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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MIRROR-IMAGE L-RNA/L-DNA APTAMER NOX-D20 IN COMPLEX WITH MOUSE C5A-DESARG COMPLEMENT ANAPHYLATOXIN
 
Authors :  L. Yatime, C. Maasch, K. Hoehlig, S. Klussmann, A. Vater, G. R. Andersen
Date :  02 Sep 14  (Deposition) - 06 May 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C,E  (1x)
Keywords :  Protein-Rna Complex, Mirror-Image Aptamer, G-Quadruplex, Complement Anaphylatoxin, Dna-Rna Hybrid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Yatime, C. Maasch, K. Hoehlig, S. Klussmann, G. R. Andersen, A. Vate
Structural Basis For The Targeting Of Complement Anaphylatoxin C5A Using A Mixed L-Rna/L-Dna Aptamer.
Nat Commun V. 6 6481 2015
PubMed-ID: 25901944  |  Reference-DOI: 10.1038/NCOMMS7481

(-) Compounds

Molecule 1 - COMPLEMENT C5
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: SHUFFLE T7 EXPRESS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: C5, HC
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: HEMOLYTIC COMPLEMENT
 
Molecule 2 - MIXED L-RNA/L-DNA APTAMER NOX-D20 (40-MER)
    Chains: D, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A  D 
Biological Unit 2 (1x):  B   
Biological Unit 3 (1x):   C E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (11, 91)

Asymmetric Unit (11, 91)
No.NameCountTypeFull Name
10A8Mod. ResidueL-ADENOSINE-5'-MONOPHOSPHATE
20C10Mod. ResidueL-CYTIDINE-5'-MONOPHOSPHATE
30DA2OTHER2'-DEOXY-L-RIBO-FURANOSYL ADENOSINE-5'-MONOPHOSPHATE
40DC2OTHER2'-DEOXY-L-RIBO-FURANOSYL CYTOSINE-5'-MONOPHOSPHATE
50DG2OTHER2'-DEOXY-L-RIBO-FURANOSYL GUANINE-5'-MONOPHOSPHATE
60G36Mod. ResidueL-GUANOSINE-5'-MONOPHOSPHATE
70U14Mod. ResidueL-URIDINE-5'-MONOPHOSPHATE
83KA6OTHER1-(2-DEOXY-5-O-PHOSPHONO-BETA-L-ERYTHRO-PENTOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE
9ACT3Ligand/IonACETATE ION
10CA6Ligand/IonCALCIUM ION
11MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (5, 7)
No.NameCountTypeFull Name
10A-1Mod. ResidueL-ADENOSINE-5'-MONOPHOSPHATE
20C-1Mod. ResidueL-CYTIDINE-5'-MONOPHOSPHATE
30DA1OTHER2'-DEOXY-L-RIBO-FURANOSYL ADENOSINE-5'-MONOPHOSPHATE
40DC1OTHER2'-DEOXY-L-RIBO-FURANOSYL CYTOSINE-5'-MONOPHOSPHATE
50DG1OTHER2'-DEOXY-L-RIBO-FURANOSYL GUANINE-5'-MONOPHOSPHATE
60G-1Mod. ResidueL-GUANOSINE-5'-MONOPHOSPHATE
70U-1Mod. ResidueL-URIDINE-5'-MONOPHOSPHATE
83KA3OTHER1-(2-DEOXY-5-O-PHOSPHONO-BETA-L-ERYTHRO-PENTOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE
9ACT1Ligand/IonACETATE ION
10CA-1Ligand/IonCALCIUM ION
11MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
10A-1Mod. ResidueL-ADENOSINE-5'-MONOPHOSPHATE
20C-1Mod. ResidueL-CYTIDINE-5'-MONOPHOSPHATE
30DA-1OTHER2'-DEOXY-L-RIBO-FURANOSYL ADENOSINE-5'-MONOPHOSPHATE
40DC-1OTHER2'-DEOXY-L-RIBO-FURANOSYL CYTOSINE-5'-MONOPHOSPHATE
50DG-1OTHER2'-DEOXY-L-RIBO-FURANOSYL GUANINE-5'-MONOPHOSPHATE
60G-1Mod. ResidueL-GUANOSINE-5'-MONOPHOSPHATE
70U-1Mod. ResidueL-URIDINE-5'-MONOPHOSPHATE
83KA-1OTHER1-(2-DEOXY-5-O-PHOSPHONO-BETA-L-ERYTHRO-PENTOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE
9ACT2Ligand/IonACETATE ION
10CA-1Ligand/IonCALCIUM ION
11MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (4, 6)
No.NameCountTypeFull Name
10A-1Mod. ResidueL-ADENOSINE-5'-MONOPHOSPHATE
20C-1Mod. ResidueL-CYTIDINE-5'-MONOPHOSPHATE
30DA1OTHER2'-DEOXY-L-RIBO-FURANOSYL ADENOSINE-5'-MONOPHOSPHATE
40DC1OTHER2'-DEOXY-L-RIBO-FURANOSYL CYTOSINE-5'-MONOPHOSPHATE
50DG1OTHER2'-DEOXY-L-RIBO-FURANOSYL GUANINE-5'-MONOPHOSPHATE
60G-1Mod. ResidueL-GUANOSINE-5'-MONOPHOSPHATE
70U-1Mod. ResidueL-URIDINE-5'-MONOPHOSPHATE
83KA3OTHER1-(2-DEOXY-5-O-PHOSPHONO-BETA-L-ERYTHRO-PENTOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE
9ACT-1Ligand/IonACETATE ION
10CA-1Ligand/IonCALCIUM ION
11MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (0, 0)

(no "Site" information available for 4WB3)

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:702 -A:728
2A:703 -A:735
3A:715 -A:736
4B:702 -B:728
5B:703 -B:735
6B:715 -B:736
7C:702 -C:728
8C:703 -C:735
9C:715 -C:736

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WB3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WB3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WB3)

(-) Exons   (0, 0)

(no "Exon" information available for 4WB3)

(-) 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:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4wb3 A 679 NLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECCTIANKIRKES 746
                                   688       698       708       718       728       738        


Chain B from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4wb3 B 681 HLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECCTIANKIRKESPH 748
                                   690       700       710       720       730       740        


Chain C from PDB  Type:PROTEIN  Length:69
                                                                                                     
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...hhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 4wb3 C 678 ANLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECCTIANKIRKES 746
                                   687       697       707       717       727       737         


Chain D from PDB  Type:OTHER  Length:40
                                                                        
                 4wb3 D   1 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx  40
                            ||||||||10||||||||20||||||||30||||||||40
                            1-0G||||10-0U||||19-0G||||28-3KA|||37-0A
                             2-0C||||11-0G||||20-0U||||29-0G||||38-0DC
                              3-0G||| 12-0G||| 21-0U||| 30-3KA|| 39-0G
                               4-0A||  13-0U||  22-0G||  31-0C||  40-0C
                                5-0U|   14-0DG   23-0U|   32-0G|    
                                 6-0G    15-0DA   24-0U    33-0A    
                                  7-3KA   16-0A    25-0G    34-0C   
                                   8-0G    17-0G    26-0G    35-0G  
                                    9-0G    18-0G    27-0G    36-0C 


Chain E from PDB  Type:OTHER  Length:40
                                                                        
                 4wb3 E   1 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx  40
                            ||||||||10||||||||20||||||||30||||||||40
                            ||||||||9-0G||||18-0G||||27-0G||||36-0C|
                            1-0G||||10-0U||||19-0G||||28-3KA|||37-0A
                             2-0C||| 11-0G||| 20-0U||| 29-0G||| 38-0DC
                              3-0G||  12-0G||  21-0U||  30-3KA|  39-0G
                               4-0A|   13-0U|   22-0G|   31-0C|   40-0C
                                5-0U    14-0DG   23-0U    32-0G     
                                 6-0G    15-0DA   24-0U    33-0A    
                                  7-3KA   16-0A    25-0G    34-0C   
                                   8-0G    17-0G    26-0G    35-0G
   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 4WB3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WB3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WB3)

(-) Gene Ontology  (18, 18)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CO5_MOUSE | P06684: 4p3a 4p3b 4wb2

(-) Related Entries Specified in the PDB File

4wb2 4WB2 CONTAINS THE SAME L-RNA/L-DNA APTAMER IN COMPLEX WITH MOUSE C5A