NMR paper NMR analysis of the trans-activation response (TAR) RNA element of equine infectious

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[NMR paper] NMR analysis of the trans-activation response (TAR) RNA element of equine infectious

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NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

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TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

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NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

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SAVES2 or SAVES4

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NMR spectrum prediction:

FANDAS

MestReS

V-NMR

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Backbone S2

Methyl S2

B-factor

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Gromacs

Amber

Antechamber

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Shiftx2

Sparta+

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ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

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Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

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CCPN

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08-22-2010, 03:50 AM

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NMR analysis of the trans-activation response (TAR) RNA element of equine infectious

NMR analysis of the trans-activation response (TAR) RNA element of equine infectious anemia virus.

Related Articles NMR analysis of the trans-activation response (TAR) RNA element of equine infectious anemia virus.

Nucleic Acids Res. 1995 Oct 25;23(20):4058-65

Authors: Hoffman DW, White SW

Transcription of lentiviral DNA in the host cell is regulated by an interaction between the viral TAR RNA stem-loop and the viral Tat protein. Here we present a model of the three-dimensional structure of the TAR RNA stem-loop of the equine infectious anemia virus (EIAV), derived from two- and three-dimensional NMR data. This 25 nucleotide RNA consists of an A-form helical stem capped by two U-G base pairs and a four-nucleotide loop. Two loop cytidines are stacked into the loop interior and likely form a non-Watson-Crick C-C base-pair. The two nucleotides at the top of the loop, U13 and G14, appear to be excluded from the interior of the loop and solvent exposed. It is significant that now for the EIAV TAR-Tat system, three-dimensional structures are now known for both the RNA and protein components.

PMID: 7479065 [PubMed - indexed for MEDLINE]

Source: PubMed

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