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 :  CRYSTAL STRUCTURE OF THE GRASP65-GM130 C-TERMINAL PEPTIDE COMPLEX
 
Authors :  N. Shi, F. Hu, B. Li
Date :  24 Sep 14  (Deposition) - 23 Sep 15  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pdz Fold Six-Stranded Anti Parallel-Barrel Capped By Two-Helices, Protein Interaction, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Hu, X. Shi, B. Li, X. Huang, X. Morelli, N. Shi
Structural Basis For The Interaction Between The Golgi Reassembly-Stacking Protein Grasp65 And The Golgi Matrix Protein Gm130.
J. Biol. Chem. V. 290 26373 2015
PubMed-ID: 26363069  |  Reference-DOI: 10.1074/JBC.M115.657940

(-) Compounds

Molecule 1 - GOLGI REASSEMBLY-STACKING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidRSF
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentGRASP DOMAIN OF GRAS65, UNP RESIDUES 1-210
    GeneGOLPH5, GORASP1, GRASP65
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGOLGI PERIPHERAL MEMBRANE PROTEIN P65, GOLGI PHOSPHOPROTEIN 5, GOLPH5, GOLGI REASSEMBLY-STACKING PROTEIN OF 65 KDA, GRASP65
 
Molecule 2 - GOLGIN SUBFAMILY A MEMBER 2
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentGM130 C-TERMINAL DOMAIN, UNP RESIDUES 980-1002
    GeneGM130, GOLGA2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym130 KDA CIS-GOLGI MATRIX PROTEIN, GM130, GM130 AUTOANTIGEN, GOLGIN-95

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

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
1AC1SOFTWAREARG A:130 , SER A:170 , SER A:172 , HOH A:579 , HOH A:580BINDING SITE FOR RESIDUE SO4 A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:12 -Gly A:13

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4REY)

(-) 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:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...hhhhhh......eeeeee..ee.....hhhhhhhhhh....eeeeeee....eeeeeee.............eeeeeee..hhhhh.eeeeee...hhhhhhh.....eeeeee........hhhhhhhhh....eeeeeee....eeeeeee.............eeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rey A  12 GGAEGFHLHGVQENSPAQQAGLEPYFDFIITIGHSRLNKENDTLKALLKANVEKPVKLEVFNMKTMRVREVEVVPSNMWGGQGLLGASVRFCSFRRASEQVWHVLDVEPSSPAALAGLRPYTDYVVGSDQILQESEDFFTLIESHEGKPLKLMVYNSKSDSCREVTVTPNAAWGGEGSLGCGIGYGYLHRIPTQPP 207
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      

Chain B from PDB  Type:PROTEIN  Length:22
                                                      
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author ....ee.............ee. Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 4rey B 969 SNPCIPFFYRADENDEVKITVI 990
                                   978       988  

   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 4REY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (40, 47)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:12 - Gly A:13   [ RasMol ]  
 

(-) 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
  4rey
    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
  GOGA2_HUMAN | Q08379
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  GORS1_HUMAN | Q9BQQ3
    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
  GOGA2_HUMAN | Q08379
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  GORS1_HUMAN | Q9BQQ3
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4REY)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4REY)