PDBsum entry 3pys

Ribosome

PDB id: 3pys

Contents

Protein chains

234 a.a. *

206 a.a. *

208 a.a. *

151 a.a. *

101 a.a. *

155 a.a. *

138 a.a. *

127 a.a. *

98 a.a. *

119 a.a. *

124 a.a. *

116 a.a. *

60 a.a. *

88 a.a. *

83 a.a. *

99 a.a. *

70 a.a. *

78 a.a. *

99 a.a. *

24 a.a. *

DNA/RNA

Metals

_ZN ×2

* Residue conservation analysis

Obsolete entry

PDB id:

3pys

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 30s subunit of the first 70s ribosome.

Structure:

Ribosomal RNA 16s. Chain: a. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5.

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

P62662  (RS2_THET2) -  Small ribosomal subunit protein uS2 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 256 a.a.

Struc: 234 a.a.

Protein chain

P62663  (RS3_THET2) -  Small ribosomal subunit protein uS3 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 239 a.a.

Struc: 206 a.a.

Protein chain

P62664  (RS4_THET2) -  Small ribosomal subunit protein uS4 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 209 a.a.

Struc: 208 a.a.

Protein chain

P62665  (RS5_THET2) -  Small ribosomal subunit protein uS5 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 162 a.a.

Struc: 151 a.a.

Protein chain

P62666  (RS6_THET2) -  Small ribosomal subunit protein bS6 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 101 a.a.

Struc: 101 a.a.

Protein chain

P62667  (RS7_THET2) -  Small ribosomal subunit protein uS7 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 156 a.a.

Struc: 155 a.a.

Protein chain

P62668  (RS8_THET2) -  Small ribosomal subunit protein uS8 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 138 a.a.

Struc: 138 a.a.

Protein chain

P62669  (RS9_THET2) -  Small ribosomal subunit protein uS9 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 128 a.a.

Struc: 127 a.a.

Protein chain

P62653  (RS10_THET2) -  Small ribosomal subunit protein uS10 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 105 a.a.

Struc: 98 a.a.

Protein chain

P62654  (RS11_THET2) -  Small ribosomal subunit protein uS11 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 129 a.a.

Struc: 119 a.a.

Protein chain

P61941  (RS12_THET2) -  Small ribosomal subunit protein uS12 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 132 a.a.

Struc: 124 a.a.

Protein chain

P62655  (RS13_THET2) -  Small ribosomal subunit protein uS13 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 126 a.a.

Struc: 116 a.a.

Protein chain

P62656  (RS14Z_THET2) -  Small ribosomal subunit protein uS14 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 61 a.a.

Struc: 60 a.a.

Protein chain

P62657  (RS15_THET2) -  Small ribosomal subunit protein uS15 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 89 a.a.

Struc: 88 a.a.

Protein chain

P62238  (RS16_THET2) -  Small ribosomal subunit protein bS16 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 88 a.a.

Struc: 83 a.a.

Protein chain

P62658  (RS17_THET2) -  Small ribosomal subunit protein uS17 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 105 a.a.

Struc: 99 a.a.

Protein chain

P62659  (RS18_THET2) -  Small ribosomal subunit protein bS18 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 88 a.a.

Struc: 70 a.a.

Protein chain

P62660  (RS19_THET2) -  Small ribosomal subunit protein uS19 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 93 a.a.

Struc: 78 a.a.

Protein chain

P62661  (RS20_THET2) -  Small ribosomal subunit protein bS20 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 106 a.a.

Struc: 99 a.a.

Protein chain

P62613  (RSHX_THET2) -  Small ribosomal subunit protein bTHX from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 27 a.a.

Struc: 24 a.a.

DNA/RNA chains

U-G-G-A-G-A-G-U-U-U-G-A-U-C-C-U-G-G-C-U-C-A-G-G-G-U-G-A-A-C-G-C-U-G-G-C-G-G-C- ... 1506 bases

G-G-U-U-A-U-U-C-A-G-A-U-U-A-G-G-U-A-G-U-C-G-A-A-U-G-A-C-C-U-A-C-C-U 34 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.