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(-) Description

Title :  CRYSTAL STRUCTURE OF GRASP55 GRASP DOMAIN IN COMPLEX WITH JAM-B C-TERMINUS
 
Authors :  N. Shi, X. Shi, X. Morelli, S. Betzi, X. Huang
Date :  14 Jul 16  (Deposition) - 24 May 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Beta Strand Sandswish, Classic Pdz Peptide Binding Groove, Conserved Carboxylate-Binding Loop, Structural Protein-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Cartier-Michaud, A. L. Bailly, S. Betzi, X. Shi, J. C. Lissitzky, A. Zarubica, A. Serge, P. Roche, A. Lugari, V. Hamon, F. Bardin, C. Derviaux, F. Lembo, S. Audebert, S. Marchetto, B. Durand, J. P. Borg N. Shi, X. Morelli, M. Aurrand-Lions
Genetic, Structural, And Chemical Insights Into The Dual Function Of Grasp55 In Germ Cell Golgi Remodeling And Jam-C Polarized Localization During Spermatogenesis
Plos Genet. V. 13 06803 2017
PubMed-ID: 28617811  |  Reference-DOI: 10.1371/JOURNAL.PGEN.1006803

(-) Compounds

Molecule 1 - GOLGI REASSEMBLY-STACKING PROTEIN 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: GRASP DOMAIN, UNP RESIDUES 2-208
    Gene: GORASP2,GOLPH6
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: GRS2,GOLGI REASSEMBLY-STACKING PROTEIN OF 55 KDA,GRASP55
 
Molecule 2 - JUNCTIONAL ADHESION MOLECULE B
    Chains: C, D
    Engineered: YES
    Fragment: PEPTIDE OF JAMB C TERMIANL
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: JAM-B,JUNCTIONAL ADHESION MOLECULE 2,JAM-2,VASCULAR ENDOTHELIAL JUNCTION-ASSOCIATED MOLECULE,VE-JAM
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5GMJ)

(-) Sites  (0, 0)

(no "Site" information available for 5GMJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GMJ)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser A:1 -Gly A:2
2Gly A:2 -Ser A:3
3Gln A:5 -Ser A:6
4Val A:142 -Met A:143
5Glu B:145 -Ser B:146
6Pro B:160 -Leu B:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GMJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GMJ)

(-) Exons   (0, 0)

(no "Exon" information available for 5GMJ)

(-) 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:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................eeeeeeee...hhhhhhh.....eeeeee..ee.....hhhhhhhhhh....eeeeeee.....eeeeee.............eeeeeee........eeeeee...hhhhhhh.....eeeee.........hhhhh........eeeeeee....eeeeeee.............eeee.hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gmj A -14 STSLYKKAGFLVPRGSGSSQSVEIPGGGTEGYHVLRVQENSPGHRAGLEPFFDFIVSINGSRLNKDNDTLKDLLKANVEKPVKMLIYSSKTLELREASVTPSNLWGGQGLLGVSIRFCSFDGANENVWHVLEVESNSPAALAGLRPHSDYIIGADTVMNESEDLFSLIETHEAKPLKLYVYNTDTDNCREVIITPNSAWGGEGSLGCGIGYGYLHRIPTRPFE 208
                                    -5         5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205   


Chain B from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................eeeeeeee...hhhhhhh.....eeeeee..ee.....hhhhhhhhhh....eeeeeee.....eeeeee.............eeeeeee..hhhhh.eeeeee...hhhhhhh.....eeeeeee.......hhhhhhh.......eeeeee....eeeeee..............eeee.hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gmj B -15 ESTSLYKKAGFLVPRGSGSSQSVEIPGGGTEGYHVLRVQENSPGHRAGLEPFFDFIVSINGSRLNKDNDTLKDLLKANVEKPVKMLIYSSKTLELREASVTPSNLWGGQGLLGVSIRFCSFDGANENVWHVLEVESNSPAALAGLRPHSDYIIGADTVMNESEDLFSLIETHEAKPLKLYVYNTDTDNCREVIITPNSAWGGEGSLGCGIGYGYLHRIPTRPFE 208
                                    -6         4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204    


Chain C from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author .....eee Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 5gmj C  12 KHTKSFII  19


Chain D from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...eee Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5gmj D  14 TKSFII  19
   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 5GMJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GMJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GMJ)

(-) Gene Ontology  (11, 12)

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  Cis Peptide Bonds
    Gln A:5 - Ser A:6   [ RasMol ]  
    Glu B:145 - Ser B:146   [ RasMol ]  
    Gly A:2 - Ser A:3   [ RasMol ]  
    Pro B:160 - Leu B:161   [ RasMol ]  
    Ser A:1 - Gly A:2   [ RasMol ]  
    Val A:142 - Met A:143   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        GORS2_MOUSE | Q99JX3: 5gmi 5h3j

(-) Related Entries Specified in the PDB File

5gmi 5gml