1ML5 image
Entry Detail
PDB ID:
1ML5
Keywords:
Title:
Structure of the E. coli ribosomal termination complex with release factor 2
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2002-08-30
Release Date:
2003-01-14
Method Details:
Experimental Method:
Resolution:
14.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:30S 16S RIBOSOMAL RNA
Chain IDs:A
Chain Length:2916
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:T-RNA(PHE)
Chain IDs:B
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:A- AND P-SITE MESSENGER RNA CODONS
Chain IDs:C
Chain Length:228
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S2
Chain IDs:G (auth: E)
Chain Length:338
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S3
Chain IDs:H (auth: F)
Chain Length:246
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S4
Chain IDs:I (auth: G)
Chain Length:176
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S5
Chain IDs:J (auth: H)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S6
Chain IDs:K (auth: I)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S7
Chain IDs:L (auth: J)
Chain Length:156
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S8
Chain IDs:M (auth: K)
Chain Length:138
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S9
Chain IDs:N (auth: L)
Chain Length:128
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S10
Chain IDs:O (auth: M)
Chain Length:145
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S11
Chain IDs:P (auth: N)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S12
Chain IDs:Q (auth: O)
Chain Length:164
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S13
Chain IDs:R (auth: P)
Chain Length:126
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S14
Chain IDs:S (auth: Q)
Chain Length:186
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S15
Chain IDs:T (auth: R)
Chain Length:66
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S16
Chain IDs:U (auth: S)
Chain Length:113
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S17
Chain IDs:V (auth: T)
Chain Length:105
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S18
Chain IDs:W (auth: U)
Chain Length:88
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S19
Chain IDs:X (auth: V)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S20
Chain IDs:Y (auth: W)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN THX
Chain IDs:Z (auth: X)
Chain Length:26
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Peptide chain release factor 2
Chain IDs:F (auth: Z)
Chain Length:365
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:50S 23S RIBOSOMAL RNA
Chain IDs:D (auth: a)
Chain Length:2916
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:50S 5S RIBOSOMAL RNA
Chain IDs:E (auth: b)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L1
Chain IDs:AA (auth: c)
Chain Length:228
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L2
Chain IDs:BA (auth: d)
Chain Length:178
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L3
Chain IDs:CA (auth: e)
Chain Length:338
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L4
Chain IDs:DA (auth: f)
Chain Length:246
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L5
Chain IDs:EA (auth: g)
Chain Length:176
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L6
Chain IDs:FA (auth: h)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L11
Chain IDs:GA (auth: l)
Chain Length:128
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L13
Chain IDs:HA (auth: m)
Chain Length:145
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L14
Chain IDs:IA (auth: n)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L15
Chain IDs:JA (auth: o)
Chain Length:164
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L16
Chain IDs:KA (auth: p)
Chain Length:126
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L18
Chain IDs:LA (auth: q)
Chain Length:186
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L19
Chain IDs:MA (auth: r)
Chain Length:66
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L22
Chain IDs:NA (auth: s)
Chain Length:113
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L23
Chain IDs:OA (auth: t)
Chain Length:105
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L24
Chain IDs:PA (auth: u)
Chain Length:88
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L25
Chain IDs:QA (auth: v)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L29
Chain IDs:RA (auth: w)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L30
Chain IDs:SA (auth: x)
Chain Length:26
Number of Molecules:1
Biological Source:Escherichia coli
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
1MA B A ?
2MG B G 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
5MC B C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE
5MU B U 5-METHYLURIDINE 5'-MONOPHOSPHATE
7MG B G ?
H2U B U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
M2G B G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
OMC B C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
OMG B G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
PSU B U PSEUDOURIDINE-5'-MONOPHOSPHATE
YG B G WYBUTOSINE
Ligand Molecules
Primary Citation
Structure of the Escherichia coli ribosomal termination complex with release factor 2
Nature 421 90 94 (2003)
PMID: 12511961 DOI: 10.1038/nature01225

Abstact

Termination of protein synthesis occurs when the messenger RNA presents a stop codon in the ribosomal aminoacyl (A) site. Class I release factor proteins (RF1 or RF2) are believed to recognize stop codons via tripeptide motifs, leading to release of the completed polypeptide chain from its covalent attachment to transfer RNA in the ribosomal peptidyl (P) site. Class I RFs possess a conserved GGQ amino-acid motif that is thought to be involved directly in protein-transfer-RNA bond hydrolysis. Crystal structures of bacterial and eukaryotic class I RFs have been determined, but the mechanism of stop codon recognition and peptidyl-tRNA hydrolysis remains unclear. Here we present the structure of the Escherichia coli ribosome in a post-termination complex with RF2, obtained by single-particle cryo-electron microscopy (cryo-EM). Fitting the known 70S and RF2 structures into the electron density map reveals that RF2 adopts a different conformation on the ribosome when compared with the crystal structure of the isolated protein. The amino-terminal helical domain of RF2 contacts the factor-binding site of the ribosome, the 'SPF' loop of the protein is situated close to the mRNA, and the GGQ-containing domain of RF2 interacts with the peptidyl-transferase centre (PTC). By connecting the ribosomal decoding centre with the PTC, RF2 functionally mimics a tRNA molecule in the A site. Translational termination in eukaryotes is likely to be based on a similar mechanism.

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Primary Citation of related structures