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(-) Description

Title :  CRYSTAL STRUCTURE OF HFQ IN COMPLEX WITH THE SRNA RYDC
 
Authors :  D. Dimastrogiovanni, K. S. Frohlich, H. A. Bruce, K. J. Bandyra, S. Hohe J. Vogel, B. F. Luisi
Date :  14 Oct 14  (Deposition) - 14 Jan 15  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.48
Chains :  Asym. Unit :  A,B,C,D,E,F,Q
Biol. Unit 1:  A,B,C,D,E,F,Q  (1x)
Keywords :  Rna Binding Protein-Rna Complex, Natively Unstructured Protein, Protein-Rna Recognition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Dimastrogiovanni, K. S. Frohlich, K. J. Bandyra, H. A. Bruce, S. Hohensee, J. Vogel, B. F. Luisi
Recognition Of The Small Regulatory Rna Rydc By The Bacterial Hfq Protein.
Elife V. 3 2014
PubMed-ID: 25551292  |  Reference-DOI: 10.7554/ELIFE.05375

(-) Compounds

Molecule 1 - RNA-BINDING PROTEIN HFQ
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEH-10-(HFQ)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Other Details: RNA-BINDING PROTEIN
    Strain: K-12
    Synonym: HF-1, HOST FACTOR-I PROTEIN, HF-I, HFQ
 
Molecule 2 - RYDC
    Chains: Q
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 90371
    Other Details: SMALL REGULATORY RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFQ
Biological Unit 1 (1x): ABCDEFQ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4V2S)

(-) Sites  (0, 0)

(no "Site" information available for 4V2S)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4V2S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4V2S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4V2S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4V2S)

(-) Exons   (0, 0)

(no "Exon" information available for 4V2S)

(-) 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:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee...eeeee...eeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4v2s A  4 GQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSNN 74
                                    13        23        33        43        53        63        73 


Chain B from PDB  Type:PROTEIN  Length:70
                                                                                                     
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee...eeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  4v2s B  1 MAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSH 70
                                    10        20        30        40        50        60        70


Chain C from PDB  Type:PROTEIN  Length:68
                                                                                                   
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee...eeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  4v2s C  3 KGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSH 70
                                    12        22        32        42        52        62        


Chain D from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh..eeeeee....eeeeeeeee...eeeee...eeeee...eeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4v2s D  2 AKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHS 72
                                    11        21        31        41        51        61        71 


Chain E from PDB  Type:PROTEIN  Length:67
                                                                                                  
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh..eeeeee....eeeeeeeee...eeeee...eeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  4v2s E  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
                                    14        24        34        44        54        64       


Chain F from PDB  Type:PROTEIN  Length:70
                                                                                                     
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee...eeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  4v2s F  2 AKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
                                    11        21        31        41        51        61        71


Chain Q from PDB  Type:DNA/RNA  Length:58
                                                                                         
                  4v2s Q  6 AUGUAGACCCGUCCCUUCGCCUGCGUCACGGGUCCUGGUUAGACGCAGGCGUUUUCUG 65
                                    15   ||   27        37        47        57        
                                        19|                                           
                                         22
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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 4V2S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4V2S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4V2S)

(-) Gene Ontology  (8, 8)

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  4v2s
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  HFQ_ECOLI | P0A6X3
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 Related Entries

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

UniProtKB/Swiss-Prot
        HFQ_ECOLI | P0A6X3: 1hk9 1m7c 1oou 1oov 2y90 2yht 3gib 3qhs 3qo3 3rer 3res 3vu3 4jri 4jrk 4juv 4rcb 4rcc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4V2S)