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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GGA2 VHS DOMAIN
 
Authors :  G. Zhu, X. C. Zhang
Date :  20 Aug 02  (Deposition) - 11 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Super Helix, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Zhu, X. He, S. Terzyan, P. Zhai, J. Tang, X. C. Zhang
Crystal Structure Of Gga2 Vhs Domain And Its Implication In Plasticity In The Ligand Binding Pocket
Febs Lett. V. 537 171 2003
PubMed-ID: 12606052  |  Reference-DOI: 10.1016/S0014-5793(03)00095-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX2T
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: VHS DOMAIN (N-TERMINAL DOMAIN)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GOLGI-LOCALIZED, GAMMA EAR-CONTAINING, ARF- BINDING PROTEIN 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1MHQ)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:50 -A:89
2B:50 -B:89

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp B:164 -Pro B:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VHSPS50179 VHS domain profile.GGA2_HUMAN33-163
 		  2A:33-163
B:33-163
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VHSPS50179 VHS domain profile.GGA2_HUMAN33-163
 		  1A:33-163
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VHSPS50179 VHS domain profile.GGA2_HUMAN33-163
 		  1-
B:33-163

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003098591ENSE00001387864chr16:23521815-23521642174GGA2_HUMAN1-31312A:25-31
B:25-31		7
7
1.2ENST000003098592ENSE00000677056chr16:23507099-2350701585GGA2_HUMAN31-59292A:31-59
B:31-59		29
29
1.3ENST000003098593ENSE00000829602chr16:23505699-2350562476GGA2_HUMAN59-84262A:59-84
B:59-84		26
26
1.4ENST000003098594ENSE00000829603chr16:23504779-2350468199GGA2_HUMAN85-117332A:85-117
B:85-116		33
32
1.5ENST000003098595ENSE00000829604chr16:23503121-23502998124GGA2_HUMAN118-159422A:118-159
B:119-159		42
41
1.6ENST000003098596ENSE00000677063chr16:23500030-23499927104GGA2_HUMAN159-193352A:159-167
B:159-170		9
12
1.7ENST000003098597ENSE00000829606chr16:23498111-2349803181GGA2_HUMAN194-220270--
1.8ENST000003098598ENSE00000829607chr16:23497473-23497336138GGA2_HUMAN221-266460--
1.9ENST000003098599ENSE00000677067chr16:23494325-2349424482GGA2_HUMAN267-294280--
1.10ENST0000030985910ENSE00001187989chr16:23492091-23491966126GGA2_HUMAN294-336430--
1.11ENST0000030985911ENSE00001187984chr16:23491208-23491086123GGA2_HUMAN336-377420--
1.12ENST0000030985912ENSE00000914437chr16:23490232-2349020429GGA2_HUMAN377-386100--
1.13ENST0000030985913ENSE00000677071chr16:23489822-23489689134GGA2_HUMAN387-431450--
1.14ENST0000030985914ENSE00000829613chr16:23486382-23486225158GGA2_HUMAN431-484540--
1.15ENST0000030985915ENSE00000829614chr16:23481486-23481317170GGA2_HUMAN484-540570--
1.16ENST0000030985916ENSE00001187951chr16:23480317-23480207111GGA2_HUMAN541-577370--
1.17ENST0000030985917ENSE00001188037chr16:23479021-234748634159GGA2_HUMAN578-613360--

(-) Sequences/Alignments

Asymmetric 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:143
 aligned with GGA2_HUMAN | Q9UJY4 from UniProtKB/Swiss-Prot  Length:613

    Alignment length:143
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164   
           GGA2_HUMAN    25 SLELWLNKATDPSMSEQDWSAIQNFCEQVNTDPNGPTHAPWLLAHKIQSPQEKEALYALTVLEMCMNHCGEKFHSEVAKFRFLNELIKVLSPKYLGSWATGKVKGRVIEILFSWTVWFPEDIKIRDAYQMLKKQGIIKQDPKL 167
               SCOP domains d1mhqa_ A: ADP-ribosylation factor binding protein Gga2                                                                                         SCOP domains
               CATH domains 1mhqA00 A:25-167  [code=1.25.40.90, no name defined]                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------VHS  PDB: A:33-163 UniProt: 33-163                                                                                                 ---- PROSITE
           Transcript 1 (1) 1.1    ---------------------------Exon 1.3  PDB: A:59-84    Exon 1.4  PDB: A:85-117          Exon 1.5  PDB: A:118-159 UniProt: 118-159 -------- Transcript 1 (1)
           Transcript 1 (2) ------Exon 1.2  PDB: A:31-59       ---------------------------------------------------------------------------------------------------Exon 1.6  Transcript 1 (2)
                 1mhq A  25 SLELWLNKATDPSMSEQDWSAIQNFCEQVNTDPNGPTHAPWLLAHKIQSPQEKEALYALTVLEMCMNHCGEKFHSEVAKFRFLNELIKVLSPKYLGSWATGKVKGRVIEILFSWTVWFPEDIKIRDAYQMLKKQGIIKQDPKL 167
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164   


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with GGA2_HUMAN | Q9UJY4 from UniProtKB/Swiss-Prot  Length:613

    Alignment length:146
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164      
           GGA2_HUMAN    25 SLELWLNKATDPSMSEQDWSAIQNFCEQVNTDPNGPTHAPWLLAHKIQSPQEKEALYALTVLEMCMNHCGEKFHSEVAKFRFLNELIKVLSPKYLGSWATGKVKGRVIEILFSWTVWFPEDIKIRDAYQMLKKQGIIKQDPKLPVD 170
               SCOP domains d1mhqb_ B: ADP-ribosylation factor binding protein Gga2                                                                                            SCOP domains
               CATH domains 1mhqB00 B:25-170  [code=1.25.40.90, no name defined]                                                                                               CATH domains
           Pfam domains (1) VHS-1mhqB01 B:25-159                                                                                                                   ----------- Pfam domains (1)
           Pfam domains (2) VHS-1mhqB02 B:25-159                                                                                                                   ----------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.--.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------VHS  PDB: B:33-163 UniProt: 33-163                                                                                                 ------- PROSITE
           Transcript 1 (1) 1.1    ---------------------------Exon 1.3  PDB: B:59-84    Exon 1.4  PDB: B:85-116          Exon 1.5  PDB: B:119-159 UniProt: 118-159 ----------- Transcript 1 (1)
           Transcript 1 (2) ------Exon 1.2  PDB: B:31-59       ---------------------------------------------------------------------------------------------------Exon 1.6     Transcript 1 (2)
                 1mhq B  25 SLELWLNKATDPSMSEQDWSAIQNFCEQVNTDPNGPTHAPWLLAHKIQSPQEKEALYALTVLEMCMNHCGEKFHSEVAKFRFLNELIKVLSP--LGSWATGKVKGRVIEILFSWTVWFPEDIKIRDAYQMLKKQGIIKQDPKLPVD 170
                                    34        44        54        64        74        84        94       104       114 |  |  124       134       144       154       164      
                                                                                                                     116  |                                                   
                                                                                                                        119
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: ENTH_VHS (15)
(-)
Family: VHS (11)
(-)
Homo sapiens (Human) (11)
1aVHS-1mhqB01B:25-159
1bVHS-1mhqB02B:25-159

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GGA2_HUMAN | Q9UJY4)
molecular function
    GO:0030306    ADP-ribosylation factor binding    Interacting selectively and non-covalently with ARF, ADP-ribosylation factor, a small monomeric cytosolic GTPase that, when bound to GTP, binds to the membranes of cells.
    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:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    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.
cellular component
    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:0030131    clathrin adaptor complex    A membrane coat adaptor complex that links clathrin to a membrane.
    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:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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  1mhq
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