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PDBsum entry 4kbw

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protein dna_rna Protein-protein interface(s) links
Ribosome/antibiotic PDB id
4kbw
Jmol
Contents
Protein chains
228 a.a.
275 a.a.
205 a.a.
208 a.a.
181 a.a.
167 a.a.
170 a.a.
140 a.a.
122 a.a.
146 a.a.
141 a.a.
117 a.a.
99 a.a.
138 a.a.
117 a.a.
101 a.a.
113 a.a.
93 a.a.
107 a.a.
185 a.a.
84 a.a.
93 a.a.
35 a.a.
138 a.a.
71 a.a.
60 a.a.
59 a.a.
50 a.a.
49 a.a.
64 a.a.
37 a.a.
102 a.a.
31 a.a.
30 a.a.
DNA/RNA
PDB id:
4kbw
Name: Ribosome/antibiotic
Title: 70s ribosome translocation intermediate gdpnp-ii containing factor efg/gdpnp, mRNA, and tRNA bound in the pe /E state. Contains 50s ribosomal subunit b. The full asymmetric unit contains PDB entries 4kbv (30s subunit b), 4kbt (30s subuni 4kbu (50s subunit a).
Structure: 50s ribosomal protein l1. Chain: c. 50s ribosomal protein l2. Chain: d. 50s ribosomal protein l3. Chain: e. 50s ribosomal protein l4. Chain: f. Synonym: l1e.
Source: Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Strain: hb27
Resolution:
3.86Å     R-factor:   0.264     R-free:   0.317
Authors: J.Zhou,L.Lancaster,J.P.Donohue,H.F.Noller
Key ref: J.Zhou et al. (2013). Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation. Science, 340, 1236086. PubMed id: 23812722 DOI: 10.1126/science.1236086
Date:
23-Apr-13     Release date:   03-Jul-13    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q72GV9  (RL1_THET2) -  50S ribosomal protein L1
Seq:
Struc:
229 a.a.
228 a.a.*
Protein chain
Pfam   ArchSchema ?
Q72I07  (RL2_THET2) -  50S ribosomal protein L2
Seq:
Struc:
276 a.a.
275 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I04  (RL3_THET2) -  50S ribosomal protein L3
Seq:
Struc:
206 a.a.
205 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I05  (RL4_THET2) -  50S ribosomal protein L4
Seq:
Struc:
205 a.a.
208 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.
167 a.a.
Protein chain
No UniProt id for this chain
Struc: 170 a.a.
Protein chain
Pfam   ArchSchema ?
P62442  (RL11_THET2) -  50S ribosomal protein L11
Seq:
Struc:
147 a.a.
140 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.
141 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.
99 a.a.
Protein chain
Pfam   ArchSchema ?
Q72JU9  (RL19_THET2) -  50S ribosomal protein L19
Seq:
Struc:
146 a.a.
138 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.
113 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I06  (RL23_THET2) -  50S ribosomal protein L23
Seq:
Struc:
96 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I15  (RL24_THET2) -  50S ribosomal protein L24
Seq:
Struc:
110 a.a.
107 a.a.
Protein chain
Pfam   ArchSchema ?
Q72IA7  (RL25_THET2) -  50S ribosomal protein L25
Seq:
Struc:
206 a.a.
185 a.a.
Protein chain
Pfam   ArchSchema ?
Q72HR3  (RL27_THET2) -  50S ribosomal protein L27
Seq:
Struc:
85 a.a.
84 a.a.*
Protein chain
Pfam   ArchSchema ?
Q72G84  (RL28_THET2) -  50S ribosomal protein L28
Seq:
Struc:
98 a.a.
93 a.a.*
Protein chain
Pfam   ArchSchema ?
Q72JR0  (RL31_THET2) -  50S ribosomal protein L31
Seq:
Struc:
71 a.a.
35 a.a.
Protein chain
Pfam   ArchSchema ?
Q72IN1  (RL13_THET2) -  50S ribosomal protein L13
Seq:
Struc:
140 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I12  (RL29_THET2) -  50S ribosomal protein L29
Seq:
Struc:
72 a.a.
71 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I22  (RL30_THET2) -  50S ribosomal protein L30
Seq:
Struc:
60 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
P62652  (RL32_THET2) -  50S ribosomal protein L32
Seq:
Struc:
60 a.a.
59 a.a.*
Protein chain
Pfam   ArchSchema ?
Q72GW3  (RL33_THET2) -  50S ribosomal protein L33
Seq:
Struc:
54 a.a.
50 a.a.
Protein chain
Pfam   ArchSchema ?
P80340  (RL34_THET8) -  50S ribosomal protein L34
Seq:
Struc:
49 a.a.
49 a.a.
Protein chain
Pfam   ArchSchema ?
Q72L77  (RL35_THET2) -  50S ribosomal protein L35
Seq:
Struc:
65 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I28  (RL36_THET2) -  50S ribosomal protein L36
Seq:
Struc:
37 a.a.
37 a.a.
Protein chain
Pfam   ArchSchema ?
Q72GS2  (RL7_THET2) -  50S ribosomal protein L7/L12
Seq:
Struc:
125 a.a.
102 a.a.*
Protein chains
No UniProt id for this chain
Struc: 31 a.a.
Protein chain
No UniProt id for this chain
Struc: 30 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 41 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     regulation of translation   2 terms 
  Biochemical function     structural constituent of ribosome     8 terms  

 

 
DOI no: 10.1126/science.1236086 Science 340:1236086 (2013)
PubMed id: 23812722  
 
 
Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation.
J.Zhou, L.Lancaster, J.P.Donohue, H.F.Noller.
 
  ABSTRACT  
 
Translocation of messenger and transfer RNA (mRNA and tRNA) through the ribosome is a crucial step in protein synthesis, whose mechanism is not yet understood. The crystal structures of three Thermus ribosome-tRNA-mRNA-EF-G complexes trapped with β,γ-imidoguanosine 5'-triphosphate (GDPNP) or fusidic acid reveal conformational changes occurring during intermediate states of translocation, including large-scale rotation of the 30S subunit head and body. In all complexes, the tRNA acceptor ends occupy the 50S subunit E site, while their anticodon stem loops move with the head of the 30S subunit to positions between the P and E sites, forming chimeric intermediate states. Two universally conserved bases of 16S ribosomal RNA that intercalate between bases of the mRNA may act as "pawls" of a translocational ratchet. These findings provide new insights into the molecular mechanism of ribosomal translocation.