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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIGB2 TOXIN IN COMPLEX WITH NB6
 
Authors :  S. Hadzi, R. Loris
Date :  12 Apr 16  (Deposition) - 05 Apr 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Toxin-Antitoxin System, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Hadzi, A. Garcia-Pino, S. Haesaerts, D. Jurenas, K. Gerdes, J. Lah, R. Loris
Ribosome-Dependent Vibrio Cholerae Mrnase Higb2 Is Regulate By A Beta-Strand Sliding Mechanism.
Nucleic Acids Res. V. 45 4972 2017
PubMed-ID: 28334932  |  Reference-DOI: 10.1093/NAR/GKX138

(-) Compounds

Molecule 1 - TOXIN HIGB-2
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HIGB-2, VC_A0468
    Organism Scientific: VIBRIO CHOLERAE SEROTYPE O1 (STRAIN ATCC 39315 / EL TOR INABA N16961)
    Organism Taxid: 243277
    Strain: ATCC 39315 / EL TOR INABA N16961
 
Molecule 2 - NANOBODY 6
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2SO47Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2SO43Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS C:49 , ARG C:51 , ARG C:64 , SER C:88binding site for residue SO4 C 201
2AC2SOFTWAREGLY C:62 , ARG C:64binding site for residue SO4 C 202
3AC3SOFTWAREGLN C:42binding site for residue SO4 C 203
4AC4SOFTWARELYS D:49 , ARG D:64 , HOH D:306binding site for residue SO4 D 201
5AC5SOFTWARELYS D:36 , ARG D:48binding site for residue SO4 D 202
6AC6SOFTWARETHR A:29 , TYR A:33 , HOH A:301binding site for residue SO4 A 201
7AC7SOFTWAREPHE A:51 , ASN A:60 , GLU C:17 , GLU C:86binding site for residue EDO A 202
8AC8SOFTWAREPHE B:28 , THR B:29 , TYR B:33 , HOH B:301binding site for residue SO4 B 201

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:23 -A:97
2B:23 -B:97

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JA9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JA9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JA9)

(-) Exons   (0, 0)

(no "Exon" information available for 5JA9)

(-) 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:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.....eee...eeeee..hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ja9 A   2 QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYAMRWYRQAPGEEREFVAFISSVGGSTNYADSVKGRFTISRDNGKNTLYLQMNSLKPEDTAVYFCVARLSLISDSWGQGTQVTVSSHHHHHH 124
                                    11        21        31        41        51        61        71        81        91       101       111       121   


Chain B from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.....eee...eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ja9 B   2 QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYAMRWYRQAPGEEREFVAFISSVGGSTNYADSVKGRFTISRDNGKNTLYLQMNSLKPEDTAVYFCVARLSLISDSWGQGTQVTVSSHHHHH 123
                                    11        21        31        41        51        61        71        81        91       101       111       121  


Chain C from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.......eeeee...eeeeeeee....eeeeeeeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 5ja9 C   2 KSVFVESTIFEKYRDEYLSDEEYRLFQAELMLNPKLGDVIQGTGGLRKIRVASGSRIIYYFLDEKRRFYLLTIYGKNEMSDLNANQRKQLMAFMEAWRNEQ 109
                                    11        21        31        41        51  ||    68        78        88        98       108 
                                                                               54|                                               
                                                                                62                                               


Chain D from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.....eeeeee...eeeeeeee....eeeeeeeee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 5ja9 D   2 KSVFVESTIFEKYRDEYLSDEEYRLFQAELMLNPKLGDVIQGTGGLRKIRVASGSRIIYYFLDEKRRFYLLTIYGKNEMSDLNANQRKQLMAFMEAWRNE 108
                                    11        21        31        41        51  ||    68        78        88        98       108
                                                                               54|                                              
                                                                                62
   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 5JA9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JA9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JA9)

(-) Gene Ontology  (3, 3)

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  5ja9
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 Related Entries

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

UniProtKB/Swiss-Prot
        HIGB2_VIBCH | Q9KMA6: 5ja8 5jaa 5mje

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