8EMM image
Deposition Date 2022-09-28
Release Date 2023-05-31
Last Version Date 2025-02-12
Entry Detail
PDB ID:
8EMM
Keywords:
Title:
Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Method Details:
Experimental Method:
Resolution:
2.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:AA (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Chain IDs:BA (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:CA (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:DA (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:EA (auth: 4)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:HA (auth: A)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:IA (auth: B)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:JA (auth: C)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:KA (auth: D)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:LA (auth: E)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:MA (auth: F)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:NA (auth: G)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:OA (auth: H)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:PA (auth: I)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:QA (auth: J)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:RA (auth: K)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:SA (auth: L)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:TA (auth: M)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:UA (auth: N)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:VA (auth: O)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:WA (auth: P)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:XA (auth: Q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:YA (auth: R)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:ZA (auth: S)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:AB (auth: T)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Chain IDs:BB (auth: U)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:CB (auth: X)
Chain Length:28
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:Met-NH-tRNA
Chain IDs:FA (auth: Y), GA (auth: Z)
Chain Length:59
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:A (auth: a)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:B (auth: b)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C (auth: c)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Chain IDs:D (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Chain IDs:E (auth: e)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:F (auth: f)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:G (auth: g)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Chain IDs:H (auth: h)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:I (auth: i)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:J (auth: j)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:K (auth: k)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Chain IDs:L (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:M (auth: m)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:N (auth: n)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:O (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:P (auth: p)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L21
Chain IDs:Q (auth: q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:R (auth: r)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:S (auth: s)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:T (auth: t)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Chain IDs:U (auth: u)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:V (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Chain IDs:W (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:X (auth: x)
Chain Length:28
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:Y (auth: y)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:Z (auth: z)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG HA G modified residue
4D4 L ARG modified residue
4OC HA C modified residue
5MC HA C modified residue
8AN FA A modified residue
D2T SA ASP modified residue
G7M HA G modified residue
MA6 HA A modified residue
MEQ D GLN modified residue
PSU HA U modified residue
UR3 HA U modified residue
Primary Citation
Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates.
Nat.Chem. 15 913 921 (2023)
PMID: 37308707 DOI: 10.1038/s41557-023-01226-w

Abstact

As genetic code expansion advances beyond L-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-L-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 Å from the peptidyl-tRNA carbonyl with a Bürgi-Dunitz angle of 76-115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers.

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Primary Citation of related structures