spacer
spacer

PDBsum entry 4kd8

Go to PDB code: 
protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome/antibiotic PDB id
4kd8
Jmol
Contents
Protein chains
235 a.a.
207 a.a.
208 a.a.
151 a.a.
101 a.a.
155 a.a.
138 a.a.
127 a.a.
99 a.a.
119 a.a.
125 a.a.
125 a.a.
60 a.a.
88 a.a.
84 a.a.
100 a.a.
70 a.a.
79 a.a.
99 a.a.
667 a.a.
DNA/RNA
Ligands
KBE-DPP-SER-SER-
UAL-5OH
FUA
GDP
Metals
_MG
PDB id:
4kd8
Name: Ribosome/antibiotic
Title: 70s ribosome translocation intermediate fa-3.6a containing e factor efg/fusidic acid/gdp, mRNA, and tRNA bound in the pe this entry contains the 30s ribosomal subunit a. The 50s su can be found in 4kd9. Molecule b in the same asymmetric uni deposited as 4kda (30s) and 4kdb (50s).
Structure: 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5. Chain: e. 30s ribosomal protein s6.
Source: Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Escherichia coli. Organism_taxid: 562. Streptomyces. Organism_taxid: 1883
Resolution:
3.50Å     R-factor:   0.284     R-free:   0.328
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:
24-Apr-13     Release date:   03-Jul-13    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P62662  (RS2_THET2) -  30S ribosomal protein S2
Seq:
Struc:
256 a.a.
235 a.a.
Protein chain
Pfam   ArchSchema ?
P62663  (RS3_THET2) -  30S ribosomal protein S3
Seq:
Struc:
239 a.a.
207 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.
99 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.
125 a.a.
Protein chain
Pfam   ArchSchema ?
P62655  (RS13_THET2) -  30S ribosomal protein S13
Seq:
Struc:
126 a.a.
125 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.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P62658  (RS17_THET2) -  30S ribosomal protein S17
Seq:
Struc:
105 a.a.
100 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.
79 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 ?
Q72I01  (EFG_THET2) -  Elongation factor G
Seq:
Struc:
 
Seq:
Struc:
691 a.a.
667 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   5 terms 
  Biological process     translation   3 terms 
  Biochemical function     structural constituent of ribosome     11 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.