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(-) Description

Title :  CRYSTAL STRUCTURE OF A PLECTONEMIC RNA SUPERCOIL
 
Authors :  J. R. Stagno, X. Ji
Date :  01 May 12  (Deposition) - 20 Jun 12  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t
Keywords :  Transcription Elongation, Ssrna, Dsrna, Nuse Protein, Transcription, Transcription-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Stagno, B. Ma, J. Li, A. S. Altieri, R. A. Byrd, X. Ji
Crystal Structure Of A Plectonemic Rna Supercoil.
Nat Commun V. 3 901 2012
PubMed-ID: 22692544  |  Reference-DOI: 10.1038/NCOMMS1903

(-) Compounds

Molecule 1 - N UTILIZATION SUBSTANCE PROTEIN B HOMOLOG
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AQ_133, NUSB
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: PROTEIN NUSB
 
Molecule 2 - RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')
    Chains: a, c, e, g, i, j, h, f, d, b, k, m, o, q, s, t, r, p, n, l
    Engineered: YES
    Organism Taxid: 32630
    Other Details: SYNTHETIC RNA REPRESENTING THE BOXA RNA FROM AQUIFEX AEOLICUS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910111213141516171819202122232425262728
Asymmetric/Biological Unit : ABCDEFGHabcdefghijklmnopqrst

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric/Biological Unit (2, 16)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:19 , ARG A:86BINDING SITE FOR RESIDUE GOL A 201
02AC2SOFTWARELYS B:132 , GLY G:78BINDING SITE FOR RESIDUE SO4 B 201
03AC3SOFTWARETYR A:114 , GLU B:35BINDING SITE FOR RESIDUE GOL B 202
04AC4SOFTWARETYR B:16 , TYR B:114BINDING SITE FOR RESIDUE GOL B 203
05AC5SOFTWARETRP C:18 , ASP C:19 , ARG C:86BINDING SITE FOR RESIDUE GOL C 201
06AC6SOFTWARETYR C:114 , GLU D:35BINDING SITE FOR RESIDUE GOL C 202
07AC7SOFTWARELYS D:132 , GLY E:78BINDING SITE FOR RESIDUE SO4 D 201
08AC8SOFTWARETYR D:16 , TYR D:114BINDING SITE FOR RESIDUE GOL D 202
09AC9SOFTWARETRP E:18 , ASP E:19 , ARG E:86BINDING SITE FOR RESIDUE GOL E 201
10BC1SOFTWARETYR E:114 , GLU F:35BINDING SITE FOR RESIDUE GOL E 202
11BC2SOFTWAREGLY C:78 , LYS F:132BINDING SITE FOR RESIDUE SO4 F 201
12BC3SOFTWARELEU F:13 , TYR F:16 , TYR F:114BINDING SITE FOR RESIDUE GOL F 202
13BC4SOFTWARETRP G:18 , ASP G:19 , ARG G:86BINDING SITE FOR RESIDUE GOL G 201
14BC5SOFTWAREGLY A:78 , LYS H:132BINDING SITE FOR RESIDUE SO4 H 201
15BC6SOFTWARETYR G:114 , GLU H:35BINDING SITE FOR RESIDUE GOL H 202
16BC7SOFTWARETYR H:16 , TYR H:114BINDING SITE FOR RESIDUE GOL H 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EYA)

(-) 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:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4eya A   1 MRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSS 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        


Chain B from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eya B   3 YRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSS 138
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      


Chain C from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4eya C   1 MRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSS 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        


Chain D from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eya D   3 YRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSS 138
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      


Chain E from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4eya E   1 MRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSS 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        


Chain F from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eya F   3 YRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSS 138
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      


Chain G from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4eya G   1 MRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSS 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        


Chain H from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eya H   3 YRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSS 138
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      


Chain a from PDB  Type:RNA  Length:12
                                            
                 4eya a   1 GGCUCCUUGGCA  12
                                    10  


Chain b from PDB  Type:RNA  Length:12
                                            
                 4eya b   1 GGCUCCUUGGCA  12
                                    10  


Chain c from PDB  Type:RNA  Length:12
                                            
                 4eya c   1 GGCUCCUUGGCA  12
                                    10  


Chain d from PDB  Type:RNA  Length:12
                                            
                 4eya d   1 GGCUCCUUGGCA  12
                                    10  


Chain e from PDB  Type:RNA  Length:12
                                            
                 4eya e   1 GGCUCCUUGGCA  12
                                    10  


Chain f from PDB  Type:RNA  Length:12
                                            
                 4eya f   1 GGCUCCUUGGCA  12
                                    10  


Chain g from PDB  Type:RNA  Length:12
                                            
                 4eya g   1 GGCUCCUUGGCA  12
                                    10  


Chain h from PDB  Type:RNA  Length:12
                                            
                 4eya h   1 GGCUCCUUGGCA  12
                                    10  


Chain i from PDB  Type:RNA  Length:12
                                            
                 4eya i   1 GGCUCCUUGGCA  12
                                    10  


Chain j from PDB  Type:RNA  Length:12
                                            
                 4eya j   1 GGCUCCUUGGCA  12
                                    10  


Chain k from PDB  Type:RNA  Length:12
                                            
                 4eya k   1 GGCUCCUUGGCA  12
                                    10  


Chain l from PDB  Type:RNA  Length:12
                                            
                 4eya l   1 GGCUCCUUGGCA  12
                                    10  


Chain m from PDB  Type:RNA  Length:12
                                            
                 4eya m   1 GGCUCCUUGGCA  12
                                    10  


Chain n from PDB  Type:RNA  Length:12
                                            
                 4eya n   1 GGCUCCUUGGCA  12
                                    10  


Chain o from PDB  Type:RNA  Length:12
                                            
                 4eya o   1 GGCUCCUUGGCA  12
                                    10  


Chain p from PDB  Type:RNA  Length:12
                                            
                 4eya p   1 GGCUCCUUGGCA  12
                                    10  


Chain q from PDB  Type:RNA  Length:12
                                            
                 4eya q   1 GGCUCCUUGGCA  12
                                    10  


Chain r from PDB  Type:RNA  Length:12
                                            
                 4eya r   1 GGCUCCUUGGCA  12
                                    10  


Chain s from PDB  Type:RNA  Length:12
                                            
                 4eya s   1 GGCUCCUUGGCA  12
                                    10  


Chain t from PDB  Type:RNA  Length:12
                                            
                 4eya t   1 GGCUCCUUGGCA  12
                                    10
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  4eya
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 Related Entries

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

UniProtKB/Swiss-Prot
        NUSB_AQUAE | O66530: 2jr0 3r2c 3r2d

(-) Related Entries Specified in the PDB File

3r2c THE SAME PROTEIN COMPLEXED WITH SSRNA
3r2d THE SAME PROTEIN COMPLEXED WITH DSRNA