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PDBsum entry 3kcr

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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
3kcr
Jmol
Contents
Protein chains
442 a.a. *
65 a.a. *
32 a.a. *
234 a.a. *
271 a.a. *
209 a.a. *
201 a.a. *
178 a.a. *
176 a.a. *
149 a.a. *
141 a.a. *
142 a.a. *
121 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. *
79 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
* Residue conservation analysis
PDB id:
3kcr
Name: Ribosome
Title: Ribosome-secy complex. This entry 3kcr contains 50s ribosomal subnit. The 30s ribosomal subunit can be found in PDB entry 3kc4
Structure: 5s ribosomal RNA. Chain: 7. 23s ribosomal RNA. Chain: 8. Preprotein translocase secy subunit. Chain: a. Preprotein translocase sece subunit. Chain: b. Preprotein translocase subunit secg.
Source: Escherichia coli. Organism_taxid: 562. Strain: mre600. Other_details: chimeric protein: escherichia coli, methanococcus jannaschii. Methanocaldococcus jannaschii. Organism_taxid: 2190. Escherichia coli k-12. Organism_taxid: 83333.
Authors: J.C.Gumbart,L.G.Trabuco,E.Schreiner,E.Villa,K.Schulten
Key ref: J.Gumbart et al. (2009). Regulation of the protein-conducting channel by a bound ribosome. Structure, 17, 1453-1464. PubMed id: 19913480
Date:
21-Oct-09     Release date:   02-Mar-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q60175  (SECY_METJA) -  Protein translocase subunit SecY
Seq:
Struc:
436 a.a.
442 a.a.*
Protein chain
Pfam   ArchSchema ?
Q57817  (SECE_METJA) -  Protein translocase subunit SecE
Seq:
Struc:
74 a.a.
65 a.a.*
Protein chain
Pfam   ArchSchema ?
P60460  (SECG_METJA) -  Preprotein translocase subunit SecG
Seq:
Struc:
53 a.a.
32 a.a.
Protein chain
No UniProt id for this chain
Struc: 234 a.a.
Protein chain
No UniProt id for this chain
Struc: 271 a.a.
Protein chain
Pfam   ArchSchema ?
P60438  (RL3_ECOLI) -  50S ribosomal protein L3
Seq:
Struc:
209 a.a.
209 a.a.
Protein chain
No UniProt id for this chain
Struc: 201 a.a.
Protein chain
Pfam   ArchSchema ?
P62399  (RL5_ECOLI) -  50S ribosomal protein L5
Seq:
Struc:
179 a.a.
178 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG55  (RL6_ECOLI) -  50S ribosomal protein L6
Seq:
Struc:
177 a.a.
176 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R1  (RL9_ECOLI) -  50S ribosomal protein L9
Seq:
Struc:
149 a.a.
149 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7J7  (RL11_ECOLI) -  50S ribosomal protein L11
Seq:
Struc:
142 a.a.
141 a.a.
Protein chain
No UniProt id for this chain
Struc: 142 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY3  (RL14_ECOLI) -  50S ribosomal protein L14
Seq:
Struc:
123 a.a.
121 a.a.
Protein chain
Pfam   ArchSchema ?
P02413  (RL15_ECOLI) -  50S ribosomal protein L15
Seq:
Struc:
144 a.a.
143 a.a.
Protein chain
No UniProt id for this chain
Struc: 136 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG44  (RL17_ECOLI) -  50S ribosomal protein L17
Seq:
Struc:
127 a.a.
120 a.a.
Protein chain
No UniProt id for this chain
Struc: 116 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7K6  (RL19_ECOLI) -  50S ribosomal protein L19
Seq:
Struc:
115 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L3  (RL20_ECOLI) -  50S ribosomal protein L20
Seq:
Struc:
118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG48  (RL21_ECOLI) -  50S ribosomal protein L21
Seq:
Struc:
103 a.a.
103 a.a.
Protein chain
No UniProt id for this chain
Struc: 110 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADZ0  (RL23_ECOLI) -  50S ribosomal protein L23
Seq:
Struc:
100 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
P60624  (RL24_ECOLI) -  50S ribosomal protein L24
Seq:
Struc:
104 a.a.
102 a.a.
Protein chain
Pfam   ArchSchema ?
P68919  (RL25_ECOLI) -  50S ribosomal protein L25
Seq:
Struc:
94 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L8  (RL27_ECOLI) -  50S ribosomal protein L27
Seq:
Struc:
85 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M2  (RL28_ECOLI) -  50S ribosomal protein L28
Seq:
Struc:
78 a.a.
77 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M6  (RL29_ECOLI) -  50S ribosomal protein L29
Seq:
Struc:
63 a.a.
63 a.a.
Protein chain
No UniProt id for this chain
Struc: 58 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N4  (RL32_ECOLI) -  50S ribosomal protein L32
Seq:
Struc:
57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N9  (RL33_ECOLI) -  50S ribosomal protein L33
Seq:
Struc:
55 a.a.
50 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7P5  (RL34_ECOLI) -  50S ribosomal protein L34
Seq:
Struc:
46 a.a.
46 a.a.
Protein chain
No UniProt id for this chain
Struc: 64 a.a.
Protein chain
No UniProt id for this chain
Struc: 38 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 57 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   8 terms 
  Biological process     transport   16 terms 
  Biochemical function     structural constituent of ribosome     13 terms  

 

 
Structure 17:1453-1464 (2009)
PubMed id: 19913480  
 
 
Regulation of the protein-conducting channel by a bound ribosome.
J.Gumbart, L.G.Trabuco, E.Schreiner, E.Villa, K.Schulten.
 
  ABSTRACT  
 
During protein synthesis, it is often necessary for the ribosome to form a complex with a membrane-bound channel, the SecY/Sec61 complex, in order to translocate nascent proteins across a cellular membrane. Structural data on the ribosome-channel complex are currently limited to low-resolution cryo-electron microscopy maps, including one showing a bacterial ribosome bound to a monomeric SecY complex. Using that map along with available atomic-level models of the ribosome and SecY, we have determined, through molecular dynamics flexible fitting (MDFF), an atomic-resolution model of the ribosome-channel complex. We characterized computationally the sites of ribosome-SecY interaction within the complex and determined the effect of ribosome binding on the SecY channel. We also constructed a model of a ribosome in complex with a SecY dimer by adding a second copy of SecY to the MDFF-derived model. The study involved 2.7-million-atom simulations over altogether nearly 50 ns.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21499241 J.Frauenfeld, J.Gumbart, E.O.Sluis, S.Funes, M.Gartmann, B.Beatrix, T.Mielke, O.Berninghausen, T.Becker, K.Schulten, and R.Beckmann (2011).
Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.
  Nat Struct Mol Biol, 18, 614-621.
PDB codes: 3j00 3j01
20183845 J.Hsin, D.E.Chandler, J.Gumbart, C.B.Harrison, M.Sener, J.Strumpfer, and K.Schulten (2010).
Self-assembly of photosynthetic membranes.
  Chemphyschem, 11, 1154-1159.  
20462496 L.G.Trabuco, C.B.Harrison, E.Schreiner, and K.Schulten (2010).
Recognition of the regulatory nascent chain TnaC by the ribosome.
  Structure, 18, 627-637.  
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.  
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.