Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  GAMMA 2 ADAPTIN EAR DOMAIN CRYSTAL STRUCTURE WITH PHAGE PEPTIDE GEEWGPWV
 
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 :  10 Oct 12  (Deposition) - 10 Jul 13  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Transport (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, GAMMA 2 ADAPTIN EAR DOMAIN
 
Molecule 2 - PHAGE DISPLAY DERIVED GAMMA 2 ADAPTIN EAR DOMAIN BINDING PEPTIDE
    ChainsB
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP
2PDO1Ligand/Ion1,3-PROPANDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2123BINDING SITE FOR RESIDUE PDO A 1786

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YMT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YMT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YMT)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAEPS50180 Gamma-adaptin ear (GAE) domain profile.AP1G2_HUMAN665-780  1A:665-780

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 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_HUMAN620-665461A:664-6652
1.17ENST0000039712017ENSE00001385856chr14:24029627-24029464164AP1G2_HUMAN665-719551A:665-71955
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:122
 aligned with AP1G2_HUMAN | O75843 from UniProtKB/Swiss-Prot  Length:785

    Alignment length:122
                                   673       683       693       703       713       723       733       743       753       763       773       783  
          AP1G2_HUMAN   664 PAPIPDLKVFEREGVQLNLSFIRPPENPALLLITITATNFSEGDVTHFICQAAVPKSLQLQLQAPSGNTVPARGGLPITQLFRILNPNKAPLRLKLRLTYDHFHQSVQEIFEVNNLPVESWQ 785
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- 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 -GAE  PDB: A:665-780 UniProt: 665-780                                                                                ----- PROSITE
           Transcript 1 (1) 1.------------------------------------------------------Exon 1.18  PDB: A:720-752        Exon 1.19b  PDB: A:753-785        Transcript 1 (1)
           Transcript 1 (2) -Exon 1.17  PDB: A:665-719 UniProt: 665-719             ------------------------------------------------------------------ Transcript 1 (2)
                 2ymt A 664 SAPIPDLKVFEREGVQLNLSFIRPPENPALLLITITATNFSEGDVTHFICQAAVPKSLQLQLQAPSGNTVPARGGLPITQLFRILNPNKAPLRLKLRLTYDHFHQSVQEIFEVNNLPVESWQ 785
                                   673       683       693       703       713       723       733       743       753       763       773       783  

Chain B from PDB  Type:PROTEIN  Length:7
                                       
               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
                 2ymt B   0 EWGPWVx   6
                                  |
                                  6-NH2

   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  (0, 0)

(no "SCOP Domain" information available for 2YMT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YMT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YMT)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NH2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ymt)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2ymt
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AP1G2_HUMAN | O75843
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  AP1G2_HUMAN | O75843
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        AP1G2_HUMAN | O758432e9g 3zhf 4bcx

(-) Related Entries Specified in the PDB File

4bcx GAMMA 2 ADAPTIN EAR DOMAIN CRYSTAL STRUCTURE