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(-) Description

Title :  CRYSTAL STRUCTURE OF HFQ FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH ATP
 
Authors :  V. Murina, N. Lekontseva, A. Nikulin
Date :  11 Feb 13  (Deposition) - 31 Jul 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Lsm, Rna Binding Protein, Rna Chaperone, Srna, Mrna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Murina, N. Lekontseva, A. Nikulin
Hfq Binds Ribonucleotides In Three Different Rna-Binding Sites.
Acta Crystallogr. , Sect. D V. 69 1504 2013
PubMed-ID: 23897473  |  Reference-DOI: 10.1107/S090744491301010X

(-) Compounds

Molecule 1 - PROTEIN HFQ
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HFQ, PA4944
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ATP5Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2NA2Ligand/IonSODIUM ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:25 , LYS A:31 , THR A:61 , VAL A:63 , NA A:102 , HOH A:202 , HOH A:233 , HOH A:234 , ARG B:19 , LEU F:26 , ILE F:30 , LEU F:32 , GLN F:52BINDING SITE FOR RESIDUE ATP A 101
2AC2SOFTWAREGLY A:29 , ATP A:101 , HOH A:234BINDING SITE FOR RESIDUE NA A 102
3AC3SOFTWAREGLN A:52 , TYR B:25 , GLY B:29 , LYS B:31 , THR B:61 , VAL B:63 , HOH B:213BINDING SITE FOR RESIDUE ATP B 101
4AC4SOFTWAREILE B:30 , GLN B:52 , TYR C:25 , GLY C:29 , LYS C:31 , THR C:61 , HOH C:213 , HOH C:217 , HOH C:218 , HOH C:220BINDING SITE FOR RESIDUE ATP C 101
5AC5SOFTWAREARG A:19 , HOH A:218 , LEU C:26 , ILE C:30 , GLN C:52 , TYR D:25 , LYS D:31 , THR D:61 , VAL D:63 , NA D:103 , HOH D:213 , HOH D:231 , HOH D:241 , HOH D:242BINDING SITE FOR RESIDUE ATP D 101
6AC6SOFTWAREARG D:16 , SER D:38 , PHE D:39 , HOH D:219 , HOH D:226BINDING SITE FOR RESIDUE PEG D 102
7AC7SOFTWAREGLY D:29 , ATP D:101 , HOH D:213 , HOH D:233BINDING SITE FOR RESIDUE NA D 103
8AC8SOFTWAREGLN B:35 , ASN B:48 , THR B:49 , HOH B:252 , ILE E:30 , LEU E:32 , GLN E:52 , TYR F:25 , GLY F:29 , SER F:60 , THR F:61 , VAL F:63 , HOH F:216 , HOH F:218 , HOH F:223 , HOH F:231BINDING SITE FOR RESIDUE ATP F 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J5Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J5Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J5Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J5Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4J5Y)

(-) 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:68
                                                                                                   
               SCOP domains d4j5ya_ A: Pleiotropic translational regulator Hfq                   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
                  4j5y A  4 GHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLP 71
                                    13        23        33        43        53        63        


Chain B from PDB  Type:PROTEIN  Length:68
                                                                                                   
               SCOP domains d4j5yb_ B: Pleiotropic translational regulator Hfq                   SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee....eeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  4j5y B  4 GHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLP 71
                                    13        23        33        43        53        63        


Chain C from PDB  Type:PROTEIN  Length:68
                                                                                                   
               SCOP domains d4j5yc_ C: Pleiotropic translational regulator Hfq                   SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee....eeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  4j5y C  4 GHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLP 71
                                    13        23        33        43        53        63        


Chain D from PDB  Type:PROTEIN  Length:68
                                                                                                   
               SCOP domains d4j5yd_ D: Pleiotropic translational regulator Hfq                   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
                  4j5y D  5 HSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLPS 72
                                    14        24        34        44        54        64        


Chain E from PDB  Type:PROTEIN  Length:68
                                                                                                   
               SCOP domains d4j5ye_ E: Pleiotropic translational regulator Hfq                   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
                  4j5y E  4 GHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLP 71
                                    13        23        33        43        53        63        


Chain F from PDB  Type:PROTEIN  Length:69
                                                                                                    
               SCOP domains d4j5yf_ F: Pleiotropic translational regulator Hfq                    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
                  4j5y F  3 KGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLP 71
                                    12        22        32        42        52        62
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "CATH Domain" information available for 4J5Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J5Y)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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  HFQ_PSEAE | Q9HUM0
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 Related Entries

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

UniProtKB/Swiss-Prot
        HFQ_PSEAE | Q9HUM0: 1u1s 1u1t 3inz 3m4g 3qui 4j6w 4j6x 4j6y 4mmk 4mml

(-) Related Entries Specified in the PDB File

1u1s WILD-TYPE PROTEIN
1u1t WILD-TYPE PROTEIN
3gib CRYSTAL STUCTURE OF THE COMPLEX OF THE E. COLI HFQ WITH POLY(A)
3qo3 CRYSTAL STRUCTURE OF ESCHERICHIA COLI HFQ IN COMPLEX WITH ATP
3qui PAEHFQ IN COMPLEX WITH ADPNP
3rer CRYSTAL STRUCTURE OF E. COLI HFQ IN COMPLEX WITH AU6A RNA AND ADP
4j6w HFQ FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH CTP
4j6x HFQ FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH UTP
4j6y HFQ FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH GTP