› 397d

X-ray diffraction
1.3Å resolution

A 1.3 A RESOLUTION CRYSTAL STRUCTURE OF THE HIV-1 TRANS-ACTIVATION RESPONSE REGION RNA STEM REVEALS A METAL ION-DEPENDENT BULGE CONFORMATION

Released:
DOI: 10.2210/pdb397d/pdb
PDB entry 397d coloured by chain, front view.
PDB entry 397d coloured by chain, side view.
PDB entry 397d coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation.
Ippolito JA, Steitz TA
Proc Natl Acad Sci U S A 95 9819-24 (1998)
PMID: 9707559

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-196623 (preferred)
Entry contents:
2 distinct RNA molecules
Macromolecules (2 distinct):
RNA (5'-R(*GP*GP*CP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP*CP*G)-3') Chain: A
Molecule details ›
Chain: A
Length: 15 nucleotides
Theoretical weight: 4.85 KDa
Source organism: Synthetic construct
Expression system: Not provided
RNA (5'-R(*GP*CP*UP*CP*UP*CP*UP*GP*GP*CP*CP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.74 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 4 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1, RIGAKU RU300
Spacegroup: P1
Unit cell:
a: 27.1Å b: 27.1Å c: 31.6Å
α: 69.2° β: 77.5° γ: 63°
R-values:
R R work R free
0.131 not available 0.177
Expression system: Not provided

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Citations

18 review citations

Structural biology of HIV.
Turner et al. (1999)
17 more

8 mentions without citation

Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition.
Frank et al. (2009)
7 more