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(-) Description

Title :  CRYSTAL STRUCTURE OF LISTERIA MONOCYTOGENES HFQ IN COMPLEX WITH U6 RNA
 
Authors :  A. R. Kovach, R. G Brennan
Date :  13 Nov 13  (Deposition) - 10 Sep 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,R,Z
Biol. Unit 1:  A,B,D,G,H,J,R  (1x)
Biol. Unit 2:  C,E,F,I,K,L,Z  (1x)
Keywords :  Lsm/Sm Proteins, Rna Chaperone, Srna, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Kovach, K. E. Hoff, J. T. Canty, J. Orans, R. G. Brennan
Recognition Of U-Rich Rna By Hfq From The Gram-Positive Pathogen Listeria Monocytogenes.
Rna V. 20 1548 2014
PubMed-ID: 25150227  |  Reference-DOI: 10.1261/RNA.044032.113

(-) Compounds

Molecule 1 - PROTEIN HFQ
    Chains: D, A, B, C, E, F, J, G, H, I, K, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HFQ, LMHCC_1277
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 1639
 
Molecule 2 - 5'-R(*UP*UP*UP*UP*UP*U)-3'
    Chains: R, Z
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234567891011121314
Asymmetric Unit : ABCDEFGHIJKLRZ
Biological Unit 1 (1x): AB D  GH J  R 
Biological Unit 2 (1x):   C EF  I KL Z

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4NL3)

(-) Sites  (0, 0)

(no "Site" information available for 4NL3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NL3)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln E:3 -Gly E:4
2Gly I:5 -Gln I:6
3Gln K:3 -Gly K:4

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NL3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NL3)

(-) Exons   (0, 0)

(no "Exon" information available for 4NL3)

(-) 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:72
                                                                                                       
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh...eeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                  4nl3 A  2 KQGGQGLQDYYLNQLRKEKILATVFLTNGFQLRGRVVSFDNFTVLLDVEGKQQLVFKHAISTFSPQKNVALN 73
                                    11        21        31        41        51        61        71  


Chain B from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4nl3 B  2 KQGGQGLQDYYLNQLRKEKILATVFLTNGFQLRGRVVSFDNFTVLLDVEGKQQLVFKHAISTFSPQKNVAL 72
                                    11        21        31        41        51        61        71 


Chain C from PDB  Type:PROTEIN  Length:74
                                                                                                         
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  4nl3 C  1 MKQGGQGLQDYYLNQLRKEKILATVFLTNGFQLRGRVVSFDNFTVLLDVEGKQQLVFKHAISTFSPQKNVALNP 74
                                    10        20        30        40        50        60        70    


Chain D from PDB  Type:PROTEIN  Length:73
                                                                                                        
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  4nl3 D  1 MKQGGQGLQDYYLNQLRKEKILATVFLTNGFQLRGRVVSFDNFTVLLDVEGKQQLVFKHAISTFSPQKNVALN 73
                                    10        20        30        40        50        60        70   


Chain E from PDB  Type:PROTEIN  Length:72
                                                                                                       
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh...eeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                  4nl3 E  2 KQGGQGLQDYYLNQLRKEKILATVFLTNGFQLRGRVVSFDNFTVLLDVEGKQQLVFKHAISTFSPQKNVALN 73
                                    11        21        31        41        51        61        71  


Chain F from PDB  Type:PROTEIN  Length:75
                                                                                                          
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  4nl3 F  1 MKQGGQGLQDYYLNQLRKEKILATVFLTNGFQLRGRVVSFDNFTVLLDVEGKQQLVFKHAISTFSPQKNVALNPD 75
                                    10        20        30        40        50        60        70     


Chain G from PDB  Type:PROTEIN  Length:73
                                                                                                        
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh...eeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  4nl3 G  1 MKQGGQGLQDYYLNQLRKEKILATVFLTNGFQLRGRVVSFDNFTVLLDVEGKQQLVFKHAISTFSPQKNVALN 73
                                    10        20        30        40        50        60        70   


Chain H from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh...eeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4nl3 H  2 KQGGQGLQDYYLNQLRKEKILATVFLTNGFQLRGRVVSFDNFTVLLDVEGKQQLVFKHAISTFSPQKNVAL 72
                                    11        21        31        41        51        61        71 


Chain I from PDB  Type:PROTEIN  Length:74
                                                                                                         
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh...eeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  4nl3 I  1 MKQGGQGLQDYYLNQLRKEKILATVFLTNGFQLRGRVVSFDNFTVLLDVEGKQQLVFKHAISTFSPQKNVALNP 74
                                    10        20        30        40        50        60        70    


Chain J from PDB  Type:PROTEIN  Length:73
                                                                                                        
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  4nl3 J  1 MKQGGQGLQDYYLNQLRKEKILATVFLTNGFQLRGRVVSFDNFTVLLDVEGKQQLVFKHAISTFSPQKNVALN 73
                                    10        20        30        40        50        60        70   


Chain K from PDB  Type:PROTEIN  Length:73
                                                                                                        
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  4nl3 K  1 MKQGGQGLQDYYLNQLRKEKILATVFLTNGFQLRGRVVSFDNFTVLLDVEGKQQLVFKHAISTFSPQKNVALN 73
                                    10        20        30        40        50        60        70   


Chain L from PDB  Type:PROTEIN  Length:74
                                                                                                         
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  4nl3 L  1 MKQGGQGLQDYYLNQLRKEKILATVFLTNGFQLRGRVVSFDNFTVLLDVEGKQQLVFKHAISTFSPQKNVALNP 74
                                    10        20        30        40        50        60        70    


Chain R from PDB  Type:RNA  Length:6
                                     
                  4nl3 R 17 UUUUUU 22


Chain Z from PDB  Type:RNA  Length:6
                                     
                  4nl3 Z 27 UUUUUU 32
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4NL3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NL3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NL3)

(-) Gene Ontology  (2, 2)

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4nl2