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(-) Description

Title :  CRYSTAL STRUCTURE OF FULL-LENGTH HFQ FROM ESCHERICHIA COLI
 
Authors :  M. Beich-Frandsen, B. Vecerek, B. Sjoeblom, U. Blaesi, K. Djinovic-Ca
Date :  26 Jan 11  (Deposition) - 18 May 11  (Release) - 18 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  G,H,I,J,K,L  (1x)
Keywords :  Rna Binding Protein, Sm-Like, Pleiotropic Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Beich-Frandsen, B. Vecerek, B. Sjoblom, U. Blasi, K. Djinovic-Carugo
Structural Analysis Of Full-Length Hfq From Escherichia Col
Acta Crystallogr. , Sect. F V. 67 536 2011
PubMed-ID: 21543856  |  Reference-DOI: 10.1107/S174430911100786X

(-) Compounds

Molecule 1 - PROTEIN HFQ
    Chains: A, B, C, D, E, F, G, H, I, J, K, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC19
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B4172, HFQ, JW4130
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: HF-1, HOST FACTOR-I PROTEIN, HF-I

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCDEF      
Biological Unit 2 (1x):       GHIJKL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3QHS)

(-) Sites  (0, 0)

(no "Site" information available for 3QHS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln G:5 -Ser G:6
2Gln I:5 -Ser I:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QHS)

(-) 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:67
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:67
                                    14        24        34        44        54        64       
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
               SCOP domains d3qhsa_ A: automated matches                                        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
                  3qhs A  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
                                    14        24        34        44        54        64       


Chain B from PDB  Type:PROTEIN  Length:69
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:69
                                    14        24        34        44        54        64         
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSN 73
               SCOP domains d3qhsb_ B: automated matches                                          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
                  3qhs B  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSN 73
                                    14        24        34        44        54        64         


Chain C from PDB  Type:PROTEIN  Length:70
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:70
                                    13        23        33        43        53        63        73
             HFQ_ECOLI    4 GQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSN 73
               SCOP domains d3qhsc_ C: automated matches                                           SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee...eeeee...eeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  3qhs C  4 GQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSN 73
                                    13        23        33        43        53        63        73


Chain D from PDB  Type:PROTEIN  Length:68
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:68
                                    14        24        34        44        54        64        
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHS 72
               SCOP domains d3qhsd_ D: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee...eeeee...eeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  3qhs D  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHS 72
                                    14        24        34        44        54        64        


Chain E from PDB  Type:PROTEIN  Length:67
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:67
                                    14        24        34        44        54        64       
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
               SCOP domains d3qhse_ E: automated matches                                        SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eeeee....eeeeeeeee...eeeee...eeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  3qhs E  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
                                    14        24        34        44        54        64       


Chain F from PDB  Type:PROTEIN  Length:68
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:68
                                    14        24        34        44        54        64        
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHS 72
               SCOP domains d3qhsf_ F: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eeeee....eeeeeeeee...eeeee...eeeee...eeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  3qhs F  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHS 72
                                    14        24        34        44        54        64        


Chain G from PDB  Type:PROTEIN  Length:67
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:67
                                    14        24        34        44        54        64       
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
               SCOP domains d3qhsg_ G: automated matches                                        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
                  3qhs G  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
                                    14        24        34        44        54        64       


Chain H from PDB  Type:PROTEIN  Length:66
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:66
                                    15        25        35        45        55        65      
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
               SCOP domains d3qhsh_ H: automated matches                                       SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee.......eeeeee...eeeee...eeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  3qhs H  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
                                    15        25        35        45        55        65      


Chain I from PDB  Type:PROTEIN  Length:67
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:67
                                    14        24        34        44        54        64       
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
               SCOP domains d3qhsi_ I: automated matches                                        SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee...eeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  3qhs I  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
                                    14        24        34        44        54        64       


Chain J from PDB  Type:PROTEIN  Length:66
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:66
                                    15        25        35        45        55        65      
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
               SCOP domains d3qhsj_ J: automated matches                                       SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...eeeee....eeeeee......eeeee...eeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  3qhs J  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
                                    15        25        35        45        55        65      


Chain K from PDB  Type:PROTEIN  Length:69
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:69
                                    15        25        35        45        55        65         
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSNN 74
               SCOP domains d3qhsk_ K: automated matches                                          SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee...eeeee...eeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  3qhs K  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSNN 74
                                    15        25        35        45        55        65         


Chain L from PDB  Type:PROTEIN  Length:68
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:68
                                    14        24        34        44        54        64        
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHS 72
               SCOP domains d3qhsl_ L: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----LSM-3qhsL01 L:10-64                                    -------- Pfam domains (1)
           Pfam domains (2) -----LSM-3qhsL02 L:10-64                                    -------- Pfam domains (2)
           Pfam domains (3) -----LSM-3qhsL03 L:10-64                                    -------- Pfam domains (3)
           Pfam domains (4) -----LSM-3qhsL04 L:10-64                                    -------- Pfam domains (4)
           Pfam domains (5) -----LSM-3qhsL05 L:10-64                                    -------- Pfam domains (5)
           Pfam domains (6) -----LSM-3qhsL06 L:10-64                                    -------- Pfam domains (6)
           Pfam domains (7) -----LSM-3qhsL07 L:10-64                                    -------- Pfam domains (7)
           Pfam domains (8) -----LSM-3qhsL08 L:10-64                                    -------- Pfam domains (8)
           Pfam domains (9) -----LSM-3qhsL09 L:10-64                                    -------- Pfam domains (9)
          Pfam domains (10) -----LSM-3qhsL10 L:10-64                                    -------- Pfam domains (10)
          Pfam domains (11) -----LSM-3qhsL11 L:10-64                                    -------- Pfam domains (11)
          Pfam domains (12) -----LSM-3qhsL12 L:10-64                                    -------- Pfam domains (12)
         Sec.struct. author ..hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee...eeeee...eeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  3qhs L  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHS 72
                                    14        24        34        44        54        64
   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  (1, 12)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 12)

Asymmetric Unit
(-)
Clan: Sm-like (17)
(-)
Family: LSM (13)
(-)
Escherichia coli (strain K12) (1)
1aLSM-3qhsL01L:10-64
1bLSM-3qhsL02L:10-64
1cLSM-3qhsL03L:10-64
1dLSM-3qhsL04L:10-64
1eLSM-3qhsL05L:10-64
1fLSM-3qhsL06L:10-64
1gLSM-3qhsL07L:10-64
1hLSM-3qhsL08L:10-64
1iLSM-3qhsL09L:10-64
1jLSM-3qhsL10L:10-64
1kLSM-3qhsL11L:10-64
1lLSM-3qhsL12L:10-64

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J,K,L   (HFQ_ECOLI | P0A6X3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003681    bent DNA binding    Interacting selectively and non-covalently with DNA in a bent conformation.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0040033    negative regulation of translation, ncRNA-mediated    Any process, mediated by small non-coding RNAs, that stops, prevents or reduces the rate that mRNAs are effectively translated into protein.
    GO:0045975    positive regulation of translation, ncRNA-mediated    Any process, mediated by small non-coding RNAs, that activates or increases the rate that mRNAs are effectively translated into protein.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  Cis Peptide Bonds
    Gln G:5 - Ser G:6   [ RasMol ]  
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  3qhs
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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 3qo3 3rer 3res 3vu3 4jri 4jrk 4juv 4rcb 4rcc 4v2s

(-) Related Entries Specified in the PDB File

3qo3