PDBsum entry 1g2e

Transcription/RNA

PDB id: 1g2e

Contents

Protein chain

167 a.a. *

DNA/RNA

Waters ×154

* Residue conservation analysis

PDB id:

1g2e

Name:

Transcription/RNA

Title:

Crystal structure of hud and au-rich element of the tumor necrosis factor alpha RNA

Structure:

5'-r(p Up Ap Up Up Up Ap Up Up Up A)-3'. Chain: b. Fragment: fragment of au-rich element of the tumor necrosis factor alpha RNA. Engineered: yes. Paraneoplastic encephalomyelitis antigen hud. Chain: a. Fragment: n-terminal two rrm-domains. Engineered: yes

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Organ: brain. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.174 R-free: 0.238

Authors:

X.Wang,T.M.T.Hall

Key ref:

X.Wang and T.M.Tanaka Hall (2001). Structural basis for recognition of AU-rich element RNA by the HuD protein. Nat Struct Biol, 8, 141-145. PubMed id: 11175903 DOI: 10.1038/84131

Date:

18-Oct-00 Release date: 05-Feb-01

Protein chain

P26378  (ELAV4_HUMAN) -  ELAV-like protein 4 from Homo sapiens

Seq: 385 a.a.

Struc: 167 a.a.

DNA/RNA chain

U-A-U-U-U-A-U-U-U-A 10 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/84131

Nat Struct Biol 8:141-145 (2001)

PubMed id: 11175903

Structural basis for recognition of AU-rich element RNA by the HuD protein.

X.Wang, T.M.Tanaka Hall.

ABSTRACT

Hu proteins bind to adenosine-uridine (AU)-rich elements (AREs) in the 3' untranslated regions of many short-lived mRNAs, thereby stabilizing them. Here we report the crystal structures of the first two RNA recognition motif (RRM) domains of the HuD protein in complex with an 11-nucleotide fragment of a class I ARE (the c-fos ARE; to 1.8 A), and with an 11-nucleotide fragment of a class II ARE (the tumor necrosis factor alpha ARE; to 2.3 A). These structures reveal a consensus RNA recognition sequence that suggests a preference for pyrimidine-rich sequences and a requirement for a central uracil residue in the clustered AUUUA repeats found in class II AREs. Comparison to structures of other RRM domain-nucleic acid complexes reveals two base recognition pockets in all the structures that interact with bases using residues in conserved ribonucleoprotein motifs and at the C-terminal ends of RRM domains. Different conformations of nucleic acid can be bound by RRM domains by using different combinations of base recognition pockets and multiple RRM domains.

Selected figure(s)

Figure 2.
Figure 2. Protein -RNA contacts. a, Stereo diagram of the cfos-11 structure and HuD1,2 side chain contacts. b, Stereo diagram of the TNF 11 structure and HuD1,2 side chain contacts. The structures of the cfos-11 and TNF 11 RNAs are shown as ball-and-stick models colored by atom type. The bases and 5' and 3' ends of the RNA and side chains contacting the RNA are labeled. 2F[o] - F[c] maps for the cfos-11 and TNF 11 RNAs contoured at 1 are shown superimposed on their respective ball-and-stick models. Two water molecules are shown as green spheres. Hydrogen bonds within the RNA structures and with the water molecules are shown as black dotted lines and hydrogen bonds between the protein and RNAs are shown as red dashed lines. Amino acid residues are colored as in Fig. 1b. c, Summary of contacts between HuD1,2 protein and cfos-11 RNA. d, Summary of contacts between HuD1,2 protein and TNF 11 RNA. Red lines indicate side chain contacts, green lines indicate main chain contacts, and dashed orange lines indicate stacking interactions. Distances in Å are noted. Atoms on the RNA that are recognized in water-mediated contacts are highlighted with yellow. In the complex with TNF 11, the side chains of Tyr 128, Arg 166 and Lys 201 and the main chain of A203 seem to have moved away from the RNA to accommodate the A3 base. This could indicate plasticity in this site or reflect the ability to accommodate a less than ideal sequence at the concentration used for crystallization (1 mM).

Figure 4.
Figure 4. Nucleic acid recognition by RRM domains. a, Stereo diagram showing the superposition of RRM domains from HuD, Sxl, PABP, UP1, U1A, and U2B". The bases in all the structures at positions equivalent to U3/U9 (Sxl, G4/U10; PABP, A3/A6; UP1, A203/A209; U1A, C10; and U2B", C10) and U4/U10 (Sxl, U5/U11; PABP, A4/A8; UP1, G204/G210; U1A, A11; and U2B", A11) in the HuD1,2 -cfos-11 structure are shown in yellow and blue, respectively. Amino acid side chains at positions equivalent to Asn 40/Asn 126 (Sxl, Asn 126/Asn 212; PABP, Ser 12/Asn 100; and UP1, Lys 15/Lys 106), Ile 42/Tyr 128 (Sxl, Ile 124/Tyr 214; PABP, Tyr 14/Phe 102; UP1, Phe 17/Phe 108; U1A, Tyr 13; and U2B", Tyr 13), and Phe 84/Phe 170 (Sxl, Phe 170/Phe 256; PABP, Tyr 56/Phe 142; UP1, Phe 59/Phe 150; U1A, Phe 56; and U2B", Phe 56) in HuD1,2 are shown and backbone atoms at positions equivalent to Arg 116/Ala 203 of HuD1,2 (Sxl, Arg 202/Ala 289; PABP, Gln 88/Phe 173; UP1, Val 90/Leu 181; U1A, Lys 88; and U2B", Lys 88) are shown. Amino acid residues are colored as in Fig 1b. The side chains of Thr 11 in U1A and U2B", which occupy positions structurally equivalent to Asn 40/126 of HuD1,2, do not contact the RNA. Instead the side chains of Ser 91 near the C-terminus of U1A and U2B", which have no structural equivalent in the other structures, contact the RNA. b, Base recognition in the U3/U9 binding pocket. Stereo view showing the superimposed ball-and-stick models of U3 in the HuD1,2 -cfos-11 structure (green), G4 in the Sxl -tra structure (yellow), A209 in the UP1 -telomeric DNA structure (blue), and C10 in the U1A -U1 RNA structure (orange) and the residues contacting the bases. c, Base recognition in the U4/U10 binding pocket. Stereo view showing the superimposed ball-and-stick models of U10 in the HuD1,2 -cfos-11 structure (green), U5 in the Sxl -tra structure (yellow), A8 in the PABP -A[11] structure (red), and G204 in the UP1 -telomeric DNA structure (blue) and the residues contacting the bases. Hydrogen bonds are indicated by dotted lines.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 141-145) copyright 2001.

Figures were selected by the author.