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(-) Description

Title :  AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPSIN DPW PEPTIDE
 
Authors :  T. J. Brett, L. M. Traub, D. H. Fremont
Date :  04 Feb 02  (Deposition) - 12 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-2T
    Expression System Strain: BL4
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL APPENDAGE (EAR), RESIDUES 701-938
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: AP-2 CLATHRIN ADAPTOR ALPHA SUBUNIT
 
Molecule 2 - EH DOMAIN-BINDING MITOTIC PHOSPHOPROTEIN
    Chains: P
    Engineered: YES
    Fragment: RESIDUES 341-345
    Mutation: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE USED (SPDWK) IS A SINGLE MUTATION TO THE NATURALLY OCCURING SEQUENCE FROM HUMAN EPSIN (SPDWT)
    Synonym: EPSIN 1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AP

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:177 , ASP A:761 , LEU A:762 , ASN A:765 , PHE A:795 , THR A:796 , GLU A:797BINDING SITE FOR RESIDUE SO4 A 200

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002704601ENSE00001178639chr19:56186561-56186801241EPN1_HUMAN-00--
1.4ENST000002704604ENSE00001671302chr19:56189893-56190221329EPN1_HUMAN1-76760--
1.5ENST000002704605ENSE00000728185chr19:56196762-56197011250EPN1_HUMAN77-160840--
1.6ENST000002704606ENSE00000728191chr19:56200236-56200360125EPN1_HUMAN160-201420--
1.7ENST000002704607ENSE00000953972chr19:56200663-5620073775EPN1_HUMAN202-226250--
1.8ENST000002704608ENSE00000728194chr19:56201233-5620131684EPN1_HUMAN227-254280--
1.9ENST000002704609ENSE00000728198chr19:56203120-56203423304EPN1_HUMAN255-3561020--
1.10ENST0000027046010ENSE00000728203chr19:56204052-56204162111EPN1_HUMAN356-393381P:341-345 (gaps)10
1.11aENST0000027046011aENSE00000892889chr19:56204317-5620440387EPN1_HUMAN393-422300--
1.12ENST0000027046012ENSE00000728216chr19:56206092-56206349258EPN1_HUMAN422-508870--
1.13ENST0000027046013ENSE00001354396chr19:56206514-56207132619EPN1_HUMAN508-576690--

(-) 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                  da1 A                                  :692-824 Alpha-adaptin AP2 ear domain, N-terminal subdomain                                                                 d1kyda2 A:825-938 Alpa-adaptin AP2, C-terminal subdomain                                                           SCOP domains
               CATH domains 1kyd                  A01 A                                  :692-825  [code=2.60.40.1030, no name defined]                                                                               1kydA02 A:826-938  [code=3.30.310.30, no name defined]                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------Alpha_adaptinC2-1kydA01 A:712-819                                                                           -----Alpha_adaptin_C-1kydA02 A:825-933                                                                            ----- Pfam domains
         Sec.struct. author ....------------------.....----------------------------------...hhhhhh....eeeee...eeeeeeeeee..eeeeeeeeee......eeeeeeee...hhhhheeeee...........eeeeeeeeee........eeeeeeee..eeeeeeee...hhhh.eee...hhhhhhhhhh...hhh.eeeeeee.....hhhhhhhhhhhhh.ee..........eeeeeeee....eeeeeeeeeee....eeeeeeee.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kyd 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 EPN1_HUMAN | Q9Y6I3 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:10
                                   385
           EPN1_HUMAN   376 SDPWGGSPAK 385
               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 1.10  Transcript 1
                 1kyd P 341 SDPW-----K 345
                               |   345
                             344   345
   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
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) 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)
(-)
Clan: no clan defined [family: Alpha_adaptin_C] (9)

(-) Gene Ontology  (24, 30)

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   (EPN1_HUMAN | Q9Y6I3)
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).
biological process
    GO:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0048568    embryonic organ development    Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    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:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    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.
cellular component
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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 | P17427: 1b9k 1ky6 1ky7 1kyf 1kyu 1qtp 1qts 1w80 2jkr 2jkt 2vj0 3hs8
        EPN1_HUMAN | Q9Y6I3: 1inz

(-) 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
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