9SYH image
Deposition Date 2025-10-12
Release Date 2026-03-18
Last Version Date 2026-04-01
Entry Detail
PDB ID:
9SYH
Keywords:
RIBOSOME
Title:
E. coli 70S ribosome from deltaRlmE strain
Biological Source:
Source Organism(s):
Escherichia coli (Taxon ID: 562)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
1.89 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9SYH validation report
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:YA (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:ZA (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:AB (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:BB (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:CB (auth: 4)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A
Chain Length:1542
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:B
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:C
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:D
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:E
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:F
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:G
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:H
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:I
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:J
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:K
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:L
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:M
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:N
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:O
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:P
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:Q
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:R
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:S
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:T
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:U
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:V (auth: X)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:tRNA(Phe)
Chain IDs:W (auth: Y)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:tRNA(fMet)
Chain IDs:X (auth: Z), DB (auth: 5)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:Y (auth: a)
Chain Length:1542
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:Z (auth: b)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:AA (auth: c)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:BA (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:CA (auth: e)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:DA (auth: f)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:EA (auth: g)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:FA (auth: h)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:GA (auth: i)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:HA (auth: j)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:IA (auth: k)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:JA (auth: l)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:KA (auth: m)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:LA (auth: n)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:MA (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:NA (auth: p)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:OA (auth: q)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:PA (auth: r)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:QA (auth: s)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:RA (auth: t)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:SA (auth: u)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:TA (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:UA (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:VA (auth: x)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:WA (auth: y)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:XA (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 A G modified residue
4D4 JA ARG modified residue
4OC A C modified residue
4SU W U modified residue
5MC A C modified residue
5MU W U modified residue
D2T L ASP modified residue
G7M A G modified residue
H2U W U modified residue
MA6 A A modified residue
MEQ BA GLN modified residue
MIA W A modified residue
PSU A U modified residue
UR3 A U modified residue
Ligand Molecules
K
MG
PUT
SR0
ZN
Primary Citation
Ribosomal RNA modifications around the peptidyl transfer center stimulate catalytic activity and prevent the formation of alternative structures
Biorxiv ? ? ? (2026)
DOI: 10.64898/2026.03.01.708810
Primary Citation of related structures
9SYH
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