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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIGB2 TOXIN IN COMPLEX WITH NB2
 
Authors :  S. Hadzi, R. Loris
Date :  12 Apr 16  (Deposition) - 05 Apr 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (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: A, C, E, G
    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 2
    Chains: B, D, F, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4PDO2Ligand/Ion1,3-PROPANDIOL
5PO410Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4PDO-1Ligand/Ion1,3-PROPANDIOL
5PO43Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4PDO1Ligand/Ion1,3-PROPANDIOL
5PO44Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4PDO-1Ligand/Ion1,3-PROPANDIOL
5PO42Ligand/IonPHOSPHATE ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4PDO1Ligand/Ion1,3-PROPANDIOL
5PO41Ligand/IonPHOSPHATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:36 , ARG A:48binding site for residue PO4 A 201
02AC2SOFTWAREASN A:91 , ALA A:92 , ARG A:95binding site for residue PO4 A 202
03AC3SOFTWAREARG A:64 , TYR A:82binding site for residue ACT A 203
04AC4SOFTWARETHR B:116 , GLN B:117binding site for residue PO4 B 201
05AC5SOFTWAREILE A:10 , THR A:80 , MET A:87 , ALA B:99 , ASP B:100 , PHE B:101 , ARG B:107 , TRP B:112binding site for residue EDO B 202
06AC6SOFTWAREARG C:51 , ARG C:64 , TYR C:82 , LYS C:84 , ASN C:85binding site for residue PO4 C 201
07AC7SOFTWAREASN C:91 , ALA C:92 , ARG C:95binding site for residue PO4 C 202
08AC8SOFTWARETYR B:96 , TYR B:111 , GLN D:114 , GLY D:115 , THR D:116 , GLN D:117 , ARG E:51binding site for residue EPE D 201
09AC9SOFTWAREARG A:51 , ARG A:64 , HIS D:128 , HOH D:304binding site for residue PO4 D 202
10AD1SOFTWAREGLU D:7 , SER D:8 , GLY D:9 , THR D:116 , ARG E:64 , LYS E:84binding site for residue PO4 D 203
11AD2SOFTWAREILE C:10 , THR C:80 , MET C:87 , ALA D:99 , ASP D:100 , PHE D:101 , ARG D:107 , HOH D:302binding site for residue PDO D 204
12AD3SOFTWAREARG E:64 , TYR E:82 , HOH E:301binding site for residue PO4 E 201
13AD4SOFTWAREASN E:91 , ALA E:92 , ARG E:95binding site for residue PO4 E 202
14AD5SOFTWAREARG C:51 , GLN F:114 , GLY F:115 , THR F:116 , GLN F:117 , TYR H:111binding site for residue EPE F 201
15AD6SOFTWAREGLY D:48 , TYR D:109 , HIS F:128 , ARG G:51 , ARG G:64 , LYS G:84binding site for residue PO4 G 201
16AD7SOFTWARELYS G:49 , TYR G:82 , LYS G:84 , ASN G:85binding site for residue PDO G 202
17AD8SOFTWAREILE C:50 , VAL C:52 , GLY C:62 , SER C:63 , ILE C:65 , ILE C:81 , TYR C:82 , LYS C:84 , PO4 C:201 , LEU F:12 , EPE F:201binding site for Di-peptide ARG C 51 and ARG C 64

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1B:23 -B:97
2B:51 -B:103
3D:23 -D:97
4D:51 -D:103
5F:23 -F:97
6F:51 -F:103
7H:23 -H:97
8H:51 -H:103

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Cys B:103 -Pro B:104
2Cys D:103 -Pro D:104
3Cys F:103 -Pro F:104
4Cys H:103 -Pro H:104

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JA8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JA8)

(-) Exons   (0, 0)

(no "Exon" information available for 5JA8)

(-) 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:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeehhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.......eeeee.....eeeeeeee....eeeeeeee........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 5ja8 A   0 HMKSVFVESTIFEKYRDEYLSDEEYRLFQAELMLNPKLGDVIQGTGGLRKIRVASRGGSRIIYYFLDEKRRFYLLTIYGKNEMSDLNANQRKQLMAFMEAWRNEQ 109
                                     9        19        29        39        49    ||  64        74        84        94       104     
                                                                                 54|                                                 
                                                                                  60                                                 


Chain B from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee.......eeeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee...............eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ja8 B   2 QVQLQESGGGLVQPGGSLRLSCAASGFTLDYYAIGWFRQAPGKEREGVSCISSSGGTTNYADSVKGRFTVSRDNAKNTVYLQMNSLKPEDTAVYYCVADFACPLIREYDYWGQGTQVTVSS 122
                                    11        21        31        41        51        61        71        81        91       101       111       121 


Chain C from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeehhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.......eeeee.......eeeeeeee....eeeeeeee........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5ja8 C   0 HMKSVFVESTIFEKYRDEYLSDEEYRLFQAELMLNPKLGDVIQGTGGLRKIRVASKKRGGSRIIYYFLDEKRRFYLLTIYGKNEMSDLNANQRKQLMAFMEAWRNEQS 110
                                     9        19        29        39        49     || 62        72        82        92       102        
                                                                                  55|                                                   
                                                                                   59                                                   


Chain D from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee.......eeeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee...............eeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ja8 D   2 QVQLQESGGGLVQPGGSLRLSCAASGFTLDYYAIGWFRQAPGKEREGVSCISSSGGTTNYADSVKGRFTVSRDNAKNTVYLQMNSLKPEDTAVYYCVADFACPLIREYDYWGQGTQVTVSSHHHHHH 128
                                    11        21        31        41        51        61        71        81        91       101       111       121       


Chain E from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeehhhhhhhhhhhhhhhhhhhhhhhhhhh....ee......eeeeee......eeeeeeee....eeeeeeee........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 5ja8 E   0 HMKSVFVESTIFEKYRDEYLSDEEYRLFQAELMLNPKLGDVIQGTGGLRKIRVASKRGGSRIIYYFLDEKRRFYLLTIYGKNEMSDLNANQRKQLMAFMEAWRNEQS 110
                                     9        19        29        39        49     || 63        73        83        93       103       
                                                                                  55|                                                  
                                                                                   60                                                  


Chain F from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee.......eeeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee...............eeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ja8 F   2 QVQLQESGGGLVQPGGSLRLSCAASGFTLDYYAIGWFRQAPGKEREGVSCISSSGGTTNYADSVKGRFTVSRDNAKNTVYLQMNSLKPEDTAVYYCVADFACPLIREYDYWGQGTQVTVSSHHHHHH 128
                                    11        21        31        41        51        61        71        81        91       101       111       121       


Chain G from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeehhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.......eeeee....eeeeeeee....eeeeeeee........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 5ja8 G   0 HMKSVFVESTIFEKYRDEYLSDEEYRLFQAELMLNPKLGDVIQGTGGLRKIRVASGGSRIIYYFLDEKRRFYLLTIYGKNEMSDLNANQRKQLMAFMEAWRNEQS 110
                                     9        19        29        39        49    ||  65        75        85        95       105     
                                                                                 54|                                                 
                                                                                  61                                                 


Chain H from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee.......eeeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee...............eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ja8 H   2 QVQLQESGGGLVQPGGSLRLSCAASGFTLDYYAIGWFRQAPGKEREGVSCISSSGGTTNYADSVKGRFTVSRDNAKNTVYLQMNSLKPEDTAVYYCVADFACPLIREYDYWGQGTQVTVSSH 123
                                    11        21        31        41        51        61        71        81        91       101       111       121
   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 5JA8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JA8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JA8)

(-) Gene Ontology  (3, 3)

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  5ja8
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  HIGB2_VIBCH | Q9KMA6
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 Related Entries

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

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        HIGB2_VIBCH | Q9KMA6: 5ja9 5jaa 5mje

(-) Related Entries Specified in the PDB File

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