Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF A MIRROR-IMAGE RNA OLIGONUCLEOTIDE APTAMER IN COMPLEX WITH THE CHEMOKINE CCL2
 
Authors :  D. Oberthuer, J. Achenbach, A. Gabdulkhakov, S. Falke, K. Buchner, C. M D. Rehders, S. Klussmann, C. Betzel
Date :  02 Sep 14  (Deposition) - 29 Apr 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aptamer Spiegelmer L-Oligonucleotide, Cytokine-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Oberthur, J. Achenbach, A. Gabdulkhakov, K. Buchner, C. Maasch, S. Falke, D. Rehders, S. Klussmann, C. Betzel
Crystal Structure Of A Mirror-Image L-Rna Aptamer (Spiegelmer) In Complex With The Natural L-Protein Target Ccl2.
Nat Commun V. 6 6923 2015
PubMed-ID: 25901662  |  Reference-DOI: 10.1038/NCOMMS7923

(-) Compounds

Molecule 1 - C-C MOTIF CHEMOKINE 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CCL2, MCP1, SCYA2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HC11, MONOCYTE CHEMOATTRACTANT PROTEIN 1, MONOCYTE CHEMOTACTIC AND ACTIVATING FACTOR, MCAF, MONOCYTE CHEMOTACTIC PROTEIN 1, MCP-1, MONOCYTE SECRETORY PROTEIN JE, SMALL-INDUCIBLE CYTOKINE A2
 
Molecule 2 - MIRROR-IMAGE RNA OLIGONUCLEOTIDE APTAMER NOXE36
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: THE NOX-E36 L-OLIGONUCLEOTIDES WITH THE SEQUENCE 5'- GCACGUCCCUCACCGGUGCAAGUGAAGCCGUGGCUCUGCG-3' WERE SYNTHESIZED USING STANDARD PHOSPHORAMIDITE CHEMISTRY AT NOXXON PHARMA AG (BERLIN, GERMANY)
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 47)

Asymmetric/Biological Unit (8, 47)
No.NameCountTypeFull Name
10A6Mod. ResidueL-ADENOSINE-5'-MONOPHOSPHATE
20C14Mod. ResidueL-CYTIDINE-5'-MONOPHOSPHATE
30G13Mod. ResidueL-GUANOSINE-5'-MONOPHOSPHATE
50U6Mod. ResidueL-URIDINE-5'-MONOPHOSPHATE
40U11OTHER2'-METHYLSELENYL-2'-DEOXY-L-URIDINE-5'-MONOPHOSPHATE
6K5Ligand/IonPOTASSIUM ION
7NA1Ligand/IonSODIUM ION
8SR1Ligand/IonSTRONTIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARE0A B:12 , 0C B:13 , 0G B:30 , 0G B:32 , NA B:101 , HOH B:221 , HOH B:274 , HOH B:293BINDING SITE FOR RESIDUE 0U1 B 31
2AC2SOFTWARE0U1 B:31 , HOH B:221 , HOH B:245 , HOH B:246 , HOH B:248BINDING SITE FOR RESIDUE NA B 101
3AC3SOFTWARE0C B:9 , 0C B:11 , 0A B:12 , HOH B:206 , HOH B:213 , HOH B:215BINDING SITE FOR RESIDUE SR B 102
4AC4SOFTWARE0U B:6 , HOH B:230 , HOH B:256 , HOH B:283BINDING SITE FOR RESIDUE K B 103
5AC5SOFTWARE0U B:6 , 0G B:18 , HOH B:273 , HOH B:276 , HOH B:285BINDING SITE FOR RESIDUE K B 104
6AC6SOFTWAREHOH B:214 , HOH B:240 , HOH B:241 , HOH B:254 , HOH B:291BINDING SITE FOR RESIDUE K B 105
7AC7SOFTWARE0G B:32 , 0G B:33 , HOH B:235 , HOH B:236 , HOH B:271 , HOH B:272 , HOH B:296BINDING SITE FOR RESIDUE K B 106
8AC8SOFTWARE0C B:13 , HOH B:229 , HOH B:292 , HOH B:293BINDING SITE FOR RESIDUE K B 107

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:11 -A:36
2A:12 -A:52

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4R8I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R8I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R8I)

(-) Exons   (0, 0)

(no "Exon" information available for 4R8I)

(-) 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 -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhh.eeeeeee........eeeeee....eeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  4r8i A  3 DAINAPVTCCYNFTNRKISVQRLASYRRITSSKCPKEAVIFKTIVAKEICADPKQKWVQDSMDHLDKQ 70
                                    12        22        32        42        52        62        


Chain B from PDB  Type:OTHER  Length:40
                                                                       
                  4r8i B  1 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 40
                            ||||||||10||||||||20||||||||30||||||||40
                            1-0G||||10-0U||||19-0C||||28-0C||||37-0U
                             2-0C||||11-0C||||20-0A||||29-0C||||38-0G
                              3-0A||| 12-0A||| 21-0A||| 30-0G||| 39-0C
                               4-0C||  13-0C||  22-0G||  31-0U1|  40-0G
                                5-0G|   14-0C|   23-0U|   32-0G|    
                                 6-0U    15-0G    24-0G    33-0G    
                                  7-0C    16-0G    25-0A    34-0C   
                                   8-0C    17-0U    26-0A    35-0U  
                                    9-0C    18-0G    27-0G    36-0C
   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 4R8I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R8I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R8I)

(-) Gene Ontology  (113, 113)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    0A  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    0C  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    0G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    0U  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    0U1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4r8i)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4r8i
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CCL2_HUMAN | P13500
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CCL2_HUMAN | P13500
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CCL2_HUMAN | P13500: 1dok 1dol 1dom 1don 1mca 1ml0 2bdn 2nz1 3ifd 4dn4 4zk9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4R8I)