PDBsum entry 2ozb

RNA binding protein/RNA

PDB id: 2ozb

Contents

Protein chains

126 a.a. *

239 a.a. *

DNA/RNA

Metals

_CA ×3

Waters ×239

* Residue conservation analysis

PDB id:

2ozb

Name:

RNA binding protein/RNA

Title:

Structure of a human prp31-15.5k-u4 snrna complex

Structure:

RNA comprising the 5' stem-loop RNA of u4snrna. Chain: c, f. Fragment: u4 5'-sl, residues 20-52. Engineered: yes. U4/u6.U5 tri-snrnp 15.5 kda protein. Chain: a, d. Synonym: high mobility group-like nuclear protein 2 homolog 1, nhp2- like protein 1, otk27, hsnu13. Engineered: yes.

Source:

Synthetic: yes. Other_details: RNA was chemically synthesized according to gene rnu4a (residues 20-52). Homo sapiens. Human. Organism_taxid: 9606. Strain: hela cells. Gene: nhp2l1. Expressed in: escherichia coli bl21(de3).

Resolution:

2.60Å R-factor: 0.208 R-free: 0.248

Authors:

S.Liu,R.Luehrmann,M.C.Wahl

Key ref:

S.Liu et al. (2007). Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP. Science, 316, 115-120. PubMed id: 17412961 DOI: 10.1126/science.1137924

Date:

26-Feb-07 Release date: 20-Mar-07

Protein chains

P55769  (NH2L1_HUMAN) -  NHP2-like protein 1 from Homo sapiens

Seq: 128 a.a.

Struc: 126 a.a.

Protein chains

Q8WWY3  (PRP31_HUMAN) -  U4/U6 small nuclear ribonucleoprotein Prp31 from Homo sapiens

Seq: 499 a.a.

Struc: 239 a.a.

DNA/RNA chains

A-U-C-G-U-A-G-C-C-A-A-U-G-A-G-G-U-U-U-A-U-C-C-G-A-G-G-C-G-C-G-A-U 33 bases

A-U-C-G-U-A-G-C-C-A-A-U-G-A-G-G-U-U-U-A-U-C-C-G-A-G-G-C-G-C-G-A-U 33 bases

Enzyme reactions

• Enzyme class: Chains A, B, D, E: E.C.?

DOI no: 10.1126/science.1137924

Science 316:115-120 (2007)

PubMed id: 17412961

Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP.

S.Liu, P.Li, O.Dybkov, S.Nottrott, K.Hartmuth, R.Lührmann, T.Carlomagno, M.C.Wahl.

ABSTRACT

Although highly homologous, the spliceosomal hPrp31 and the nucleolar Nop56 and Nop58 (Nop56/58) proteins recognize different ribonucleoprotein (RNP) particles. hPrp31 interacts with complexes containing the 15.5K protein and U4 or U4atac small nuclear RNA (snRNA), whereas Nop56/58 associate with 15.5K-box C/D small nucleolar RNA complexes. We present structural and biochemical analyses of hPrp31-15.5K-U4 snRNA complexes that show how the conserved Nop domain in hPrp31 maintains high RNP binding selectivity despite relaxed RNA sequence requirements. The Nop domain is a genuine RNP binding module, exhibiting RNA and protein binding surfaces. Yeast two-hybrid analyses suggest a link between retinitis pigmentosa and an aberrant hPrp31-hPrp6 interaction that blocks U4/U6-U5 tri-snRNP formation.

Selected figure(s)

Figure 1.
Fig. 1. (A) Schematics of the 5'-SLs of U4 snRNA (left), U4atac snRNA (middle), and the K-turn region of box C/D snoRNAs (right). N indicates any nucleotide; R, purine. Binding of 15.5K and the secondary binding proteins is indicated. Stem II of the K turn in the box C/D snoRNAs is longer by one base pair (20), and a single additional base pair in stem II is known to interfere with hPrp31 binding (21). Box C/D snoRNPs act as sequence-specific 2'-O methyltransferases, which posttranscriptionally modify several functional RNAs. (B)(Left) ^1H-^15N heteronuclear singlequantum coherence spectra of 15.5K in the binary 15.5K–U4 5'-SL complex (black) and in the ternary complex containing full-length hPrp31 (red). Assignments of selected resonances are indicated. ppm, parts per million. (Middle) Mapping of NMR chemical shift changes elicited by the addition of hPrp31 on the structure of the 15.5K-RNA complex [coordinates from (12); PDB ID 1E7K]. Dashed line is the disordered pentaloop of the RNA; 15.5K, light gray; and RNA, dark gray. All structure figures were prepared with PyMOL (34). (Right) Mapping of saturation transfer from hPrp31 to RNA-bound 15.5K, indicating residues of 15.5K that are directly contacted by hPrp31. Apparent contacts to the central ß sheet of 15.5K arise from spin diffusion. Degrees of chemical shift changes and saturation transfer are color-coded: red, strong; orange, intermediate; and yellow, weak. A similar picture is obtained when mapping the contacts of hPrp31^78-333 on 15.5K in the framework of the 15.5K–U4 5'-SL complex (SOM text), confirming that the hPrp31^78-333 fragment interacts with 15.5K in the same way as the full-length protein.

Figure 2.
Fig. 2. (A) Overview of the hPrp31^78-333–15.5K–U4 5'-SL complex (left). hPrp31^78-333, blue; 15.5K, red; RNA, gold. RNA elements not seen in the binary 15.5K–22-mer RNA complex with a shorter stem I [right (12); PDB ID 1E7K] are in green. Positions A194 and A216, at which missense mutations have been linked to the RP11 form of retinitis pigmentosa, are shown as space-filling models and colored cyan. Dashed line in hPrp31^78-333, disordered loop. Dashed line in the binary complex, unstructured pentaloop. Although induced-fit interactions are the hallmark of most RNA-protein complexes (32), the structuring of the RNA pentaloop upon hPrp31^78-333 binding observed here is particularly pronounced. The crystal structure contains two crystallographically independent ternary complexes per asymmetric unit that are largely identical (table S2). (B) Close-up views of the complex from the back (left) and from the bottom (right). Main contact regions between hPrp31^78-333 and 15.5K and between hPrp31^78-333 and the RNA are indicated by connecting lines and are labeled by letters and numbers, respectively. Regions of the RNA are color-coded: distal portion of stem I, gray; K-turn region, gold; distal portion of stem II, brown; and pentaloop, beige. The bulged-out U31 denotes the tip of the K turn and is shown in sticks.

The above figures are reprinted by permission from the AAAs: Science (2007, 316, 115-120) copyright 2007.

Figures were selected by an automated process.