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(-) Description

Title :  GAMMA 2 ADAPTIN EAR DOMAIN CRYSTAL STRUCTURE
 
Authors :  M. C. Juergens, J. Voros, G. Rautureau, D. Shepherd, V. E. Pye, J. Muldoo C. M. Johnson, A. Ashcroft, S. M. V. Freund, N. Ferguson
Date :  03 Oct 12  (Deposition) - 10 Jul 13  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Transport, Gae, Gamma Adaptin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. C. Jurgens, J. Voros, G. J. P. Rautureau, D. A. Shepherd, V. E. Pye, J. Muldoon, C. M. Johnson, A. E. Ashcroft, S. M. V. Freund, N. Ferguson
The Hepatitis B Virus Pres1 Domain Hijacks Host Trafficking Proteins By Motif Mimicry.
Nat. Chem. Biol. V. 9 540 2013
PubMed-ID: 23851574  |  Reference-DOI: 10.1038/NCHEMBIO.1294

(-) Compounds

Molecule 1 - AP-1 COMPLEX SUBUNIT GAMMA-LIKE 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantC41
    Expression System VectorMODIFIED PRSETA
    FragmentEAR DOMAIN, RESIDUES 665-785
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGAMMA2-ADAPTIN, G2AD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE
2PDO1Ligand/Ion1,3-PROPANDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:716 , LYS A:758 , GLU A:775BINDING SITE FOR RESIDUE IMD A 1786
2AC2SOFTWAREHOH A:2110BINDING SITE FOR RESIDUE PDO A 1787

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BCX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BCX)

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003971201bENSE00001527366chr14:24036987-2403694840AP1G2_HUMAN-00--
1.1eENST000003971201eENSE00002163144chr14:24036528-24036320209AP1G2_HUMAN1-68680--
1.2ENST000003971202ENSE00001380724chr14:24035895-24035771125AP1G2_HUMAN69-110420--
1.3ENST000003971203ENSE00000889289chr14:24035628-24035487142AP1G2_HUMAN110-157480--
1.4aENST000003971204aENSE00001387199chr14:24035369-2403527397AP1G2_HUMAN158-190330--
1.4cENST000003971204cENSE00000889287chr14:24035101-2403502577AP1G2_HUMAN190-215260--
1.5ENST000003971205ENSE00001382639chr14:24034910-2403481596AP1G2_HUMAN216-247320--
1.6ENST000003971206ENSE00000889285chr14:24034408-2403432881AP1G2_HUMAN248-274270--
1.7ENST000003971207ENSE00001379613chr14:24033869-2403377199AP1G2_HUMAN275-307330--
1.8ENST000003971208ENSE00000889283chr14:24033597-2403354256AP1G2_HUMAN308-326190--
1.9cENST000003971209cENSE00001384905chr14:24033368-24033255114AP1G2_HUMAN326-364390--
1.9dENST000003971209dENSE00001268068chr14:24033065-24032925141AP1G2_HUMAN364-411480--
1.10ENST0000039712010ENSE00001389733chr14:24032847-2403279355AP1G2_HUMAN411-429190--
1.11ENST0000039712011ENSE00001389075chr14:24032711-24032589123AP1G2_HUMAN430-470410--
1.12ENST0000039712012ENSE00000889278chr14:24031802-2403171390AP1G2_HUMAN471-500300--
1.13bENST0000039712013bENSE00001379347chr14:24031624-24031497128AP1G2_HUMAN501-543430--
1.14ENST0000039712014ENSE00000889276chr14:24031275-24031171105AP1G2_HUMAN543-578360--
1.15ENST0000039712015ENSE00001268569chr14:24030844-24030721124AP1G2_HUMAN578-619420--
1.16ENST0000039712016ENSE00001370277chr14:24030640-24030505136AP1G2_HUMAN620-665460--
1.17ENST0000039712017ENSE00001385856chr14:24029627-24029464164AP1G2_HUMAN665-719551A:666-71954
1.18ENST0000039712018ENSE00000654059chr14:24029245-2402914799AP1G2_HUMAN720-752331A:720-75233
1.19bENST0000039712019bENSE00001404703chr14:24029059-24028777283AP1G2_HUMAN753-785331A:753-78533

(-) 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:120
 aligned with AP1G2_HUMAN | O75843 from UniProtKB/Swiss-Prot  Length:785

    Alignment length:120
                                   675       685       695       705       715       725       735       745       755       765       775       785
          AP1G2_HUMAN   666 PIPDLKVFEREGVQLNLSFIRPPENPALLLITITATNFSEGDVTHFICQAAVPKSLQLQLQAPSGNTVPARGGLPITQLFRILNPNKAPLRLKLRLTYDHFHQSVQEIFEVNNLPVESWQ 785
               SCOP domains d4bcxa_ A: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeee.......eeeeeeeeee.....eeeeeeeee.....eeee...............eeeeeeee.........eeeeeeee..eeeeeeee....hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.17  PDB: A:666-719 UniProt: 665-719            Exon 1.18  PDB: A:720-752        Exon 1.19b  PDB: A:753-785        Transcript 1
                 4bcx A 666 PIPDLKVFEREGVQLNLSFIRPPENPALLLITITATNFSEGDVTHFICQAAVPKSLQLQLQAPSGNTVPARGGLPITQLFRILNPNKAPLRLKLRLTYDHFHQSVQEIFEVNNLPVESWQ 785
                                   675       685       695       705       715       725       735       745       755       765       775       785

   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/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AP1G2_HUMAN | O75843)
molecular function
    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:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
    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: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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0030121    AP-1 adaptor complex    A heterotetrameric AP-type membrane coat adaptor complex that consists of beta1, gamma, mu1 and sigma1 subunits and links clathrin to the membrane surface of a vesicle; vesicles with AP-1-containing coats are normally found primarily in the trans-Golgi network. In at least humans, the AP-1 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different genes (gamma1 and gamma2, mu1A and mu1B, and sigma1A, sigma1B and sigma1C).
    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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005798    Golgi-associated vesicle    Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell.
    GO:0030131    clathrin adaptor complex    A membrane coat adaptor complex that links clathrin to a membrane.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    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:0030133    transport vesicle    Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AP1G2_HUMAN | O758432e9g 2ymt 3zhf

(-) Related Entries Specified in the PDB File

2ymt GAMMA 2 ADAPTIN EAR DOMAIN CRYSTAL STRUCTURE WITH PHAGE PEPTIDE GEEWGPWV