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(-) Description

Title :  AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPS15 DPF PEPTIDE
 
Authors :  T. J. Brett, L. M. Traub, D. H. Fremont
Date :  05 Feb 02  (Deposition) - 12 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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 - EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15
    ChainsP
    EngineeredYES
    FragmentRESIDUES 628-632
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE IS A NATURALLY OCCURING SEQUENCE IN EPS15 (MOUSE)
    SynonymPROTEIN EPS15, AF-1P PROTEIN
    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 1KYU)

(-) Sites  (0, 0)

(no "Site" information available for 1KYU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KYU)

(-) 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                  ua1 A                                  :692-824 Alpha-adaptin AP2 ear domain, N-terminal subdomain                                                                 d1kyua2 A:825-938 Alpa-adaptin AP2, C-terminal subdomain                                                           SCOP domains
               CATH domains 1kyu                  A01 A                                  :692-825  [code=2.60.40.1030, no name defined]                                                                               1kyuA02 A:826-938  [code=3.30.310.30, no name defined]                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------Alpha_adaptinC2-1kyuA01 A:712-819                                                                           -----Alpha_adaptin_C-1kyuA02 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
                 1kyu 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:5
 aligned with EPS15_MOUSE | P42567 from UniProtKB/Swiss-Prot  Length:897

    Alignment length:5
          EPS15_MOUSE   628 SDPFK 632
               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 ----- Transcript
                 1kyu P 628 SDPFK 632

   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  (36, 43)

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   (EPS15_MOUSE | P42567)
molecular function
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0031593    polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination of the target protein.
    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:0006895    Golgi to endosome transport    The directed movement of substances from the Golgi to early sorting endosomes. Clathrin vesicles transport substances from the trans-Golgi to endosomes.
    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: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:0019065    receptor-mediated endocytosis of virus by host cell    Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the cell.
    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:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
cellular component
    GO:0030122    AP-2 adaptor complex    A heterotetrameric AP-type membrane coat adaptor complex that consists of alpha, beta2, mu2 and sigma2 subunits, and links clathrin to the membrane surface of a vesicle, and the cargo receptors during receptor/clathrin mediated endocytosis. Vesicles with AP-2-containing coats are normally found primarily near the plasma membrane, on endocytic vesicles. In at least humans, the AP-2 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different alpha genes (alphaA and alphaC).
    GO:0016235    aggresome    An inclusion body formed by dynein-dependent retrograde transport of an aggregated protein on microtubules.
    GO:0060170    ciliary membrane    The portion of the plasma membrane surrounding a cilium.
    GO:0030132    clathrin coat of coated pit    The coat found on coated pits and the coated vesicles derived from coated pits; comprises clathrin and the AP-2 adaptor complex.
    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: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:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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
        AP2A2_MOUSE | P174271b9k 1ky6 1ky7 1kyd 1kyf 1qtp 1qts 1w80 2jkr 2jkt 2vj0 3hs8
        EPS15_MOUSE | P425671kyf 1qjt

(-) 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