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(-) Description

Title :  THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH AMPHIPHYSIN FXDXF
 
Authors :  T. J. Brett, L. M. Traub, D. H. Fremont
Date :  03 Feb 02  (Deposition) - 12 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,P
Keywords :  Protein-Peptide Complex, Endocytosis, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. J. Brett, L. M. Traub, D. H. Fremont
Accessory Protein Recruitment Motifs In Clathrin-Mediated Endocytosis.
Structure V. 10 797 2002
PubMed-ID: 12057195  |  Reference-DOI: 10.1016/S0969-2126(02)00784-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-ADAPTIN C
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-2T
    Expression System StrainBL4
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL APPENDAGE (EAR) RESIDUES 701-938
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymAP-2 CLATHRIN ADAPTOR ALPHA SUBUNIT
 
Molecule 2 - AMPHIPHYSIN
    ChainsP
    EngineeredYES
    FragmentRESIDUES 322-330
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE IS A NATURALLY OCCURING SEQUENCE IN AMPHIPHYSIN (HOMO SAPIENS)
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1KY7)

(-) Sites  (0, 0)

(no "Site" information available for 1KY7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KY7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KY7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KY7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KY7)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003562641aENSE00001865805chr7:38671167-38670883285AMPH_HUMAN1-23230--
1.2ENST000003562642ENSE00001646088chr7:38574611-3857453181AMPH_HUMAN24-50270--
1.3ENST000003562643ENSE00001611965chr7:38543304-3854325055AMPH_HUMAN51-69190--
1.4ENST000003562644ENSE00001792437chr7:38534127-3853403395AMPH_HUMAN69-100320--
1.5ENST000003562645ENSE00001770901chr7:38530745-3853065096AMPH_HUMAN101-132320--
1.6ENST000003562646ENSE00001607557chr7:38516569-38516462108AMPH_HUMAN133-168360--
1.7ENST000003562647ENSE00001792678chr7:38515016-3851493186AMPH_HUMAN169-197290--
1.8ENST000003562648ENSE00001727100chr7:38505848-3850577376AMPH_HUMAN197-222260--
1.9ENST000003562649ENSE00001723487chr7:38505149-3850506783AMPH_HUMAN223-250280--
1.10ENST0000035626410ENSE00001772878chr7:38502713-38502575139AMPH_HUMAN250-296470--
1.11ENST0000035626411ENSE00001605286chr7:38501011-38500883129AMPH_HUMAN297-339431P:322-3309
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/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:247
 aligned with AP2A2_MOUSE | P17427 from UniProtKB/Swiss-Prot  Length:938

    Alignment length:299
                                   649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929         
          AP2A2_MOUSE   640 GGPEPVPASTSAASTPSPSADLLGLGAVPPAPTGPPPSSGGGLLVDVFSDSASAVAPLAPGSEDNFARFVCKNNGVLFENQLLQIGLKSEFRQNLGRMFIFYGNKTSTQFLNFTPTLICADDLQTNLNLQTKPVDPTVDGGAQVQQVVNIECISDFTEAPVLNIQFRYGGTFQNVSVKLPITLNKFFQPTEMASQDFFQRWKQLSNPQQEVQNIFKAKHPMDTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQMYRLTLRTSKDTVSQRLCELLSEQF 938
               SCOP domains d1ky                  7a1 A                                  :692-824 Alpha-adaptin AP2 ear domain, N-terminal subdomain                                                                 d1ky7a2 A:825-938 Alpa-adaptin AP2, C-terminal subdomain                                                           SCOP domains
               CATH domains 1ky7                  A01 A                                  :692-825  [code=2.60.40.1030, no name defined]                                                                               1ky7A02 A:826-938  [code=3.30.310.30, no name defined]                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------Alpha_adaptinC2-1ky7A01 A:712-819                                                                           -----Alpha_adaptin_C-1ky7A02 A:825-933                                                                            ----- Pfam domains
         Sec.struct. author ....------------------.....----------------------------------...hhhhhh....eeeee...eeeeeeeeee..eeeeeeeeee......eeeeeeee.hhhhhhheeeee...........eeeeeeeeee........eeeeeeee..eeeeeeee...hhhh.eee...hhhhhhhhhh...hhh.eeeeeee.....hhhhhhhhhhhhh.eee.........eeeeeeee....eeeeeeeeeee....eeeeeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ky7 A 692 GSPG------------------IRLGS----------------------------------SEDNFARFVCKNNGVLFENQLLQIGLKSEFRQNLGRMFIFYGNKTSTQFLNFTPTLICADDLQTNLNLQTKPVDPTVDGGAQVQQVVNIECISDFTEAPVLNIQFRYGGTFQNVSVKLPITLNKFFQPTEMASQDFFQRWKQLSNPQQEVQNIFKAKHPMDTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQMYRLTLRTSKDTVSQRLCELLSEQF 938
                               |     -         -  |   |  -         -         -         - |     709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929         
                             695                696 700                                701                                                                                                                                                                                                                                             

Chain P from PDB  Type:PROTEIN  Length:9
 aligned with AMPH_HUMAN | P49418 from UniProtKB/Swiss-Prot  Length:695

    Alignment length:9
           AMPH_HUMAN   322 SFFEDNFVP 330
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
               Transcript 1 Exon 1.11 Transcript 1
                 1ky7 P 322 SFFEDNFVP 330

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: E-set (290)

(-) Gene Ontology  (31, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AP2A2_MOUSE | P17427)
molecular function
    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).
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
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:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    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:1902036    regulation of hematopoietic stem cell differentiation    Any process that modulates the frequency, rate or extent of hematopoietic stem cell differentiation.
    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.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030117    membrane coat    Any of several different proteinaceous coats that can associate with membranes. Membrane coats include those formed by clathrin plus an adaptor complex, the COPI and COPII complexes, and possibly others. They are found associated with membranes on many vesicles as well as other membrane features such as pits and perhaps tubules.
    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.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

Chain P   (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 | P494181utc 3sog 4atm 5m5s 5m61
        AP2A2_MOUSE | P174271b9k 1ky6 1kyd 1kyf 1kyu 1qtp 1qts 1w80 2jkr 2jkt 2vj0 3hs8

(-) Related Entries Specified in the PDB File

1ky6 AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPSIN DPW PEPTIDE
1ky7 THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH AMPHIPHYSIN FXDXF
1kyd AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPSIN DPW PEPTIDE
1kyf AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPS15 DPF PEPTIDE
1qtp CRYSTAL STRUCTURE OF THE AP-2 CLATHRIN ADAPTOR ALPHA- APPENDAGE
1qts CRYSTAL STRUCTURE OF THE AP-2 CLATHRIN ADAPTOR ALPHA- APPENDAGE