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(-) Description

Title :  CRYSTALLOGRAPHIC ANALYSIS OF AN RNA-POLYMERASE SIGMA-SUBUNIT FRAGMENT COMPLEXED WITH -10 PROMOTER ELEMENT SSDNA
 
Authors :  A. Feklistov, Darst S. A.
Date :  01 May 13  (Deposition) - 04 Sep 13  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,D,E,F,G
Biol. Unit 1:  A,D,G  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Ssdna, G-Quartet, G-Quadruplex, Promoter Recognition, Promoter Opening, Transcription Initiation, Protein-Dna Binding, Ssdna- Binding, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Feklistov, S. A. Darst
Crystallographic Analysis Of An Rna Polymerase Sigma-Subuni Fragment Complexed With -10 Promoter Element Ssdna: Quadruplex Formation As A Possible Tool For Engineering Crystal Contacts In Protein-Ssdna Complexes.
Acta Crystallogr. , Sect. F V. 69 950 2013
PubMed-ID: 23989139  |  Reference-DOI: 10.1107/S1744309113020368

(-) Compounds

Molecule 1 - DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3')
    Chains: D, E, F, G
    Engineered: YES
    Other Details: -10 ELEMENT NON-TEMPLATE STRAND SSDNA
    Other Details - Source: SEQUENCE FROM NON-TEMPLATE STRAND OF -10 BACTERIAL PROMOTER ELEMENT
    Synthetic: YES
 
Molecule 2 - RNA POLYMERASE SIGMA FACTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: DOMAINS 2-3, (UNP RESIDUES 92-332)
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABDEFG
Biological Unit 1 (1x): A D  G
Biological Unit 2 (1x):  B EF 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1K5Ligand/IonPOTASSIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG D:10 , DG D:11 , K D:102 , DG E:10 , DG E:11BINDING SITE FOR RESIDUE K D 101
2AC2SOFTWAREDG D:9 , DG D:10 , K D:101 , K D:103 , DG E:9 , DG E:10BINDING SITE FOR RESIDUE K D 102
3AC3SOFTWAREDG D:9 , K D:102 , DG E:9 , DG F:11 , DG G:11 , K G:101BINDING SITE FOR RESIDUE K D 103
4AC4SOFTWAREK D:103 , DG F:10 , DG F:11 , DG G:10 , DG G:11 , K G:102BINDING SITE FOR RESIDUE K G 101
5AC5SOFTWAREDG F:9 , DG F:10 , DG G:9 , DG G:10 , K G:101BINDING SITE FOR RESIDUE K G 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KI2)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:165 -Pro A:166
2Ile B:273 -Arg B:274
3Gly B:311 -Pro B:312

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KI2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KI2)

(-) Exons   (0, 0)

(no "Exon" information available for 4KI2)

(-) 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:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ki2 A  93 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQA 270
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262        


Chain B from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ki2 B  93 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIA 326
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322    


Chain D from PDB  Type:DNA  Length:11
                                           
                 4ki2 D   1 TGTACAATGGG  11
                                    10 


Chain E from PDB  Type:DNA  Length:10
                                          
                 4ki2 E   2 GTACAATGGG  11
                                    11


Chain F from PDB  Type:DNA  Length:3
                                   
                 4ki2 F   9 GGG  11


Chain G from PDB  Type:DNA  Length:3
                                   
                 4ki2 G   9 GGG  11
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4KI2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KI2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KI2)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        SIGA_THEAQ | Q9EZJ8: 1ku2 1ku3 1ku7 1l9u 1l9z 1rio 3les 3lev 3n97 3ugo 3ugp 4xln 4xlp 4xlq 4xlr 4xls 5tjg

(-) Related Entries Specified in the PDB File

3ugo 3ugp