PDBsum entry 3pyv

Ribosome

PDB id: 3pyv

Contents

Protein chains

271 a.a. *

204 a.a. *

202 a.a. *

181 a.a. *

159 a.a. *

145 a.a. *

32 a.a. *

137 a.a. *

122 a.a. *

146 a.a. *

136 a.a. *

117 a.a. *

98 a.a. *

137 a.a. *

116 a.a. *

101 a.a. *

112 a.a. *

92 a.a. *

100 a.a. *

188 a.a. *

76 a.a. *

88 a.a. *

62 a.a. *

59 a.a. *

30 a.a. *

52 a.a. *

44 a.a. *

48 a.a. *

63 a.a. *

DNA/RNA

* Residue conservation analysis

Obsolete entry

PDB id:

3pyv

Name:

Ribosome

Title:

Crystal structure of a complex containing domain 3 of crpv igr ires RNA bound to the 70s ribosome. This file contains the 50s subunit of the second 70s ribosome.

Structure:

23s ribosomal RNA. Chain: a. 5s ribosomal RNA. Chain: b. 50s ribosomal protein l2. Chain: c. 50s ribosomal protein l3. Chain: d. 50s ribosomal protein l4.

Source:

Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Strain: hb27

Resolution:

3.40Å R-factor: 0.228 R-free: 0.266

Authors:

J.Zhu,A.Korostelev,D.Costantino,H.F.Noller,J.S.Kieft

Key ref:

J.Zhu et al. (2011). Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome. Proc Natl Acad Sci U S A, 108, 1839-1844. PubMed id: 21245352

Date:

13-Dec-10 Release date: 09-Feb-11

Protein chain

Q72I07  (RL2_THET2) -  50S ribosomal protein L2 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 276 a.a.

Struc: 271 a.a.

Protein chain

Q72I04  (RL3_THET2) -  50S ribosomal protein L3 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 206 a.a.

Struc: 204 a.a.

Protein chain

Q72I05  (RL4_THET2) -  50S ribosomal protein L4 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 205 a.a.

Struc: 202 a.a.

Protein chain

Q72I16  (RL5_THET2) -  50S ribosomal protein L5 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 182 a.a.

Struc: 181 a.a.

Protein chain

Q72I19  (RL6_THET2) -  50S ribosomal protein L6 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 180 a.a.

Struc: 159 a.a.

Protein chain

Q72GV5  (RL9_THET2) -  50S ribosomal protein L9 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 148 a.a.

Struc: 145 a.a.

Protein chain

Q72GS1  (RL10_THET2) -  50S ribosomal protein L10 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 173 a.a.

Struc: 32 a.a.*

Protein chain

Q72IN1  (RL13_THET2) -  50S ribosomal protein L13 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 140 a.a.

Struc: 137 a.a.

Protein chain

Q72I14  (RL14_THET2) -  50S ribosomal protein L14 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 122 a.a.

Struc: 122 a.a.

Protein chain

Q72I23  (RL15_THET2) -  50S ribosomal protein L15 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 150 a.a.

Struc: 146 a.a.

Protein chain

Q72I11  (RL16_THET2) -  50S ribosomal protein L16 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 141 a.a.

Struc: 136 a.a.

Protein chain

Q72I33  (RL17_THET2) -  50S ribosomal protein L17 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 118 a.a.

Struc: 117 a.a.

Protein chain

Q72I20  (RL18_THET2) -  50S ribosomal protein L18 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 112 a.a.

Struc: 98 a.a.

Protein chain

Q72JU9  (RL19_THET2) -  50S ribosomal protein L19 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 146 a.a.

Struc: 137 a.a.

Protein chain

Q72L76  (RL20_THET2) -  50S ribosomal protein L20 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 118 a.a.

Struc: 116 a.a.

Protein chain

Q72HR2  (RL21_THET2) -  50S ribosomal protein L21 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 101 a.a.

Struc: 101 a.a.

Protein chain

Q72I09  (RL22_THET2) -  50S ribosomal protein L22 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 113 a.a.

Struc: 112 a.a.

Protein chain

Q72I06  (RL23_THET2) -  50S ribosomal protein L23 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 96 a.a.

Struc: 92 a.a.

Protein chain

Q72I15  (RL24_THET2) -  50S ribosomal protein L24 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 110 a.a.

Struc: 100 a.a.

Protein chain

Q72IA7  (RL25_THET2) -  50S ribosomal protein L25 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 206 a.a.

Struc: 188 a.a.

Protein chain

Q72HR3  (RL27_THET2) -  50S ribosomal protein L27 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 85 a.a.

Struc: 76 a.a.

Protein chain

Q72G84  (RL28_THET2) -  50S ribosomal protein L28 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 98 a.a.

Struc: 88 a.a.

Protein chain

Q72I12  (RL29_THET2) -  50S ribosomal protein L29 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 72 a.a.

Struc: 62 a.a.

Protein chain

Q72I22  (RL30_THET2) -  50S ribosomal protein L30 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 60 a.a.

Struc: 59 a.a.

Protein chain

Q72JR0  (RL31_THET2) -  50S ribosomal protein L31 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 71 a.a.

Struc: 30 a.a.

Protein chain

P62652  (RL32_THET2) -  50S ribosomal protein L32 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 60 a.a.

Struc: 52 a.a.

Protein chain

Q72GW3  (RL33_THET2) -  50S ribosomal protein L33 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 54 a.a.

Struc: 44 a.a.

Protein chain

P80340  (RL34_THET8) -  50S ribosomal protein L34 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 49 a.a.

Struc: 48 a.a.

Protein chain

Q72L77  (RL35_THET2) -  50S ribosomal protein L35 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 65 a.a.

Struc: 63 a.a.

* PDB and UniProt seqs differ at 12 residue positions (black crosses)

DNA/RNA chains

A-G-A-U-G-G-U-A-A-G-G-G-C-C-C-A-C-G-G-U-G-G-A-U-G-C-C-U-C-G-G-C-A-C-C-C-G-A-G- ... 2760 bases

U-C-C-C-C-C-G-U-G-C-C-C-A-U-A-G-C-G-G-C-G-U-G-G-A-A-C-C-A-C-C-C-G-U-U-C-C-C-A- 119 bases

Proc Natl Acad Sci U S A 108:1839-1844 (2011)

PubMed id: 21245352

Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.

J.Zhu, A.Korostelev, D.A.Costantino, J.P.Donohue, H.F.Noller, J.S.Kieft.

ABSTRACT

Internal ribosome entry site (IRES) RNAs are elements of viral or cellular mRNAs that bypass steps of canonical eukaryotic cap-dependent translation initiation. Understanding of the structural basis of IRES mechanisms is limited, partially due to a lack of high-resolution structures of IRES RNAs bound to their cellular targets. Prompted by the universal phylogenetic conservation of the ribosomal P site, we solved the crystal structures of proposed P site binding domains from two intergenic region IRES RNAs bound to bacterial 70S ribosomes. The structures show that these IRES domains nearly perfectly mimic a tRNA • mRNA interaction. However, there are clear differences in the global shape and position of this IRES domain in the intersubunit space compared to those of tRNA, supporting a mechanism for IRES action that invokes hybrid state mimicry to drive a noncanonical mode of translocation. These structures suggest how relatively small structured RNAs can manipulate complex biological machines.