180 (Lap)                                                                                                                     d1hx8b1 B:167-299 AP180 (Lap)                                                                                                         SCOP domains
               CATH domains 1hx8B01 B:22-142  [code=1.25.40.90, no name defined]                                                                     -----------------1hx    8B02 B:160-299  [code=1.20.58.150, no name defined]                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.......hhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..............-----......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......----.......hhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hx8 B  22 QGLAKSVCKATTEECIGPKKKHLDYLVHCANEPNVSIPHLANLLIERSQNANWVVVYKSLITTHHLMAYGNERFMQYLASSNSTFNLSSFLDKGT-----MGVPGGRMGYDMSPFIRRYAKYLNEKSLSYRAMAFDFCKVK----EGSLRSMNAEKLLKTLPVLQAQLDALLEFDCQSNDLSNGVINMSFMLLFRDLIRLFACYNDGIINLLEKYFDMNKKHARDALDLYKKFLVRMDRVGEFLKVAENVGIDKGDIPDLTKAPSSLLDALEQHLATL 299
                                    31        41        51        61        71        81        91       101       111    |    -|      131       141       151       161|    | 171       181       191       201       211       221       231       241       251       261       271       281       291        
                                                                                                                        116   122                                     162  167                                                                                                                                    

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HX8)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PICAL_DROME | Q9VI75)
molecular function
    GO:0005545    1-phosphatidylinositol binding    Interacting selectively and non-covalently with phosphatidylinositol, any glycophospholipid with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0030276    clathrin binding    Interacting selectively and non-covalently with a clathrin heavy or light chain, the main components of the coat of coated vesicles and coated pits, and which also occurs in synaptic vesicles.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
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:0048268    clathrin coat assembly    The process that results in the assembly of clathrin triskelia into the ordered structure known as a clathrin cage.
    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:0007270    neuron-neuron synaptic transmission    The process of synaptic transmission from a neuron to another neuron across a synapse.
    GO:0007269    neurotransmitter secretion    The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission.
    GO:0042331    phototaxis    The directed movement of a motile cell or organism in response to light.
    GO:2000370    positive regulation of clathrin-dependent endocytosis    Any process that activates or increases the frequency, rate or extent of clathrin-mediated endocytosis.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0016183    synaptic vesicle coating    The formation of clathrin coated pits in the presynaptic membrane endocytic zone, triggered by the presence of high concentrations of synaptic vesicle components. This process leads to, but does not include budding of the membrane to form new vesicles.
    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.
    GO:0048489    synaptic vesicle transport    The directed movement of synaptic vesicles.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0030131    clathrin adaptor complex    A membrane coat adaptor complex that links clathrin to a membrane.
    GO:0005905    clathrin-coated pit    A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
    GO:0030136    clathrin-coated vesicle    A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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1dvp THE GEOMETRY OF THE FIRST FOUR HELICIES IS SIMILAR