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PDBsum entry 3pyv

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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
3pyv
Jmol
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
PDB id:
3pyv
Name: Ribosome
Title: Crystal structure of a complex containing domain 3 of crpv i RNA bound to the 70s ribosome. This file contains the 50s s 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    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q72I07  (RL2_THET2) -  50S ribosomal protein L2
Seq:
Struc:
276 a.a.
271 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I04  (RL3_THET2) -  50S ribosomal protein L3
Seq:
Struc:
206 a.a.
204 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I05  (RL4_THET2) -  50S ribosomal protein L4
Seq:
Struc:
205 a.a.
202 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I16  (RL5_THET2) -  50S ribosomal protein L5
Seq:
Struc:
182 a.a.
181 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I19  (RL6_THET2) -  50S ribosomal protein L6
Seq:
Struc:
180 a.a.
159 a.a.
Protein chain
Pfam   ArchSchema ?
Q72GV5  (RL9_THET2) -  50S ribosomal protein L9
Seq:
Struc:
148 a.a.
145 a.a.
Protein chain
Pfam   ArchSchema ?
Q72GS1  (RL10_THET2) -  50S ribosomal protein L10
Seq:
Struc:
173 a.a.
32 a.a.*
Protein chain
Pfam   ArchSchema ?
Q72IN1  (RL13_THET2) -  50S ribosomal protein L13
Seq:
Struc:
140 a.a.
137 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I14  (RL14_THET2) -  50S ribosomal protein L14
Seq:
Struc:
122 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I23  (RL15_THET2) -  50S ribosomal protein L15
Seq:
Struc:
150 a.a.
146 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I11  (RL16_THET2) -  50S ribosomal protein L16
Seq:
Struc:
141 a.a.
136 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I33  (RL17_THET2) -  50S ribosomal protein L17
Seq:
Struc:
118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I20  (RL18_THET2) -  50S ribosomal protein L18
Seq:
Struc:
112 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
Q72JU9  (RL19_THET2) -  50S ribosomal protein L19
Seq:
Struc:
146 a.a.
137 a.a.
Protein chain
Pfam   ArchSchema ?
Q72L76  (RL20_THET2) -  50S ribosomal protein L20
Seq:
Struc:
118 a.a.
116 a.a.
Protein chain
Pfam   ArchSchema ?
Q72HR2  (RL21_THET2) -  50S ribosomal protein L21
Seq:
Struc:
101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I09  (RL22_THET2) -  50S ribosomal protein L22
Seq:
Struc:
113 a.a.
112 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I06  (RL23_THET2) -  50S ribosomal protein L23
Seq:
Struc:
96 a.a.
92 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I15  (RL24_THET2) -  50S ribosomal protein L24
Seq:
Struc:
110 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
Q72IA7  (RL25_THET2) -  50S ribosomal protein L25
Seq:
Struc:
206 a.a.
188 a.a.
Protein chain
Pfam   ArchSchema ?
Q72HR3  (RL27_THET2) -  50S ribosomal protein L27
Seq:
Struc:
85 a.a.
76 a.a.
Protein chain
Pfam   ArchSchema ?
Q72G84  (RL28_THET2) -  50S ribosomal protein L28
Seq:
Struc:
98 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I12  (RL29_THET2) -  50S ribosomal protein L29
Seq:
Struc:
72 a.a.
62 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I22  (RL30_THET2) -  50S ribosomal protein L30
Seq:
Struc:
60 a.a.
59 a.a.
Protein chain
Pfam   ArchSchema ?
Q72JR0  (RL31_THET2) -  50S ribosomal protein L31
Seq:
Struc:
71 a.a.
30 a.a.
Protein chain
Pfam   ArchSchema ?
P62652  (RL32_THET2) -  50S ribosomal protein L32
Seq:
Struc:
60 a.a.
52 a.a.
Protein chain
Pfam   ArchSchema ?
Q72GW3  (RL33_THET2) -  50S ribosomal protein L33
Seq:
Struc:
54 a.a.
44 a.a.
Protein chain
Pfam   ArchSchema ?
P80340  (RL34_THET8) -  50S ribosomal protein L34
Seq:
Struc:
49 a.a.
48 a.a.
Protein chain
Pfam   ArchSchema ?
Q72L77  (RL35_THET2) -  50S ribosomal protein L35
Seq:
Struc:
65 a.a.
63 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 12 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     ribosome biogenesis   2 terms 
  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.