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(-) Description

Title :  CRYSTAL STRUCTURE OF E COLI HFQ IN COMPLEX WITH ADP
 
Authors :  W. W. Wang, J. H. Wu, Y. Y. Shi
Date :  05 Apr 11  (Deposition) - 19 Oct 11  (Release) - 19 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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 :  Adp, Hfq, Sm Fold, Rna Chaperone, Rna Binding, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Wang, L. Wang, Y. Zou, J. Zhang, Q. Gong, J. Wu, Y. Shi
Cooperation Of Escherichia Coli Hfq Hexamers In Dsra Binding.
Genes Dev. V. 25 2106 2011
PubMed-ID: 21979921  |  Reference-DOI: 10.1101/GAD.16746011

(-) 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: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-65
    Gene: B21_04001, HFQ
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 511693
    Strain: BL21
    Synonym: HF-1, HOST FACTOR-I PROTEIN

 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  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1ADP8Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:25 , GLY B:29 , LYS B:31 , SER B:60 , THR B:61 , HOH B:177 , LEU C:26 , ILE C:30 , LEU C:32 , GLN C:52BINDING SITE FOR RESIDUE ADP B 66
2AC2SOFTWARETYR C:25 , GLY C:29 , SER C:60 , THR C:61 , HOH C:275 , LEU D:26 , ILE D:30 , LEU D:32 , GLN D:52BINDING SITE FOR RESIDUE ADP C 66
3AC3SOFTWARETYR E:25 , GLY E:29 , LYS E:31 , SER E:60 , THR E:61 , HOH E:76 , LEU F:26 , ASN F:28 , ILE F:30 , LEU F:32 , GLN F:41BINDING SITE FOR RESIDUE ADP E 66
4AC4SOFTWAREASP A:9 , LEU A:26 , ILE A:30 , LEU A:32 , GLN A:52 , HOH A:265 , TYR F:25 , GLY F:29 , SER F:60 , THR F:61 , HOH F:247BINDING SITE FOR RESIDUE ADP F 66
5AC5SOFTWARETYR H:25 , GLY H:29 , SER H:60 , THR H:61 , HOH H:160 , LEU I:26 , ILE I:30 , LEU I:32 , GLN I:52BINDING SITE FOR RESIDUE ADP H 66
6AC6SOFTWAREARG I:16 , TYR I:25 , GLY I:29 , SER I:60 , THR I:61 , HOH I:266 , ILE J:30 , LEU J:32 , GLN J:52BINDING SITE FOR RESIDUE ADP I 66
7AC7SOFTWARETYR K:25 , GLY K:29 , LYS K:31 , SER K:60 , THR K:61 , HOH K:242 , HOH K:260 , LEU L:26 , ASN L:28 , ILE L:30 , GLN L:41BINDING SITE FOR RESIDUE ADP K 66
8AC8SOFTWAREASP G:9 , LEU G:26 , ILE G:30 , LEU G:32 , GLN G:52 , TYR L:25 , GLY L:29 , SER L:60 , THR L:61BINDING SITE FOR RESIDUE ADP L 66

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RES)

(-) 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:62
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:62
                                    13        23        33        43        53        63  
             HFQ_ECOLI    4 GQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3resa_ 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
                  3res A  4 GQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    13        23        33        43        53        63  


Chain B from PDB  Type:PROTEIN  Length:60
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:60
                                    15        25        35        45        55        65
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3resb_ B: 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
                  3res B  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    15        25        35        45        55        65


Chain C from PDB  Type:PROTEIN  Length:61
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:61
                                    14        24        34        44        54        64 
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3resc_ C: 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
                  3res C  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    14        24        34        44        54        64 


Chain D from PDB  Type:PROTEIN  Length:61
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:61
                                    14        24        34        44        54        64 
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3resd_ D: 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
                  3res D  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    14        24        34        44        54        64 


Chain E from PDB  Type:PROTEIN  Length:60
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:60
                                    15        25        35        45        55        65
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3rese_ E: 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
                  3res E  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    15        25        35        45        55        65


Chain F from PDB  Type:PROTEIN  Length:60
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:60
                                    15        25        35        45        55        65
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3resf_ F: 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
                  3res F  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    15        25        35        45        55        65


Chain G from PDB  Type:PROTEIN  Length:60
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:60
                                    15        25        35        45        55        65
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3resg_ G: 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
                  3res G  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    15        25        35        45        55        65


Chain H from PDB  Type:PROTEIN  Length:60
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:60
                                    15        25        35        45        55        65
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3resh_ H: 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
                  3res H  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    15        25        35        45        55        65


Chain I from PDB  Type:PROTEIN  Length:60
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:60
                                    15        25        35        45        55        65
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3resi_ I: 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
                  3res I  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    15        25        35        45        55        65


Chain J from PDB  Type:PROTEIN  Length:61
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:61
                                    14        24        34        44        54        64 
             HFQ_ECOLI    5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3resj_ J: 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
                  3res J  5 QSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    14        24        34        44        54        64 


Chain K from PDB  Type:PROTEIN  Length:60
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:60
                                    15        25        35        45        55        65
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3resk_ 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
                  3res K  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    15        25        35        45        55        65


Chain L from PDB  Type:PROTEIN  Length:60
 aligned with HFQ_ECOLI | P0A6X3 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:60
                                    15        25        35        45        55        65
             HFQ_ECOLI    6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
               SCOP domains d3resl_ L: 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
                  3res L  6 SLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPS 65
                                    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 3RES)

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        HFQ_ECOLI | P0A6X3: 1hk9 1m7c 1oou 1oov 2y90 2yht 3gib 3qhs 3qo3 3rer 3vu3 4jri 4jrk 4juv 4rcb 4rcc 4v2s

(-) Related Entries Specified in the PDB File

3rer