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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF THE E. COLI HFQ WITH POLY(A)
 
Authors :  T. M. Link, P. Valentin-Hansen, R. G. Brennan
Date :  05 Mar 09  (Deposition) - 17 Nov 09  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,H
Biol. Unit 1:  A,B,C,H  (2x)
Keywords :  Rna Binding Protein, Hfq-Rna Complex, Degradosome Component, Dna- Binding, Rna-Binding, Stress Response, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. M. Link, P. Valentin-Hansen, R. G. Brennan
Structure Of Escherichia Coli Hfq Bound To Polyriboadenylat Rna
Proc. Natl. Acad. Sci. Usa V. 106 19292 2009
PubMed-ID: 19889981  |  Reference-DOI: 10.1073/PNAS.0908744106

(-) Compounds

Molecule 1 - PROTEIN HFQ
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTYB11
    Expression System StrainBL21 NULL HFQ
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL FRAGMENT (2-69)
    GeneB4172, HFQ, JW4130
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK-12
    SynonymHOST FACTOR-I PROTEIN, HF-I, HF-1
 
Molecule 2 - 5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
    ChainsH
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCH
Biological Unit 1 (2x)ABCH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NHE3Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1NHE6Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:57BINDING SITE FOR RESIDUE NHE A 70
2AC2SOFTWAREHIS A:57 , LYS C:56BINDING SITE FOR RESIDUE NHE A 71
3AC3SOFTWAREHIS C:57BINDING SITE FOR RESIDUE NHE C 70

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GIB)

(-) 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: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 d3giba_ A: automated matches                                     SCOP domains
               CATH domains 3gibA00 A:6-69  [code=2.30.30.100, no name defined]              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
                  3gib A  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVS 69
                                    15        25        35        45        55        65    

Chain B from PDB  Type:PROTEIN  Length:65
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:65
                                    13        23        33        43        53        63     
             HFQ_ECOLI    4 GQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
               SCOP domains d3gibb_ B: automated matches                                      SCOP domains
               CATH domains 3gibB00 B:4-68  [code=2.30.30.100, no name defined]               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
                  3gib B  4 GQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPV 68
                                    13        23        33        43        53        63     

Chain C from PDB  Type:PROTEIN  Length:62
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:62
                                    15        25        35        45        55        65  
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRP 67
               SCOP domains d3gibc_ C: automated matches                                   SCOP domains
               CATH domains 3gibC00 C:6-67  [code=2.30.30.100, no name defined]            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
                  3gib C  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRP 67
                                    15        25        35        45        55        65  

Chain H from PDB  Type:RNA  Length:9
                                        
                  3gib H  1 AAAAAAAAA  9

   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, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HFQ_ECOLI | P0A6X31hk9 1m7c 1oou 1oov 2y90 2yht 3qhs 3qo3 3rer 3res 3vu3 4jri 4jrk 4juv 4rcb 4rcc 4v2s

(-) Related Entries Specified in the PDB File

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