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(-) Description

Title :  CRYSTAL STRUCTURE OF HEPATITIS C VIRUS IRES SUBDOMAIN IIA
 
Authors :  Q. Zhao, Q. Han, C. R. Kissinger, P. A. Thompson
Date :  23 Apr 07  (Deposition) - 01 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hcv, Ires, Subdoamin Iia, Rna, Strontium, Hepatitis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Zhao, Q. Han, C. R. Kissinger, T. Hermann, P. A. Thompson
Structure Of Hepatitis C Virus Ires Subdomain Iia.
Acta Crystallogr. , Sect. D V. 64 436 2008
PubMed-ID: 18391410  |  Reference-DOI: 10.1107/S0907444908002011

(-) Compounds

Molecule 1 - 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP *CP*AP*CP*GP*CP*C)-3'
    Chains: A, C
    Engineered: YES
    Fragment: HCV IRES SUBDOMAIN IIA (RESIDUE 47-70)
    Mutation: YES
    Other Details: THIS SEQUENCE OF RNA NATURALLY EXISTS IN HEPATITIS C VIRUS
    Synthetic: YES
 
Molecule 2 - 5'-R(*GP*CP*GP*(5BU) P*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*(5BU)P*CP*CP*GP*G)-3'
    Chains: B, D
    Engineered: YES
    Fragment: HCV IRES SUBDOMAIN IIA (RESIDUE 98-117)
    Mutation: YES
    Other Details: THIS SEQUENCE OF RNA NATURALLY EXISTS IN HEPATITIS C VIRUS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
15BU4Mod. Nucleotide5-BROMO-URIDINE-5'-MONOPHOSPHATE
2SR10Ligand/IonSTRONTIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
15BU2Mod. Nucleotide5-BROMO-URIDINE-5'-MONOPHOSPHATE
2SR-1Ligand/IonSTRONTIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
15BU2Mod. Nucleotide5-BROMO-URIDINE-5'-MONOPHOSPHATE
2SR-1Ligand/IonSTRONTIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1046 , HOH B:126BINDING SITE FOR RESIDUE SR A 1001
2AC2SOFTWAREHOH A:1038BINDING SITE FOR RESIDUE SR A 1002
3AC3SOFTWAREHOH C:1032BINDING SITE FOR RESIDUE SR C 1003
4AC4SOFTWAREHOH A:1035BINDING SITE FOR RESIDUE SR C 1022
5AC5SOFTWAREHOH A:1036BINDING SITE FOR RESIDUE SR A 1027
6AC6SOFTWAREHOH A:1032 , HOH A:1045BINDING SITE FOR RESIDUE SR A 1005
7AC7SOFTWAREHOH C:1028 , HOH C:1034BINDING SITE FOR RESIDUE SR C 1008

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PN4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PN4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2PN4)

(-) 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    
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Chain A from PDB  Type:RNA  Length:24
                                                        
                 2pn4 A  47 CGGAGGAACUACUGUCUUCACGCC  70
                                    56        66    


Chain B from PDB  Type:RNA  Length:20
                                                    
                 2pn4 B  98 GCGuGUCGUGCAGCCuCCGG 117
                               |   107     | 117
                             101-5BU     113-5BU


Chain C from PDB  Type:RNA  Length:24
                                                        
                 2pn4 C  47 CGGAGGAACUACUGUCUUCACGCC  70
                                    56        66    


Chain D from PDB  Type:RNA  Length:20
                                                    
                 2pn4 D  98 GCGuGUCGUGCAGCCuCCGG 117
                               |   107     | 117
                             101-5BU     113-5BU
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2PN4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PN4)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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  2pn4
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