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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HFQ PROTEIN FROM ESCHERICHIA COLI
 
Authors :  C. Sauter, J. Basquin, D. Suck
Date :  06 Mar 03  (Deposition) - 24 Jul 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Rna-Binding Protein, Sm-Like, Pleiotropic Regulator, Rna Binding Protein, Rna Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Sauter, J. Basquin, D. Suck
Sm-Like Proteins In Eubacteria: The Crystal Structure Of The Hfq Protein From Escherichia Coli
Nucleic Acids Res. V. 31 4091 2003
PubMed-ID: 12853626  |  Reference-DOI: 10.1093/NAR/GKG480
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN HFQ
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET24D
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-72
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: C-TERMINAL RESIDUES 73-102 DELETED
    Other Details - Source: SYNTHETIC GENE
    Synonym: HOST FACTOR-I PROTEIN, HF-1, HF-I

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1HK9)

(-) Sites  (0, 0)

(no "Site" information available for 1HK9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HK9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HK9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HK9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HK9)

(-) Exons   (0, 0)

(no "Exon" information available for 1HK9)

(-) Sequences/Alignments

Asymmetric/Biological 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:65
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:65
                                    15        25        35        45        55        65     
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSH 70
               SCOP domains d1hk9a_ A: Pleiotropic translational regulator Hfq                SCOP domains
               CATH domains 1hk9A00 A:6-70  [code=2.30.30.100, no name defined]               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
                  1hk9 A  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSH 70
                                    15        25        35        45        55        65     


Chain B from PDB  Type:PROTEIN  Length:64
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:64
                                    15        25        35        45        55        65    
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVS 69
               SCOP domains d1hk9b_ B: Pleiotropic translational regulator Hfq               SCOP domains
               CATH domains 1hk9B00 B:6-69  [code=2.30.30.100, no name defined]              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
                  1hk9 B  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVS 69
                                    15        25        35        45        55        65    


Chain C from PDB  Type:PROTEIN  Length:64
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:64
                                    15        25        35        45        55        65    
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVS 69
               SCOP domains d1hk9c_ C: Pleiotropic translational regulator Hfq               SCOP domains
               CATH domains 1hk9C00 C:6-69  [code=2.30.30.100, no name defined]              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
                  1hk9 C  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVS 69
                                    15        25        35        45        55        65    


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

    Alignment length:67
                                    13        23        33        43        53        63       
             HFQ_ECOLI    4 GQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSH 70
               SCOP domains d1hk9d_ D: Pleiotropic translational regulator Hfq                  SCOP domains
               CATH domains 1hk9D00 D:4-70  [code=2.30.30.100, no name defined]                 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
                  1hk9 D  4 GQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSH 70
                                    13        23        33        43        53        63       


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

    Alignment length:68
                                    13        23        33        43        53        63        
             HFQ_ECOLI    4 GQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
               SCOP domains d1hk9e_ E: Pleiotropic translational regulator Hfq                   SCOP domains
               CATH domains 1hk9E00 E:4-71  [code=2.30.30.100, no name defined]                  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
                  1hk9 E  4 GQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHH 71
                                    13        23        33        43        53        63        


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

    Alignment length:66
                                    16        26        36        46        56        66      
             HFQ_ECOLI    7 LQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHS 72
               SCOP domains d1hk9f_ F: Pleiotropic translational regulator Hfq                 SCOP domains
               CATH domains 1hk9F00 F:7-72  [code=2.30.30.100, no name defined]                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
                  1hk9 F  7 LQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHS 72
                                    16        26        36        46        56        66
   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, 6)

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

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HK9)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (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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  1hk9
    Family and Domain Information: ProDom | SYSTERS
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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: 1m7c 1oou 1oov 2y90 2yht 3gib 3qhs 3qo3 3rer 3res 3vu3 4jri 4jrk 4juv 4rcb 4rcc 4v2s

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1HK9)