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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DUPLEX FORM OF THE HIV-1(LAI) RNA DIMERIZATION INITIATION SITE MN SOAKED
 
Authors :  E. Ennifar, P. Walter, P. Dumas
Date :  12 Jan 07  (Deposition) - 25 Dec 07  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hiv-1, Dis, Rna, Dimerization, Metal Ions (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Ennifar, P. Walter, P. Dumas
Cation-Dependent Cleavage Of The Duplex Form Of The Subtype-B Hiv-1 Rna Dimerization Initiation Site.
Nucleic Acids Res. V. 38 5807 2010
PubMed-ID: 20460458  |  Reference-DOI: 10.1093/NAR/GKQ344

(-) Compounds

Molecule 1 - 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP *GP*CP*AP*AP*G)-3'
    Chains: A, B
    Engineered: YES
    Other Details: HIV-1 SUBTYPE-B DIS RNA, DIMERIZATION INITIATION SITE
    Other Details - Source: HIV-1 GENOMIC RNA LAI ISOLATE (HIV-1 SUBTYPE B)
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1K5Ligand/IonPOTASSIUM ION
2MN3Ligand/IonMANGANESE (II) ION
3NA3Ligand/IonSODIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:4BINDING SITE FOR RESIDUE K A 201
02AC2SOFTWAREG A:19 , U B:3BINDING SITE FOR RESIDUE K B 202
03AC3SOFTWAREU A:6 , G A:7 , C B:17 , G B:18BINDING SITE FOR RESIDUE K A 203
04AC4SOFTWAREA B:9 , G B:10 , HOH B:240BINDING SITE FOR RESIDUE MN B 204
05AC5SOFTWAREHOH A:373BINDING SITE FOR RESIDUE MN A 205
06AC6SOFTWAREC A:11 , G B:14 , HOH B:244BINDING SITE FOR RESIDUE MN B 206
07AC7SOFTWAREG A:4 , G B:4 , C B:20 , A B:21BINDING SITE FOR RESIDUE K B 207
08AC8SOFTWAREG A:10 , HOH A:330 , G B:10BINDING SITE FOR RESIDUE K B 208
09AC9SOFTWAREC B:11 , HOH B:219BINDING SITE FOR RESIDUE NA B 209
10BC1SOFTWAREA A:8 , G A:12 , C A:13 , HOH A:381 , HOH A:390BINDING SITE FOR RESIDUE NA A 315

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OJ0)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:RNA  Length:23
                                                      
                  2oj0 A  1 CUUGCUGAAGCGCGCACGGCAAG 23
                                    10        20   


Chain B from PDB  Type:RNA  Length:23
                                                      
                  2oj0 B  1 CUUGCUGAAGCGCGCACGGCAAG 23
                                    10        20
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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 Related Entries

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(-) Related Entries Specified in the PDB File

2oij HIV-1 SUBTYPE B DIS RNA DUPLEX (AUCL3 SOAKED)
2oiy HIV-1 SUBTYPE B DIS RNA DUPLEX (NATIVE)