11DG image
Deposition Date 2026-02-18
Release Date 2026-04-08
Last Version Date 2026-04-08
Entry Detail
PDB ID:
11DG
Keywords:
RIBOSOME
Title:
Chimeric Escherichia coli 70S ribosome containing an evolved Vibrio cholerae 16S rRNA (VC-S4.4)
Biological Source:
Source Organism(s):
Escherichia coli (Taxon ID: 562)
Expression System(s):
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
11DG validation report
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:A (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:B (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:C (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:D (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Chain IDs:E (auth: 4)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:E-site tRNA
Chain IDs:F (auth: 5)
Chain Length:2
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:G (auth: A)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:H (auth: B)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:I (auth: C)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:J (auth: D)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:K (auth: E)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:L (auth: F)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:M (auth: G)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:N (auth: H)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:O (auth: I)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:P (auth: J)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:Q (auth: K)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:R (auth: L)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:S (auth: M)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:T (auth: N)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:U (auth: O)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:V (auth: P)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:W (auth: Q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:X (auth: R)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:Y (auth: S)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:Z (auth: T)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:AA (auth: U)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:BA (auth: a)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:CA (auth: b)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Chain IDs:DA (auth: c)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Chain IDs:EA (auth: d)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:FA (auth: e)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:GA (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:HA (auth: g)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:IA (auth: h)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:JA (auth: i)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:KA (auth: j)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:LA (auth: k)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:MA (auth: l)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:NA (auth: m)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:OA (auth: n)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:PA (auth: o)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:QA (auth: p)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:RA (auth: q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:SA (auth: r)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:TA (auth: s)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:UA (auth: t)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:VA (auth: u)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:WA (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Chain IDs:XA (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:YA (auth: x)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:ZA (auth: y)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:AB (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
4D4 MA ARG modified residue
D2T R ASP modified residue
MEQ EA GLN modified residue
MS6 MA MET modified residue
Ligand Molecules
MG
SPD
SPM
ZN
Primary Citation
Structural adaptations for enhanced translation kinetics in evolved ribosomes.
Biorxiv ? ? ? (2026)
PMID: 41846938 DOI: 10.64898/2026.03.05.706023
Primary Citation of related structures
11DG
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