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(-) Description

Title :  CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS HFQ AT 1.5A
 
Authors :  K. Stanek, J. Patterson, P. S. Randolph, C. Mura
Date :  13 Aug 16  (Deposition) - 19 Apr 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
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)
Biol. Unit 3:  A,B,C,D,E,F,G,H,I,J,K,L  (1x)
Keywords :  Hfq, Aquifex, Rna-Binding, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. A. Stanek, J. Patterson-West, P. S. Randolph, C. Mura
Crystal Structure And Rna-Binding Properties Of An Hfq Homolog From The Deep-Branching Aquificae: Conservation Of The Lateral Rna-Binding Mode.
Acta Crystallogr D Struct V. 73 294 2017 Biol
PubMed-ID: 28375142  |  Reference-DOI: 10.1107/S2059798317000031

(-) Compounds

Molecule 1 - RNA-BINDING PROTEIN HFQ
    Chains: A, B, C, D, E, F, G, H, I, J, K, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HFQ, AQ_108, AQ_108B
    Organism Scientific: AQUIFEX AEOLICUS (STRAIN VF5)
    Organism Taxid: 224324
    Strain: VF5

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCDEF      
Biological Unit 2 (1x):       GHIJKL
Biological Unit 3 (1x): ABCDEFGHIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 44)

Asymmetric Unit (5, 44)
No.NameCountTypeFull Name
1CL7Ligand/IonCHLORIDE ION
2GAI8Ligand/IonGUANIDINE
3MPD12Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD13Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
5PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GAI6Ligand/IonGUANIDINE
3MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD7Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
5PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (4, 19)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GAI2Ligand/IonGUANIDINE
3MPD7Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD6Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
5PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (4, 37)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GAI8Ligand/IonGUANIDINE
3MPD12Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD13Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
5PEG4Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (44, 44)

Asymmetric Unit (44, 44)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:43 , TYR A:57 , HIS A:59 , HOH A:215 , GLN B:9 , LEU B:42binding site for residue MRD A 101
02AC2SOFTWAREHIS A:3 , GLN F:9 , GLU F:10 , PHE F:40 , ASP F:41 , LEU F:42 , LYS F:58binding site for residue MRD A 102
03AC3SOFTWAREGLN A:9 , PHE A:40 , ASP A:41 , LEU A:42 , LYS A:58binding site for residue MPD A 103
04AC4SOFTWAREASN A:29 , GLY A:30 , LEU I:42 , TYR J:6binding site for residue GAI A 104
05AC5SOFTWARETYR A:6binding site for residue GAI A 105
06AC6SOFTWAREPHE B:43 , TYR B:57 , HIS B:59 , HOH B:219 , GLN C:9 , LEU C:42binding site for residue MRD B 101
07AC7SOFTWAREGLN B:9 , GLU B:10 , PHE B:40 , ASP B:41 , LEU B:42 , LYS B:58 , PRO C:5binding site for residue MPD B 102
08AC8SOFTWAREASN B:29 , GLY B:30 , TYR K:6binding site for residue GAI B 103
09AC9SOFTWAREPHE C:43 , TYR C:57 , HIS C:59 , HOH C:218 , GLN D:9 , LEU D:42binding site for residue MRD C 101
10AD1SOFTWAREGLN C:9 , GLU C:10 , PHE C:40 , ASP C:41 , LEU C:42 , LYS C:58binding site for residue MPD C 102
11AD2SOFTWAREASN C:29 , GLY C:30 , LEU K:42 , TYR L:6binding site for residue GAI C 103
12AD3SOFTWAREPHE D:43 , TYR D:57 , HIS D:59 , HOH D:213 , GLN E:9 , LEU E:42binding site for residue MRD D 101
13AD4SOFTWAREGLN D:9 , GLU D:10 , PHE D:40 , ASP D:41 , LEU D:42 , LYS D:58binding site for residue MPD D 102
14AD5SOFTWAREPHE E:43 , TYR E:57 , HIS E:59 , HOH E:216 , GLN F:9 , LEU F:42binding site for residue MRD E 101
15AD6SOFTWAREGLN E:9 , GLU E:10 , PHE E:40 , ASP E:41 , LEU E:42 , LYS E:58 , HOH E:207binding site for residue MPD E 102
16AD7SOFTWAREASN E:29 , GLY E:30 , HOH E:222 , TYR H:6binding site for residue GAI E 103
17AD8SOFTWAREGLN A:9 , LEU A:42 , PHE F:43 , TYR F:57 , HIS F:59 , HOH F:216binding site for residue MRD F 101
18AD9SOFTWAREMET F:4 , PRO F:5 , TYR F:6 , LYS F:7 , HOH F:201binding site for residue CL F 102
19AE1SOFTWAREASN F:29 , GLY F:30 , HOH F:206 , LEU H:42 , TYR I:6binding site for residue GAI F 103
20AE2SOFTWAREPHE G:43 , TYR G:57 , HIS G:59 , HOH G:216 , GLN H:9 , LEU H:42binding site for residue MRD G 101
21AE3SOFTWAREGLN G:9 , PHE G:40 , ASP G:41 , LYS G:58 , HOH G:214binding site for residue MPD G 102
22AE4SOFTWAREHOH D:207 , HOH D:217 , MET G:4 , TYR G:6 , HOH G:215binding site for residue CL G 103
23AE5SOFTWAREASN D:29 , GLY D:30 , HOH D:216 , TYR G:6binding site for residue GAI G 104
24AE6SOFTWARETYR G:26 , LEU G:27 , THR G:62 , THR G:63 , HOH G:208 , ASN L:29 , VAL L:31binding site for residue PEG G 105
25AE7SOFTWAREPHE H:43 , TYR H:57 , HIS H:59 , HOH H:217 , GLN I:9 , LEU I:42binding site for residue MRD H 101
26AE8SOFTWAREGLN H:9 , GLU H:10 , PHE H:40 , ASP H:41 , LYS H:58 , HOH H:221 , SER I:2binding site for residue MPD H 102
27AE9SOFTWAREGLN G:52 , TYR H:26 , THR H:63binding site for residue MPD H 103
28AF1SOFTWAREHOH E:210 , HOH E:214 , MET H:4 , TYR H:6 , HOH H:202binding site for residue CL H 104
29AF2SOFTWARETYR H:26 , GLY H:30binding site for residue GAI H 105
30AF3SOFTWAREPHE I:43 , TYR I:57 , HIS I:59 , HOH I:216 , GLN J:9 , LEU J:42binding site for residue MRD I 101
31AF4SOFTWAREGLN I:9 , PHE I:40 , ASP I:41 , LEU I:42 , LYS I:58 , HOH I:214 , SER J:2binding site for residue MPD I 102
32AF5SOFTWAREHOH F:208 , HOH F:214 , MET I:4 , TYR I:6 , HOH I:209binding site for residue CL I 103
33AF6SOFTWAREPHE J:43 , TYR J:57 , HIS J:59 , HOH J:216 , GLN K:9 , LEU K:42binding site for residue MRD J 101
34AF7SOFTWAREGLN J:9 , PHE J:40 , ASP J:41 , LYS J:58 , HOH J:214 , SER K:2binding site for residue MPD J 102
35AF8SOFTWAREHOH A:207 , HOH A:214 , MET J:4 , TYR J:6 , LYS J:7 , HOH J:206binding site for residue CL J 103
36AF9SOFTWAREASN I:29 , TYR J:26 , LEU J:27 , THR J:62 , THR J:63 , HOH J:201binding site for residue PEG J 104
37AG1SOFTWAREPHE K:43 , TYR K:57 , HIS K:59 , HOH K:211 , GLN L:9 , LEU L:42binding site for residue MRD K 101
38AG2SOFTWAREGLN K:9 , PHE K:40 , ASP K:41 , LYS K:58 , HOH K:209 , SER L:2binding site for residue MPD K 102
39AG3SOFTWAREHOH B:213 , HOH B:216 , MET K:4 , TYR K:6 , LYS K:7 , HOH K:207binding site for residue CL K 103
40AG4SOFTWARELEU J:27 , ASN J:29 , LEU J:33 , LEU K:27 , THR K:62 , THR K:63 , HOH K:201 , HOH K:222binding site for residue PEG K 104
41AG5SOFTWAREGLN G:9 , LEU G:42 , PHE L:43 , TYR L:57 , HIS L:59 , HOH L:222binding site for residue MRD L 101
42AG6SOFTWARESER G:2 , GLN L:9 , PHE L:40 , ASP L:41 , LEU L:42 , LYS L:58 , HOH L:218binding site for residue MPD L 102
43AG7SOFTWAREHOH C:207 , HOH C:215 , MET L:4 , TYR L:6 , LYS L:7 , HOH L:213binding site for residue CL L 103
44AG8SOFTWARELEU K:27 , ASN K:29 , VAL K:31 , TYR L:26 , LEU L:27 , THR L:62 , THR L:63 , HOH L:206 , HOH L:208binding site for residue PEG L 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5SZD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5SZD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5SZD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5SZD)

(-) Exons   (0, 0)

(no "Exon" information available for 5SZD)

(-) 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:72
                                                                                                       
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                  5szd A  1 GSHMPYKLQESFLNTARKKRVKVSVYLVNGVRLQGRIRSFDLFTILLEDGKQQTLVYKHAITTIVPHERLEI 72
                                    10        20        30        40        50        60        70  


Chain B from PDB  Type:PROTEIN  Length:70
                                                                                                     
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  5szd B  3 HMPYKLQESFLNTARKKRVKVSVYLVNGVRLQGRIRSFDLFTILLEDGKQQTLVYKHAITTIVPHERLEI 72
                                    12        22        32        42        52        62        72


Chain C from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh.eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  5szd C  2 SHMPYKLQESFLNTARKKRVKVSVYLVNGVRLQGRIRSFDLFTILLEDGKQQTLVYKHAITTIVPHERLEI 72
                                    11        21        31        41        51        61        71 


Chain D from PDB  Type:PROTEIN  Length:69
                                                                                                    
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  5szd D  4 MPYKLQESFLNTARKKRVKVSVYLVNGVRLQGRIRSFDLFTILLEDGKQQTLVYKHAITTIVPHERLEI 72
                                    13        23        33        43        53        63         


Chain E from PDB  Type:PROTEIN  Length:69
                                                                                                    
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  5szd E  4 MPYKLQESFLNTARKKRVKVSVYLVNGVRLQGRIRSFDLFTILLEDGKQQTLVYKHAITTIVPHERLEI 72
                                    13        23        33        43        53        63         


Chain F from PDB  Type:PROTEIN  Length:72
                                                                                                       
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                  5szd F  1 GSHMPYKLQESFLNTARKKRVKVSVYLVNGVRLQGRIRSFDLFTILLEDGKQQTLVYKHAITTIVPHERLEI 72
                                    10        20        30        40        50        60        70  


Chain G from PDB  Type:PROTEIN  Length:70
                                                                                                     
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeeee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  5szd G  2 SHMPYKLQESFLNTARKKRVKVSVYLVNGVRLQGRIRSFDLFTILLEDGKQQTLVYKHAITTIVPHERLE 71
                                    11        21        31        41        51        61        71


Chain H from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  5szd H  2 SHMPYKLQESFLNTARKKRVKVSVYLVNGVRLQGRIRSFDLFTILLEDGKQQTLVYKHAITTIVPHERLEI 72
                                    11        21        31        41        51        61        71 


Chain I from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  5szd I  2 SHMPYKLQESFLNTARKKRVKVSVYLVNGVRLQGRIRSFDLFTILLEDGKQQTLVYKHAITTIVPHERLEI 72
                                    11        21        31        41        51        61        71 


Chain J from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  5szd J  2 SHMPYKLQESFLNTARKKRVKVSVYLVNGVRLQGRIRSFDLFTILLEDGKQQTLVYKHAITTIVPHERLEI 72
                                    11        21        31        41        51        61        71 


Chain K from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  5szd K  2 SHMPYKLQESFLNTARKKRVKVSVYLVNGVRLQGRIRSFDLFTILLEDGKQQTLVYKHAITTIVPHERLEI 72
                                    11        21        31        41        51        61        71 


Chain L from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeeee..eeeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  5szd L  2 SHMPYKLQESFLNTARKKRVKVSVYLVNGVRLQGRIRSFDLFTILLEDGKQQTLVYKHAITTIVPHERLEI 72
                                    11        21        31        41        51        61        71
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

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(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5SZD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5SZD)

(-) Gene Ontology  (2, 2)

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 Related Entries

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

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        HFQ_AQUAE | O66512: 5sze

(-) Related Entries Specified in the PDB File

5sze