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(-) Description

Title :  STRUCTURE OF CAULOBACTER CRESCENTUS VAPBC1 (APO 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 :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (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
    Engineered: YES
    Expression System: ESCHERICHIA COLI B
    Expression System Plasmid: PKW912HB
    Expression System Taxid: 37762
    Expression System Variant: B834(DE3)
    Gene: CC_0032
    Organism Scientific: CAULOBACTER CRESCENTUS
    Organism Taxid: 190650
    Strain: ATCC 19089 / CB15
 
Molecule 2 - RIBONUCLEASE VAPC
    Chains: B, C
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI B
    Expression System Plasmid: PKW912HB
    Expression System Taxid: 37762
    Expression System Variant: B834(DE3)
    Gene: VAPC, CC_0031
    Organism Scientific: CAULOBACTER CRESCENTUS
    Organism Taxid: 190650
    Strain: ATCC 19089 / CB15
    Synonym: RNASE VAPC,TOXIN VAPC

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL B:68 , ASP B:70 , HOH B:339 , HOH B:384 , ASP C:72 , GLY C:73 , GLY D:37 , HOH D:108binding site for residue GOL B 201
2AC2SOFTWARETYR B:3 , LEU B:27 , ASN B:28 , THR C:108 , LEU C:125 , HOH C:348 , HOH C:392binding site for residue GOL C 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K8J)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly D:12 -Asn D:13

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K8J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K8J)

(-) Exons   (0, 0)

(no "Exon" information available for 5K8J)

(-) 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:80
                                                                                                                
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.ee....eeeee...........eeeeee..eeeeee...hhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 5k8j A   0 HHARATGKTFRSGNSEAVRLPRDLAFGADVELTLIRSGDVLTIYPSKGSIADLVATLNQmPRPDSVEIRDEDLFPERPGL  79
                                     9        19        29        39        49        59        69        79
                                                                                      59-MSE                


Chain B from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.ee..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee.hhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k8j B   2 AYVLDTNVAIHLRDGDPEVTTRVTALNGAILLSIISRVELEGGVYREAAQAGLRRSRLDVmLKVLPVLDFDGAAADEYRRIVESAGYSRRKVVDRmIAAQALAHRATFVTFNADDFRDIPGLSLLAW 128
                                    11        21        31        41        51        61|       71        81        91     | 101       111       121       
                                                                                       62-MSE                             97-MSE                           


Chain C from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhh.hhhhhhhhh.....eeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhh.ee..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.eeee.hhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k8j C   2 AYVLDTNVAIHLRDGDPEVTTRVTALNGAILLSIISRVELEGGVYREAAQAGLRRSRLDVmLKVLPVLDFDGAAADEYRRIVESAGYSRRKVVDRmIAAQALAHRATFVTFNADDFRDIPGLSLLAW 128
                                    11        21        31        41        51        61|       71        81        91     | 101       111       121       
                                                                                       62-MSE                             97-MSE                           


Chain D from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..ee....eeeee..........eeeeeee..eeeeee...hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 5k8j D  -4 HHHHHHARATGKTFRSGNSEAVRLPRDLAFGADVELTLIRSGDVLTIYPSKGSIADLVATLNQmPRPD  63
                                     5        15        25        35        45        55   |    
                                                                                          59-MSE
   Legend:   → Mismatch (orange background)
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  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 5K8J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K8J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K8J)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q9AC34_CAUCR | Q9AC34: 5l6l 5l6m
        Q9AC35_CAUCR | Q9AC35: 5l6l 5l6m

(-) Related Entries Specified in the PDB File

5l6l CONTAINS A DNA-BOUND FORM OF THE VAPBC COMPLEX
5l6m CONTAINS A MUTATED VERSION OF THE APO, VAPBC COMPLEX