spacer
spacer

PDBsum entry 3pyu

Go to PDB code: 
protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
3pyu
Jmol
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
PDB id:
3pyu
Name: Ribosome
Title: Crystal structure of a complex containing domain 3 of crpv i RNA bound to the 70s ribosome. This file contains the 30s s the second 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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P62662  (RS2_THET2) -  30S ribosomal protein S2
Seq:
Struc:
256 a.a.
234 a.a.
Protein chain
Pfam   ArchSchema ?
P62663  (RS3_THET2) -  30S ribosomal protein S3
Seq:
Struc:
239 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P62664  (RS4_THET2) -  30S ribosomal protein S4
Seq:
Struc:
209 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
P62665  (RS5_THET2) -  30S ribosomal protein S5
Seq:
Struc:
162 a.a.
151 a.a.
Protein chain
Pfam   ArchSchema ?
P62666  (RS6_THET2) -  30S ribosomal protein S6
Seq:
Struc:
101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P62667  (RS7_THET2) -  30S ribosomal protein S7
Seq:
Struc:
156 a.a.
155 a.a.
Protein chain
Pfam   ArchSchema ?
P62668  (RS8_THET2) -  30S ribosomal protein S8
Seq:
Struc:
138 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P62669  (RS9_THET2) -  30S ribosomal protein S9
Seq:
Struc:
128 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
P62653  (RS10_THET2) -  30S ribosomal protein S10
Seq:
Struc:
105 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P62654  (RS11_THET2) -  30S ribosomal protein S11
Seq:
Struc:
129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P61941  (RS12_THET2) -  30S ribosomal protein S12
Seq:
Struc:
132 a.a.
124 a.a.
Protein chain
Pfam   ArchSchema ?
P62655  (RS13_THET2) -  30S ribosomal protein S13
Seq:
Struc:
126 a.a.
116 a.a.
Protein chain
Pfam   ArchSchema ?
P62656  (RS14Z_THET2) -  30S ribosomal protein S14 type Z
Seq:
Struc:
61 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
P62657  (RS15_THET2) -  30S ribosomal protein S15
Seq:
Struc:
89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
P62238  (RS16_THET2) -  30S ribosomal protein S16
Seq:
Struc:
88 a.a.
83 a.a.
Protein chain
Pfam   ArchSchema ?
P62658  (RS17_THET2) -  30S ribosomal protein S17
Seq:
Struc:
105 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P62659  (RS18_THET2) -  30S ribosomal protein S18
Seq:
Struc:
88 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
P62660  (RS19_THET2) -  30S ribosomal protein S19
Seq:
Struc:
93 a.a.
78 a.a.
Protein chain
Pfam   ArchSchema ?
P62661  (RS20_THET2) -  30S ribosomal protein S20
Seq:
Struc:
106 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P62613  (RSHX_THET2) -  30S ribosomal protein Thx
Seq:
Struc:
27 a.a.
24 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     translation   1 term 
  Biochemical function     structural constituent of ribosome     7 terms  

 

 
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.