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(-) Description

Title :  STRUCTURE OF CAULOBACTER CRESCENTUS VAPBC1 (VAPB1DELTAC:VAPC1 FORM)
 
Authors :  K. L. Bendtsen, K. Xu, M. Luckmann, D. E. Brodersen
Date :  30 May 16  (Deposition) - 28 Dec 16  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D,E,F,G,H  (1x)
Biol. Unit 2:  I,J,K,L  (2x)
Keywords :  Pin Domain, Toxin-Antitoxin, Ribonuclease, Dna-Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. L. Bendtsen, K. Xu, M. Luckmann, K. S. Winther, S. A. Shah, C. N. S. Pedersen, D. E. Brodersen
Toxin Inhibition In C. Crescentus Vapbc1 Is Mediated By A Flexible Pseudo-Palindromic Protein Motif And Modulated By Dna Binding.
Nucleic Acids Res. V. 45 2875 2017
PubMed-ID: 27998932  |  Reference-DOI: 10.1093/NAR/GKW1266

(-) Compounds

Molecule 1 - VAPB FAMILY PROTEIN
    Chains: A, D, E, H, I, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: CC_0032
    Organism Scientific: CAULOBACTER CRESCENTUS (STRAIN ATCC 19089 / CB15)
    Organism Taxid: 190650
    Strain: ATCC 19089 / CB15
 
Molecule 2 - RIBONUCLEASE VAPC
    Chains: B, C, F, G, J, K
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: VAPC, CC_0031
    Organism Scientific: CAULOBACTER CRESCENTUS (STRAIN ATCC 19089 / CB15)
    Organism Taxid: 190650
    Strain: ATCC 19089 / CB15
    Synonym: RNASE VAPC,TOXIN VAPC

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCDEFGH    
Biological Unit 2 (2x):         IJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MLI3Ligand/IonMALONATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MLI3Ligand/IonMALONATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MLI-1Ligand/IonMALONATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:43 , GLY A:47 , SER A:48 , ILE A:49 , HOH A:203 , ILE B:31 , LEU B:66 , PRO B:67 , ARG D:3 , HOH D:104binding site for residue MLI A 101
2AC2SOFTWAREVAL B:68 , ASP B:70 , HOH B:326 , ASP C:72 , GLY C:73 , ASP D:38binding site for residue GOL B 201
3AC3SOFTWAREILE C:11 , ARG C:14 , GLU C:40 , LEU C:41 , GLY C:44 , ARG C:47 , HOH C:304 , GLU H:66 , ILE H:67 , ARG H:68 , ASP H:69 , HOH H:102binding site for residue MLI C 201
4AC4SOFTWAREGLU D:66 , ILE D:67 , ASP D:69 , ILE G:11 , ARG G:14 , GLU G:40 , LEU G:41 , GLY G:44 , ARG G:47 , HOH G:311binding site for residue MLI G 201
5AC5SOFTWAREHIS I:0 , VAL J:68 , ASP J:70 , HOH J:322 , HOH J:323 , ASP K:72 , GLY K:73 , ASP L:38 , HOH L:109binding site for residue GOL J 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L6M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5L6M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L6M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L6M)

(-) Exons   (0, 0)

(no "Exon" information available for 5L6M)

(-) 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:66
                                                                                                  
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.eee..eeeeee...........eeeeee..eeeeee...hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 5l6m A   2 ARATGKTFRSGNSEAVRLPRDLAFGADVELTLIRSGDVLTIYPSKGSIADLVATLNQMPRPDSVEI  67
                                    11        21        31        41        51        61      


Chain B from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee.hhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l6m B   2 AYVLDTNVAIHLRDGDPEVTTRVTALNGAILLSIISRVELEGGVYREAAQAGLRRSRLDVMLKVLPVLDFDGAAADEYRRIVESAGYSRRKVVDRMIAAQALAHRATFVTFNADDFRDIPGLSLLAW 128
                                    11        21        31        41        51        61        71        81        91       101       111       121       


Chain C from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhh.hhhhhhhhhh....eeeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.ee..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee.hhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l6m C   2 AYVLDTNVAIHLRDGDPEVTTRVTALNGAILLSIISRVELEGGVYREAAQAGLRRSRLDVMLKVLPVLDFDGAAADEYRRIVESAGYSRRKVVDRMIAAQALAHRATFVTFNADDFRDIPGLSLLAW 128
                                    11        21        31        41        51        61        71        81        91       101       111       121       


Chain D from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee..eeeeee..........eeeeeee..eeeeee...hhhhhhhhhhhh........hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 5l6m D   2 ARATGKTFRSGNSEAVRLPRDLAFGADVELTLIRSGDVLTIYPSKGSIADLVATLNQMPRPDSVEIRDEDL  72
                                    11        21        31        41        51        61        71 


Chain E from PDB  Type:PROTEIN  Length:66
                                                                                                  
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.eee..eeeeeehhhhh......eeeeee..eeeeee.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 5l6m E  -1 HHHARATGKTFRSGNSEAVRLPRDLAFGADVELTLIRSGDVLTIYPSKGSIADLVATLNQMPRPDS  64
                                     8        18        28        38        48        58      


Chain F from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhh.hhhhhhhhhhh...eeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.ee..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee.hhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l6m F   2 AYVLDTNVAIHLRDGDPEVTTRVTALNGAILLSIISRVELEGGVYREAAQAGLRRSRLDVMLKVLPVLDFDGAAADEYRRIVESAGYSRRKVVDRMIAAQALAHRATFVTFNADDFRDIPGLSLLAW 128
                                    11        21        31        41        51        61        71        81        91       101       111       121       


Chain G from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhh.hhhhhhhhhh....eeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.ee..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..eeee.hhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l6m G   2 AYVLDTNVAIHLRDGDPEVTTRVTALNGAILLSIISRVELEGGVYREAAQAGLRRSRLDVMLKVLPVLDFDGAAADEYRRIVESAGYSRRKVVDRMIAAQALAHRATFVTFNADDFRDIPGLSLLAW 128
                                    11        21        31        41        51        61        71        81        91       101       111       121       


Chain H from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee..eeeeeehhhhh.....eeeeeee..eeeeee...hhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 5l6m H   1 HARATGKTFRSGNSEAVRLPRDLAFGADVELTLIRSGDVLTIYPSKGSIADLVATLNQMPRPDSVEIRDE  70
                                    10        20        30        40        50        60        70


Chain I from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.eee..eeeeeehhhhh.....eeeeeee..eeeeee...hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 5l6m I  -1 HHHARATGKTFRSGNSEAVRLPRDLAFGADVELTLIRSGDVLTIYPSKGSIADLVATLNQMPRPDSVE  66
                                     8        18        28        38        48        58        


Chain J from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eeee.hhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l6m J   2 AYVLDTNVAIHLRDGDPEVTTRVTALNGAILLSIISRVELEGGVYREAAQAGLRRSRLDVMLKVLPVLDFDGAAADEYRRIVESAGYSRRKVVDRMIAAQALAHRATFVTFNADDFRDIPGLSLLAW 128
                                    11        21        31        41        51        61        71        81        91       101       111       121       


Chain K from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhh.hhhhhhhhhh....eeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.ee..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee.............eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l6m K   2 AYVLDTNVAIHLRDGDPEVTTRVTALNGAILLSIISRVELEGGVYREAAQAGLRRSRLDVMLKVLPVLDFDGAAADEYRRIVESAGYSRRKVVDRMIAAQALAHRATFVTFNADDFRDIPGLSLLAW 128
                                    11        21        31        41        51        61        71        81        91       101       111       121       


Chain L from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeee..........eeeeeee..eeeeee...hhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 5l6m L   1 HARATGKTFRSGNSEAVRLPRDLAFGADVELTLIRSGDVLTIYPSKGSIADLVATLNQMPRPDSVEIRDE  70
                                    10        20        30        40        50        60        70
   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 5L6M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L6M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L6M)

(-) Gene Ontology  (8, 8)

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 Related Entries

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

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        Q9AC34_CAUCR | Q9AC34: 5k8j 5l6l
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(-) Related Entries Specified in the PDB File

5k8j NON-TRUNCATED, APO FORM OF THE VAPBC HALF TAIL COMPLEX
5l6l NON-TRUNCATED, DNA-BOUND FORM OF THE VAPBC HALF TAIL COMPLEX