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(-) Description

Title :  CRYSTAL STRUCTURE OF SOPD2, A TYPE III SECRETED VIRULENCE EFFECTOR FROM SALMONELLA ENTERICA
 
Authors :  R. Shi, M. Cygler, Montreal-Kingston Bacterial Structural Genomi Initiative (Bsgi)
Date :  21 Jul 15  (Deposition) - 09 Sep 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  T3Ss Effector Protein, Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Cell Invasion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. M. D'Costa, V. Braun, M. Landekic, R. Shi, A. Proteau, L. Mcdonald, M. Cygler, S. Grinstein, J. H. Brumell
Salmonella Disrupts Host Endocytic Trafficking By Sopd2-Mediated Inhibition Of Rab7.
Cell Rep V. 12 1508 2015
PubMed-ID: 26299973  |  Reference-DOI: 10.1016/J.CELREP.2015.07.063

(-) Compounds

Molecule 1 - SECRETED EFFECTOR PROTEIN SOPD2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SOPD2, STM0972
    Organism Scientific: SALMONELLA TYPHIMURIUM (STRAIN LT2 / SGSC1412 / ATCC 700720)
    Organism Taxid: 99287
    Strain: LT2 / SGSC1412 / ATCC 700720
    Synonym: SALMONELLA OUTER PROTEIN D 2
 
Molecule 2 - 11-MER PEPTIDE
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 90371

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 20)

Asymmetric Unit (1, 20)
No.NameCountTypeFull Name
1UNK20Mod. Amino Acid
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1UNK-1Mod. Amino Acid
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1UNK-1Mod. Amino Acid

(-) Sites  (0, 0)

(no "Site" information available for 5CQ9)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:200 -B:314

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CQ9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CQ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CQ9)

(-) Exons   (0, 0)

(no "Exon" information available for 5CQ9)

(-) 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:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhh.eeeee.....eeeeee..eeeeeeehhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.........ee.....hhhhhhhhhhhhh...........eeeeee..eeeeee.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cq9 A  36 VWDRFKDCFRTHKKQEVLEVLYTLIHGTGMEKIHAFTQLKEYANPSQQDRFVMRFDMNQTQVLFEIDGKVIDKCNLHRLLNVSENCIFKVMEEDEEELFLKICIKYGEKISRYPELLEGFANKLKDAVNEDDDVKDEVYKLMRSGEDRKMECVEWNGTLTEEEKNKLRCLQMGSFNITTQFFKIGYWELEGEVLFDMVHPTLSYLLQAYKPSLDLIETNTMLFSDVLNKDYDDYQNNKREIDAILRRIYRSHNNTLFISEKSSCRNMLI 319
                                    45        55      ||78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  ||   270       280       290       300       310         
                                                     62|                                                                                                                                                                                      261|                                                       
                                                      76                                                                                                                                                                                       264                                                       


Chain B from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........eeeee.....eeeeee..eeeeeeehhhhh...........hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh.........ee.....hhhhhhhhhhhhh...hhhhh...eeeeee..eeeeee.hhhhhhhhhh.......hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5cq9 B  36 VWDRFKDCFRTHKKQEVLEVLYTLIHGCTGMEKIHAFTQLKEYANPSQQDRFVMRFDMNQTQVLFEIDGKVIDKCNLHRLLNVSENCIFKVMEEDEEELFLKICIKYGEKISRYPELLEGFANKLKDAVNEDDDVKDEVYKLMRSGEDRKMECVEWNGTLTEEEKNKLRCLQMGSFNITTQFFKIGYWELEGEVLFDMVHPTLSYLLQAYKPSLSLIETNTMLFSDVLNKDYDDYQNNKREIDAILRRIYRSHNNTLFISEKSSCRNMLI 319
                                    45        55       |77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257    || 269       279       289       299       309       319
                                                      63|                                                                                                                                                                                       262|                                                      
                                                       76                                                                                                                                                                                        265                                                      


Chain C from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author .hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 5cq9 C  16 xxxxxxxxx  24
                            |||||||||
                           16-UNK||||
                            17-UNK|||
                             18-UNK||
                              19-UNK|
                               20-UNK
                                21-UNK
                                 22-UNK
                                  23-UNK
                                   24-UNK


Chain D from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5cq9 D  15 xxxxxxxxxxx  25
                            ||||||||24|
                            |||||||23-UNK
                           15-UNK|||24-UNK
                            16-UNK|| 25-UNK
                             17-UNK|   
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                               19-UNK  
                                20-UNK 
                                 21-UNK
                                  22-UNK
   Legend:   → Mismatch (orange background)
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  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 5CQ9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CQ9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CQ9)

(-) Gene Ontology  (6, 6)

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 Related Entries

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(-) Related Entries Specified in the PDB File

5cpc 5CPC CONTAINS THE STRUCTURE OF SOPD