PDBsum entry 2w2h

RNA binding protein

PDB id: 2w2h

Contents

Protein chains

263 a.a. *

29 a.a. *

DNA/RNA

Metals

_MN ×2

Waters ×6

* Residue conservation analysis

PDB id:

2w2h

Name:

RNA binding protein

Title:

Structural basis of transcription activation by the cyclin t1-tat-tar RNA complex from eiav

Structure:

Cyclin-t1. Chain: a, b. Fragment: residues 5-267. Synonym: cyct1, cyclin-t. Engineered: yes. Other_details: genbank\: af137509. Protein tat. Chain: c, d. Fragment: cyclin box domain of equine cyclin t1, residues 47-75.

Source:

Equus caballus. Horse. Organism_taxid: 9796. Expressed in: escherichia coli. Expression_system_taxid: 469008. Equine infectious anemia virus. Organism_taxid: 11665. Strain: pgex-4t1. Synthetic: yes.

Resolution:

3.25Å R-factor: 0.245 R-free: 0.278

Authors:

K.Anand,M.Geyer

Key ref:

K.Anand et al. (2008). Structural insights into the cyclin T1-Tat-TAR RNA transcription activation complex from EIAV. Nat Struct Biol, 15, 1287-1292. PubMed id: 19029897 DOI: 10.1038/nsmb.1513

Date:

30-Oct-08 Release date: 09-Dec-08

Protein chains

Q9XT26  (CCNT1_HORSE) -  Cyclin-T1 from Equus caballus

Seq: 727 a.a.

Struc: 263 a.a.*

Protein chains

P20920  (TAT_EIAVY) -  Protein Tat from Equine infectious anemia virus (strain Wyoming)

Seq: 75 a.a.

Struc: 29 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chains

G-C-U-C-A-G-A-U-U-C-U-G-C-G-G-U-C-U-G-A-G-C 22 bases

G-C-U-C-A-G-A-U-U-C-U-G-C-G-G-U-C-U-G-A-G-C 22 bases

DOI no: 10.1038/nsmb.1513

Nat Struct Biol 15:1287-1292 (2008)

PubMed id: 19029897

Structural insights into the cyclin T1-Tat-TAR RNA transcription activation complex from EIAV.

K.Anand, A.Schulte, K.Vogel-Bachmayr, K.Scheffzek, M.Geyer.

ABSTRACT

The replication of many retroviruses is mediated by a transcriptional activator protein, Tat, which activates RNA polymerase II at the level of transcription elongation. Tat interacts with Cyclin T1 of the positive transcription-elongation factor P-TEFb to recruit the transactivation-response TAR RNA, which acts as a promoter element in the transcribed 5' end of the viral long terminal repeat. Here we present the structure of the cyclin box domain of Cyclin T1 in complex with the Tat protein from the equine infectious anemia virus and its corresponding TAR RNA. The basic RNA-recognition motif of Tat adopts a helical structure whose flanking regions interact with a cyclin T-specific loop in the first cyclin box repeat. Together, both proteins coordinate the stem-loop structure of TAR. Our findings show that Tat binds to a surface on Cyclin T1 similar to where recognition motifs from substrate and inhibitor peptides were previously found to interact within Cdk-cyclin pairs.

Selected figure(s)

Figure 2.
(a) Sequence alignment of Tat from HIV-1 and EIAV. The basic ARM that is required for RNA binding is highlighted in blue. Cysteine and histidine residues proposed to form zinc-finger motifs are indicated. (b) Tat interacts with the first cyclin box repeat of CycT1. The basic ARM is suspended by its flanking regions on helices H1 and H4 as well as H3 and H5 of CycT1, thus wrapping around a CycT–specific insert in between H4 and H5 (yellow) that forms the Tat-interacting loop. (c) The C-terminal leucine of Tat inserts into a hydrophobic groove formed between helices H4 and H5 of CycT1. (d) Detailed view of the interaction between Ile41, Asp42 and Tyr43 of Tat with Asn43, Asp47 of CycT1 and residues Arg251 and Lys253 of the CycT1 TRM.

Figure 5.
Left, binding and specificity of the kinase substrate Cdc6 to Cdk2–CycA heterodimers is achieved by interaction with a substrate-recognition site on CycA^41. Middle, inhibition of Cdk2–CycA by p27-Kip1 requires the cooperative interaction with both subunits^42. Right, activation of Cdk9–CycT for transcription elongation by the viral Tat–TAR complex is achieved by interaction with CycT1 and recruitment to the RNA element at RNA polymerase II. In all three complexes, a similar surface on the first cyclin box repeat structure is covered for substrate recognition, inhibitor binding and transcription stimulation.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2008, 15, 1287-1292) copyright 2008.

Figures were selected by an automated process.