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(-) Description

Title :  STRUCTURE OF STAPHYLOCOCCUS AUREUS HFQ IN COMPLEX WITH A7 RNA
 
Authors :  R. Brennan, N. Horstmann, T. M. Link
Date :  21 Feb 11  (Deposition) - 12 Sep 12  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,M,N,P,R,S
Biol. Unit 1:  A,B,H,I,K,M,R  (1x)
Biol. Unit 2:  C,D,E,F,G,J,P  (1x)
Biol. Unit 3:  N,S  (3x)
Keywords :  Hexamer, Sm/Lsm Family, Rna Chaperone, Translational Regulator, Mrna, Srna, Cytoplasma, Chaperone-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Horstmann, J. Orans, P. Valentin-Hansen, S. A. Shelburne, R. G. Brennan
Structural Mechanism Of Staphylococcus Aureus Hfq Binding T An Rna A-Tract.
Nucleic Acids Res. V. 40 11023 2012
PubMed-ID: 22965117  |  Reference-DOI: 10.1093/NAR/GKS809

(-) Compounds

Molecule 1 - RNA CHAPERONE HFQ
    Chains: A, B, H, I, K, M, C, D, E, F, G, J, N, S
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB11
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ECTR2_1161, HFQ
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 889933
    Strain: SUBSP. AUREUS ECT-R 2
 
Molecule 2 - RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')
    Chains: R, P
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910111213141516
Asymmetric Unit : ABCDEFGHIJKMNPRS
Biological Unit 1 (1x): AB     HI KM  R 
Biological Unit 2 (1x):   CDEFG  J   P  
Biological Unit 3 (3x):             N  S

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 29)

Asymmetric Unit (1, 29)
No.NameCountTypeFull Name
1ZN29Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:53 , HOH A:134BINDING SITE FOR RESIDUE ZN A 78
02AC2SOFTWAREHIS A:58 , HOH A:82 , HOH A:83 , HOH A:84BINDING SITE FOR RESIDUE ZN A 79
03AC3SOFTWARELYS B:51 , HIS B:53BINDING SITE FOR RESIDUE ZN B 78
04AC4SOFTWAREHIS B:58 , HOH B:82 , HOH B:83 , HOH B:84BINDING SITE FOR RESIDUE ZN B 79
05AC5SOFTWAREHIS H:53BINDING SITE FOR RESIDUE ZN H 78
06AC6SOFTWAREHIS H:58 , HOH H:80 , HOH H:108 , A R:4 , HOH R:163BINDING SITE FOR RESIDUE ZN H 79
07AC7SOFTWAREHIS I:53 , HOH I:87 , HOH I:88 , HOH I:119BINDING SITE FOR RESIDUE ZN I 78
08AC8SOFTWAREHIS I:58 , HOH I:82 , HOH I:83 , HOH I:112BINDING SITE FOR RESIDUE ZN I 79
09AC9SOFTWAREHIS K:58 , HOH K:85 , HOH K:86 , HOH K:128 , HOH K:175BINDING SITE FOR RESIDUE ZN K 78
10BC1SOFTWAREHIS K:53BINDING SITE FOR RESIDUE ZN K 79
11BC2SOFTWARELYS M:51 , HIS M:53BINDING SITE FOR RESIDUE ZN M 78
12BC3SOFTWAREHIS M:58 , HOH M:82 , HOH M:83 , HOH M:84BINDING SITE FOR RESIDUE ZN M 79
13BC4SOFTWAREASP C:9BINDING SITE FOR RESIDUE ZN C 78
14BC5SOFTWAREHIS C:53 , HOH C:120 , HOH C:121BINDING SITE FOR RESIDUE ZN C 79
15BC6SOFTWAREHIS C:58 , HOH C:83 , HOH C:84 , HOH C:136BINDING SITE FOR RESIDUE ZN C 80
16BC7SOFTWAREGLN D:49 , HIS D:53BINDING SITE FOR RESIDUE ZN D 78
17BC8SOFTWAREHIS D:58 , HOH D:82 , HOH D:83 , HOH D:84BINDING SITE FOR RESIDUE ZN D 79
18BC9SOFTWAREHIS E:53BINDING SITE FOR RESIDUE ZN E 78
19CC1SOFTWAREHIS E:58 , HOH E:81 , HOH E:82BINDING SITE FOR RESIDUE ZN E 79
20CC2SOFTWAREHIS F:53BINDING SITE FOR RESIDUE ZN F 78
21CC3SOFTWAREHIS F:58 , HOH F:81 , HOH F:82 , HOH F:83BINDING SITE FOR RESIDUE ZN F 79
22CC4SOFTWAREHIS G:53 , HOH J:94 , HOH J:95 , HOH J:109BINDING SITE FOR RESIDUE ZN G 78
23CC5SOFTWAREHIS G:58 , HOH G:81 , HOH G:82 , HOH G:125BINDING SITE FOR RESIDUE ZN G 79
24CC6SOFTWAREHIS J:58 , HOH J:84 , HOH J:85 , HOH J:182BINDING SITE FOR RESIDUE ZN J 78
25CC7SOFTWAREHIS J:53BINDING SITE FOR RESIDUE ZN J 79
26CC8SOFTWAREHIS N:53BINDING SITE FOR RESIDUE ZN N 78
27CC9SOFTWAREHIS N:58 , HOH N:82 , HOH N:83 , HOH N:84 , HOH N:130BINDING SITE FOR RESIDUE ZN N 79
28DC1SOFTWARELYS S:51 , HIS S:53 , HOH S:89 , HOH S:133BINDING SITE FOR RESIDUE ZN S 78
29DC2SOFTWAREHIS S:58 , HOH S:82 , HOH S:83 , HOH S:84BINDING SITE FOR RESIDUE ZN S 79

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QSU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QSU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QSU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QSU)

(-) Exons   (0, 0)

(no "Exon" information available for 3QSU)

(-) 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:60
                                                                                           
               SCOP domains d3qsua_ A: Pleiotropic translational regulator Hfq           SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  3qsu A  6 NIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQHLIYKHAISTYTV 65
                                    15        25        35        45        55        65


Chain B from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains d3qsub_ B: Pleiotropic translational regulator Hfq            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
                  3qsu B  6 NIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQHLIYKHAISTYTVE 66
                                    15        25        35        45        55        65 


Chain C from PDB  Type:PROTEIN  Length:60
                                                                                           
               SCOP domains d3qsuc_ C: Pleiotropic translational regulator Hfq           SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...eeeee....eeeeeeeee...eeeeee..eeeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  3qsu C  6 NIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQHLIYKHAISTYTV 65
                                    15        25        35        45        55        65


Chain D from PDB  Type:PROTEIN  Length:62
                                                                                             
               SCOP domains d3qsud_ D: Pleiotropic translational regulator Hfq             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
                  3qsu D  5 ENIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQHLIYKHAISTYTVE 66
                                    14        24        34        44        54        64  


Chain E from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains d3qsue_ E: Pleiotropic translational regulator Hfq            SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3qsu E  5 ENIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQHLIYKHAISTYTV 65
                                    14        24        34        44        54        64 


Chain F from PDB  Type:PROTEIN  Length:60
                                                                                           
               SCOP domains d3qsuf_ F: Pleiotropic translational regulator Hfq           SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.eeeeee....eeeeeeeee...eeeee....eeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  3qsu F  6 NIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQHLIYKHAISTYTV 65
                                    15        25        35        45        55        65


Chain G from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains d3qsug_ G: Pleiotropic translational regulator Hfq            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
                  3qsu G  6 NIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQHLIYKHAISTYTVE 66
                                    15        25        35        45        55        65 


Chain H from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains d3qsuh_ H: Pleiotropic translational regulator Hfq            SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3qsu H  6 NIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQHLIYKHAISTYTVE 66
                                    15        25        35        45        55        65 


Chain I from PDB  Type:PROTEIN  Length:60
                                                                                           
               SCOP domains d3qsui_ I: Pleiotropic translational regulator Hfq           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
                  3qsu I  6 NIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQHLIYKHAISTYTV 65
                                    15        25        35        45        55        65


Chain J from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains d3qsuj_ J: Pleiotropic translational regulator Hfq            SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3qsu J  6 NIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQHLIYKHAISTYTVE 66
                                    15        25        35        45        55        65 


Chain K from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains d3qsuk_ K: Pleiotropic translational regulator Hfq            SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3qsu K  6 NIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQHLIYKHAISTYTVE 66
                                    15        25        35        45        55        65 


Chain M from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains d3qsum_ M: Pleiotropic translational regulator Hfq            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
                  3qsu M  5 ENIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQHLIYKHAISTYTV 65
                                    14        24        34        44        54        64 


Chain N from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains d3qsun_ N: Pleiotropic translational regulator Hfq            SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3qsu N  6 NIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQHLIYKHAISTYTVE 66
                                    15        25        35        45        55        65 


Chain P from PDB  Type:RNA  Length:4
                                   
                  3qsu P  5 AAAA  8


Chain R from PDB  Type:RNA  Length:4
                                   
                  3qsu R  1 AAAA  4


Chain S from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains d3qsus_ S: Pleiotropic translational regulator Hfq            SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh...eeee....eee..eeee...eeeeee..eeeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3qsu S  6 NIQDKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQGKQHLIYKHAISTYTVE 66
                                    15        25        35        45        55        65
   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  (1, 14)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QSU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QSU)

(-) Gene Ontology  (0, 0)

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  3qsu
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 Related Entries

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(-) Related Entries Specified in the PDB File

1kq1 1.55A CRYSTAL STRUCTURE OF THE PLEIOTROPIC TRANSLATIONAL REGULATOR, HFQ
1kq2 CRYSTAL STRUCTURE OF AN HFQ-RNA COMPLEX
3gib CRYSTAL STRUCTURE OF THE COMPLEX OF THE E.COLI HFQ WITH POLY(A)
3hsb CRYSTAL STRUCTURE OF YMAH (HFQ) FROM BACILLUS SUBTILIS IN COMPLEX WITH AN RNA APTAMER