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PDBsum entry 3f1f

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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
3f1f
Jmol
Contents
Protein chains
271 a.a. *
204 a.a. *
202 a.a. *
181 a.a. *
159 a.a. *
145 a.a. *
147 a.a. *
137 a.a. *
122 a.a. *
146 a.a. *
134 a.a. *
117 a.a. *
98 a.a. *
137 a.a. *
117 a.a. *
101 a.a. *
112 a.a. *
92 a.a. *
100 a.a. *
187 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
Metals
_MG ×1060
* Residue conservation analysis
PDB id:
3f1f
Name: Ribosome
Title: Crystal structure of a translation termination complex forme release factor rf2. This file contains the 50s subunit of o ribosome. The entire crystal structure contains two 70s rib described in remark 400.
Structure: 23s rrna. Chain: a. 5s rrna. Chain: b. 50s ribosomal protein l2. Chain: d. 50s ribosomal protein l3. Chain: e. 50s ribosomal protein l4.
Source: Thermus thermophilus. Organism_taxid: 274. Strain: hb27. Strain: hb27
Resolution:
3.00Å     R-factor:   0.281     R-free:   0.316
Authors: A.Korostelev,H.Asahara,L.Lancaster,M.Laurberg,A.Hirschi,H.F.
Key ref:
A.Korostelev et al. (2008). Crystal structure of a translation termination complex formed with release factor RF2. Proc Natl Acad Sci U S A, 105, 19684-19689. PubMed id: 19064930 DOI: 10.1073/pnas.0810953105
Date:
27-Oct-08     Release date:   23-Dec-08    
PROCHECK
Go to PROCHECK summary
 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 ?
P36238  (RL11_THETH) -  50S ribosomal protein L11
Seq:
Struc:
147 a.a.
147 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.
134 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.
117 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.
187 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

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     translation   1 term 
  Biochemical function     structural constituent of ribosome     9 terms  

 

 
DOI no: 10.1073/pnas.0810953105 Proc Natl Acad Sci U S A 105:19684-19689 (2008)
PubMed id: 19064930  
 
 
Crystal structure of a translation termination complex formed with release factor RF2.
A.Korostelev, H.Asahara, L.Lancaster, M.Laurberg, A.Hirschi, J.Zhu, S.Trakhanov, W.G.Scott, H.F.Noller.
 
  ABSTRACT  
 
We report the crystal structure of a translation termination complex formed by the Thermus thermophilus 70S ribosome bound with release factor RF2, in response to a UAA stop codon, solved at 3 A resolution. The backbone of helix alpha5 and the side chain of serine of the conserved SPF motif of RF2 recognize U1 and A2 of the stop codon, respectively. A3 is unstacked from the first 2 bases, contacting Thr-216 and Val-203 of RF2 and stacking on G530 of 16S rRNA. The structure of the RF2 complex supports our previous proposal that conformational changes in the ribosome in response to recognition of the stop codon stabilize rearrangement of the switch loop of the release factor, resulting in docking of the universally conserved GGQ motif in the PTC of the 50S subunit. As seen for the RF1 complex, the main-chain amide nitrogen of glutamine in the GGQ motif is positioned to contribute directly to catalysis of peptidyl-tRNA hydrolysis, consistent with mutational studies, which show that most side-chain substitutions of the conserved glutamine have little effect. We show that when the H-bonding capability of the main-chain N-H of the conserved glutamine is eliminated by substitution with proline, peptidyl-tRNA esterase activity is abolished, consistent with its proposed role in catalysis.
 
  Selected figure(s)  
 
Figure 1.
Comparison of the structures of the RF1 and RF2 termination complexes. (A) RF2 termination complex (this work), showing RF2 (yellow), P-site tRNA (orange), E-site tRNA (red), mRNA (green), 16S rRNA (cyan), 23S and 5S rRNA (gray), 30S proteins (blue), and 50S proteins (magenta). (B) RF1 termination complex (9); molecular components are colored similarly as in A. (C) RF2 in its ribosome-bound conformation, rotated ≈180° from the view shown in A, with domains numbered. The GGQ and SPF motifs are shown in red, and the switch loop is shown in orange. (D) RF1 in its ribosome-bound conformation. The GGQ and PVT motifs are indicated in red and the switch loop is shown in orange.
Figure 2.
Interactions with the UAA stop codon in the decoding center in the RF1 and RF2 termination complexes. (A) Stereoview of the σ[A]-weighted 3F[obs] − 2F[calc] electron density map of the stop codon and surrounding elements of RF2 and the ribosome. Electron density is contoured at 1.0 σ for RF2, and at 1.5 σ for rRNA and mRNA, and colored yellow (RF1), green (mRNA), and blue (16S rRNA). (B) Interaction of the hydroxyl group of Ser-206 of the SPF motif of RF2 with A2 of the stop codon. (C) Interaction of Thr-216 of RF2 with A3 of the stop codon. (D) Comparison of the positions of Thr-186 of the PVT motif of RF1 (gray) and Ser-206 of the SPF motif of RF2 (yellow), showing their different modes of recognition of U1 and A2 of the UAA stop codon. The structures of the two termination complexes were globally superimposed. (E) Packing of RF2 around A3 of the UAA stop codon. Val-203 would be positioned to exclude water from H-bonding to O6 of guanine, helping to discriminate against guanine at position 3. The structure model is represented as Van der Waals surfaces for RF2 (yellow) and mRNA (green); 16S rRNA is shown in blue.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21420300 B.P.Klaholz (2011).
Molecular recognition and catalysis in translation termination complexes.
  Trends Biochem Sci, 36, 282-292.  
21245352 J.Zhu, A.Korostelev, D.A.Costantino, J.P.Donohue, H.F.Noller, and J.S.Kieft (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.
PDB codes: 3pyn 3pyo 3pyq 3pyr 3pys 3pyt 3pyu 3pyv
21281690 K.Kipper, S.Sild, C.Hetényi, J.Remme, and A.Liiv (2011).
Pseudouridylation of 23S rRNA helix 69 promotes peptide release by release factor RF2 but not by release factor RF1.
  Biochimie, 93, 834-844.  
21804565 S.Kuhlenkoetter, W.Wintermeyer, and M.V.Rodnina (2011).
Different substrate-dependent transition states in the active site of the ribosome.
  Nature, 476, 351-354.  
21623367 T.Becker, J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, H.Sieber, B.A.Motaal, T.Mielke, O.Berninghausen, and R.Beckmann (2011).
Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome.
  Nat Struct Mol Biol, 18, 715-720.
PDB code: 3izq
20588254 A.Korostelev, J.Zhu, H.Asahara, and H.F.Noller (2010).
Recognition of the amber UAG stop codon by release factor RF1.
  EMBO J, 29, 2577-2585.
PDB codes: 3mr8 3mrz 3ms0 3ms1
20852642 C.L.Ng, K.Lang, N.A.Meenan, A.Sharma, A.C.Kelley, C.Kleanthous, and V.Ramakrishnan (2010).
Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3.
  Nat Struct Mol Biol, 17, 1241-1246.
PDB codes: 2xfz 2xg0 2xg1 2xg2
20668033 D.E.Burakovsky, P.V.Sergiev, M.A.Steblyanko, A.V.Kubarenko, A.L.Konevega, A.A.Bogdanov, M.V.Rodnina, and O.A.Dontsova (2010).
Mutations at the accommodation gate of the ribosome impair RF2-dependent translation termination.
  RNA, 16, 1848-1853.  
20584893 D.J.Young, C.D.Edgar, E.S.Poole, and W.P.Tate (2010).
The codon specificity of eubacterial release factors is determined by the sequence and size of the recognition loop.
  RNA, 16, 1623-1633.  
20421313 D.J.Young, C.D.Edgar, J.Murphy, J.Fredebohm, E.S.Poole, and W.P.Tate (2010).
Bioinformatic, structural, and functional analyses support release factor-like MTRF1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria.
  RNA, 16, 1146-1155.  
20421507 H.Jin, A.C.Kelley, D.Loakes, and V.Ramakrishnan (2010).
Structure of the 70S ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release.
  Proc Natl Acad Sci U S A, 107, 8593-8598.
PDB codes: 2x9r 2x9s 2x9t 2x9u
20603079 H.S.Zaher, and R.Green (2010).
Hyperaccurate and error-prone ribosomes exploit distinct mechanisms during tRNA selection.
  Mol Cell, 39, 110-120.  
20724456 H.S.Zaher, and R.Green (2010).
Kinetic basis for global loss of fidelity arising from mismatches in the P-site codon:anticodon helix.
  RNA, 16, 1980-1989.  
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
20512119 J.Sund, M.Andér, and J.Aqvist (2010).
Principles of stop-codon reading on the ribosome.
  Nature, 465, 947-950.  
20688868 K.N.Bulygin, Y.S.Khairulina, P.M.Kolosov, A.G.Ven'yaminova, D.M.Graifer, Y.N.Vorobjev, L.Y.Frolova, L.L.Kisselev, and G.G.Karpova (2010).
Three distinct peptides from the N domain of translation termination factor eRF1 surround stop codon in the ribosome.
  RNA, 16, 1902-1914.  
20400952 L.B.Jenner, N.Demeshkina, G.Yusupova, and M.Yusupov (2010).
Structural aspects of messenger RNA reading frame maintenance by the ribosome.
  Nat Struct Mol Biol, 17, 555-560.
PDB codes: 3i8f 3i8g 3i8h 3i8i 3i9b 3i9c 3i9d 3i9e
20694005 L.Jenner, N.Demeshkina, G.Yusupova, and M.Yusupov (2010).
Structural rearrangements of the ribosome at the tRNA proofreading step.
  Nat Struct Mol Biol, 17, 1072-1078.  
20427512 P.C.Whitford, P.Geggier, R.B.Altman, S.C.Blanchard, J.N.Onuchic, and K.Y.Sanbonmatsu (2010).
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.
  RNA, 16, 1196-1204.  
20154709 R.E.Stanley, G.Blaha, R.L.Grodzicki, M.D.Strickler, and T.A.Steitz (2010).
The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.
  Nat Struct Mol Biol, 17, 289-293.
PDB codes: 3knh 3kni 3knj 3knk 3knl 3knm 3knn 3kno
20208546 S.L.He, and R.Green (2010).
Visualization of codon-dependent conformational rearrangements during translation termination.
  Nat Struct Mol Biol, 17, 465-470.  
20699303 S.P.McClory, J.M.Leisring, D.Qin, and K.Fredrick (2010).
Missense suppressor mutations in 16S rRNA reveal the importance of helices h8 and h14 in aminoacyl-tRNA selection.
  RNA, 16, 1925-1934.  
19822758 A.Korostelev, M.Laurberg, and H.F.Noller (2009).
Multistart simulated annealing refinement of the crystal structure of the 70S ribosome.
  Proc Natl Acad Sci U S A, 106, 18195-18200.  
19874047 B.Hetrick, K.Lee, and S.Joseph (2009).
Kinetics of stop codon recognition by release factor 1.
  Biochemistry, 48, 11178-11184.  
19239893 H.S.Zaher, and R.Green (2009).
Fidelity at the molecular level: lessons from protein synthesis.
  Cell, 136, 746-762.  
19595805 M.Simonović, and T.A.Steitz (2009).
A structural view on the mechanism of the ribosome-catalyzed peptide bond formation.
  Biochim Biophys Acta, 1789, 612-623.  
19329641 R.Yang, L.R.Cruz-Vera, and C.Yanofsky (2009).
23S rRNA nucleotides in the peptidyl transferase center are essential for tryptophanase operon induction.
  J Bacteriol, 191, 3445-3450.  
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
19846563 W.Niu, Z.Chen, L.A.Bush-Pelc, A.Bah, P.S.Gandhi, and E.Di Cera (2009).
Mutant N143P reveals how Na+ activates thrombin.
  J Biol Chem, 284, 36175-36185.
PDB codes: 3jz1 3jz2
19696352 W.Zhang, J.A.Dunkle, and J.H.Cate (2009).
Structures of the ribosome in intermediate states of ratcheting.
  Science, 325, 1014-1017.
PDB codes: 3i1m 3i1n 3i1o 3i1p 3i1q 3i1r 3i1s 3i1t 3i1z 3i20 3i21 3i22
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.