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PDBsum entry 3r8s
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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
3r8s

 

 

 

 

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Contents
Protein chains
271 a.a.
209 a.a.
201 a.a.
177 a.a.
176 a.a.
149 a.a.
141 a.a.
142 a.a.
122 a.a.
143 a.a.
136 a.a.
120 a.a.
116 a.a.
114 a.a.
117 a.a.
103 a.a.
110 a.a.
93 a.a.
102 a.a.
94 a.a.
76 a.a.
77 a.a.
63 a.a.
58 a.a.
56 a.a.
50 a.a.
46 a.a.
64 a.a.
38 a.a.
DNA/RNA
Metals
_MG ×199
_ZN
Waters ×668
Obsolete entry
PDB id:
3r8s
Name: Ribosome
Title: Structures of the bacterial ribosome in classical and hybrid states of tRNA binding
Structure: 23s rrna. Chain: a. 5s rrna. Chain: b. 50s ribosomal protein l2. Chain: c. 50s ribosomal protein l3. Chain: d. 50s ribosomal protein l4.
Source: Escherichia coli. Organism_taxid: 562. Organism_taxid: 83333. Strain: k-12. Strain: k-12
Resolution:
3.00Å     R-factor:   0.203     R-free:   0.260
Authors: J.A.Dunkle,L.Wang,M.B.Feldman,A.Pulk,V.B.Chen,G.J.Kapral,J.Noeske, J.S.Richardson,S.C.Blanchard,J.H.D.Cate
Key ref: J.A.Dunkle et al. (2011). Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science, 332, 981-984. PubMed id: 21596992
Date:
24-Mar-11     Release date:   01-Jun-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P60422  (RL2_ECOLI) -  50S ribosomal protein L2 from Escherichia coli (strain K12)
Seq:
Struc: 		273 a.a.
271 a.a.
Protein chain
Pfam   ArchSchema ?
P60438  (RL3_ECOLI) -  50S ribosomal protein L3 from Escherichia coli (strain K12)
Seq:
Struc: 		209 a.a.
209 a.a.
Protein chain
Pfam   ArchSchema ?
P60723  (RL4_ECOLI) -  50S ribosomal protein L4 from Escherichia coli (strain K12)
Seq:
Struc: 		201 a.a.
201 a.a.
Protein chain
Pfam   ArchSchema ?
P62399  (RL5_ECOLI) -  50S ribosomal protein L5 from Escherichia coli (strain K12)
Seq:
Struc: 		179 a.a.
177 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG55  (RL6_ECOLI) -  50S ribosomal protein L6 from Escherichia coli (strain K12)
Seq:
Struc: 		177 a.a.
176 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R1  (RL9_ECOLI) -  50S ribosomal protein L9 from Escherichia coli (strain K12)
Seq:
Struc: 		149 a.a.
149 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7J7  (RL11_ECOLI) -  50S ribosomal protein L11 from Escherichia coli (strain K12)
Seq:
Struc: 		142 a.a.
141 a.a.
Protein chain
Pfam   ArchSchema ?
P0AA10  (RL13_ECOLI) -  50S ribosomal protein L13 from Escherichia coli (strain K12)
Seq:
Struc: 		142 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY3  (RL14_ECOLI) -  50S ribosomal protein L14 from Escherichia coli (strain K12)
Seq:
Struc: 		123 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
P02413  (RL15_ECOLI) -  50S ribosomal protein L15 from Escherichia coli (strain K12)
Seq:
Struc: 		144 a.a.
143 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY7  (RL16_ECOLI) -  50S ribosomal protein L16 from Escherichia coli (strain K12)
Seq:
Struc: 		136 a.a.
136 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG44  (RL17_ECOLI) -  50S ribosomal protein L17 from Escherichia coli (strain K12)
Seq:
Struc: 		127 a.a.
120 a.a.
Protein chain
Pfam   ArchSchema ?
P0C018  (RL18_ECOLI) -  50S ribosomal protein L18 from Escherichia coli (strain K12)
Seq:
Struc: 		117 a.a.
116 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7K6  (RL19_ECOLI) -  50S ribosomal protein L19 from Escherichia coli (strain K12)
Seq:
Struc: 		115 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L3  (RL20_ECOLI) -  50S ribosomal protein L20 from Escherichia coli (strain K12)
Seq:
Struc: 		118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG48  (RL21_ECOLI) -  50S ribosomal protein L21 from Escherichia coli (strain K12)
Seq:
Struc: 		103 a.a.
103 a.a.
Protein chain
Pfam   ArchSchema ?
P61175  (RL22_ECOLI) -  50S ribosomal protein L22 from Escherichia coli (strain K12)
Seq:
Struc: 		110 a.a.
110 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADZ0  (RL23_ECOLI) -  50S ribosomal protein L23 from Escherichia coli (strain K12)
Seq:
Struc: 		100 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
P60624  (RL24_ECOLI) -  50S ribosomal protein L24 from Escherichia coli (strain K12)
Seq:
Struc: 		104 a.a.
102 a.a.
Protein chain
Pfam   ArchSchema ?
P68919  (RL25_ECOLI) -  50S ribosomal protein L25 from Escherichia coli (strain K12)
Seq:
Struc: 		94 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L8  (RL27_ECOLI) -  50S ribosomal protein L27 from Escherichia coli (strain K12)
Seq:
Struc: 		85 a.a.
76 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M2  (RL28_ECOLI) -  50S ribosomal protein L28 from Escherichia coli (strain K12)
Seq:
Struc: 		78 a.a.
77 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M6  (RL29_ECOLI) -  50S ribosomal protein L29 from Escherichia coli (strain K12)
Seq:
Struc: 		63 a.a.
63 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG51  (RL30_ECOLI) -  50S ribosomal protein L30 from Escherichia coli (strain K12)
Seq:
Struc: 		59 a.a.
58 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N4  (RL32_ECOLI) -  50S ribosomal protein L32 from Escherichia coli (strain K12)
Seq:
Struc: 		57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N9  (RL33_ECOLI) -  50S ribosomal protein L33 from Escherichia coli (strain K12)
Seq:
Struc: 		55 a.a.
50 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7P5  (RL34_ECOLI) -  50S ribosomal protein L34 from Escherichia coli (strain K12)
Seq:
Struc: 		46 a.a.
46 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Q1  (RL35_ECOLI) -  50S ribosomal protein L35 from Escherichia coli (strain K12)
Seq:
Struc: 		65 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Q6  (RL36_ECOLI) -  50S ribosomal protein L36 from Escherichia coli (strain K12)
Seq:
Struc: 		38 a.a.
38 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  G-G-U-U-A-A-G-C-G-A-C-U-A-A-G-C-G-U-A-C-A-C-G-G-U-G-G-A-U-G-C-C-C-U-G-G-C-A-G- ... 2897 bases
  U-G-C-C-U-G-G-C-G-G-C-C-G-U-A-G-C-G-C-G-G-U-G-G-U-C-C-C-A-C-C-U-G-A-C-C-C-C-A- 119 bases

 

 
Science 332:981-984 (2011)
PubMed id: 21596992  
 
 
Structures of the bacterial ribosome in classical and hybrid states of tRNA binding.
J.A.Dunkle, L.Wang, M.B.Feldman, A.Pulk, V.B.Chen, G.J.Kapral, J.Noeske, J.S.Richardson, S.C.Blanchard, J.H.Cate.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22622583 D.J.Ramrath, H.Yamamoto, K.Rother, D.Wittek, M.Pech, T.Mielke, J.Loerke, P.Scheerer, P.Ivanov, Y.Teraoka, O.Shpanchenko, K.H.Nierhaus, and C.M.Spahn (2012).
The complex of tmRNA-SmpB and EF-G on translocating ribosomes.
  Nature, 485, 526-529.
PDB codes: 3j18 3j19
22337051 E.A.Dethoff, J.Chugh, A.M.Mustoe, and H.M.Al-Hashimi (2012).
Functional complexity and regulation through RNA dynamics.
  Nature, 482, 322-330.  
22902368 L.Wang, A.Pulk, M.R.Wasserman, M.B.Feldman, R.B.Altman, J.H.Doudna Cate, and S.C.Blanchard (2012).
Allosteric control of the ribosome by small-molecule antibiotics.
  Nat Struct Mol Biol, 19, 957-963.
PDB codes: 4gaq 4gar 4gas 4gau
22664983 S.Melnikov, A.Ben-Shem, N.Garreau de Loubresse, L.Jenner, G.Yusupova, and M.Yusupov (2012).
One core, two shells: bacterial and eukaryotic ribosomes.
  Nat Struct Mol Biol, 19, 560-567.  
21857664 J.Fei, A.C.Richard, J.E.Bronson, and R.L.Gonzalez (2011).
Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis.
  Nat Struct Mol Biol, 18, 1043-1051.  
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.

 

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