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(-) Description

Title :  CRYSTAL STRUCTURE OF HFQ RIBOREGULATOR FROM E. COLI (P1 SPACE GROUP)
 
Authors :  J. Basquin, C. Sauter
Date :  06 May 11  (Deposition) - 16 Nov 11  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
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 :  Chaperone, Rna Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Bonnefond, P. Schellenberger, J. Basquin, G. Demangeat, C. Ritzenthaler, R. Chenevert, C. Balg, M. Frugier, J. Rudinger-Thirion, R. Giege, B. Lorber, C. Sauter
Exploiting Protein Engineering And Crystal Polymorphism For Successful X-Ray Structure Determination
Cryst. Growth Des. V. 11 4334 2011
PubMed: search  |  Reference-DOI: 10.1021/CG101468P
(for further references see the PDB file header)

(-) 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 Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector: PETM11
    Expression System Vector Type: PLASMID
    Fragment: SM-LIKE FOLD, RESIDUES 1-72
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    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 2YHT)

(-) Sites  (0, 0)

(no "Site" information available for 2YHT)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YHT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YHT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YHT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YHT)

(-) Exons   (0, 0)

(no "Exon" information available for 2YHT)

(-) 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:63
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:63
                                    15        25        35        45        55        65   
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
               SCOP domains d2yhta_ A: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  2yht A  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
                                    15        25        35        45        55        65   


Chain B from PDB  Type:PROTEIN  Length:63
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:63
                                    15        25        35        45        55        65   
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
               SCOP domains d2yhtb_ B: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  2yht B  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
                                    15        25        35        45        55        65   


Chain C from PDB  Type:PROTEIN  Length:63
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:63
                                    15        25        35        45        55        65   
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
               SCOP domains d2yhtc_ C: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  2yht C  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
                                    15        25        35        45        55        65   


Chain D from PDB  Type:PROTEIN  Length:63
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:63
                                    15        25        35        45        55        65   
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
               SCOP domains d2yhtd_ D: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  2yht D  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
                                    15        25        35        45        55        65   


Chain E from PDB  Type:PROTEIN  Length:63
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:63
                                    15        25        35        45        55        65   
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
               SCOP domains d2yhte_ E: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  2yht E  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
                                    15        25        35        45        55        65   


Chain F from PDB  Type:PROTEIN  Length:63
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:63
                                    15        25        35        45        55        65   
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
               SCOP domains d2yhtf_ F: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  2yht F  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
                                    15        25        35        45        55        65   


Chain G from PDB  Type:PROTEIN  Length:63
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:63
                                    15        25        35        45        55        65   
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
               SCOP domains d2yhtg_ G: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  2yht G  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
                                    15        25        35        45        55        65   


Chain H from PDB  Type:PROTEIN  Length:63
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:63
                                    15        25        35        45        55        65   
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
               SCOP domains d2yhth_ H: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  2yht H  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
                                    15        25        35        45        55        65   


Chain I from PDB  Type:PROTEIN  Length:63
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:63
                                    15        25        35        45        55        65   
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
               SCOP domains d2yhti_ I: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  2yht I  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
                                    15        25        35        45        55        65   


Chain J from PDB  Type:PROTEIN  Length:63
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:63
                                    15        25        35        45        55        65   
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
               SCOP domains d2yhtj_ J: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  2yht J  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
                                    15        25        35        45        55        65   


Chain K from PDB  Type:PROTEIN  Length:63
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:63
                                    15        25        35        45        55        65   
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
               SCOP domains d2yhtk_ K: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  2yht K  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
                                    15        25        35        45        55        65   


Chain L from PDB  Type:PROTEIN  Length:63
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:63
                                    15        25        35        45        55        65   
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
               SCOP domains d2yhtl_ L: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  2yht L  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
                                    15        25        35        45        55        65
   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 2YHT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YHT)

(-) 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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 Databases and Analysis Tools

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  2yht
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
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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 3gib 3qhs 3qo3 3rer 3res 3vu3 4jri 4jrk 4juv 4rcb 4rcc 4v2s

(-) Related Entries Specified in the PDB File

1hk9 CRYSTAL STRUCTURE OF THE HFQ PROTEIN FROM ESCHERICHIA COLI
1m7c STUCTURAL MODEL OF E. COLI HFQ
1oou STRUCTURAL MODELLING OF E. COLI HFQ
1oov COMPLEX OF E. COLI HFQ WITH A RA7 OLIGONUCLEOTIDE
2y90 CRYSTAL STRUCTURE OF HFQ RIBOREGULATOR FROM E. COLI ( P6 SPACE GROUP)