8B0X image
Deposition Date 2022-09-08
Release Date 2022-11-30
Last Version Date 2025-04-16
Entry Detail
PDB ID:
8B0X
Keywords:
Title:
Translating 70S ribosome in the unrotated state (P and E, tRNAs)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.55 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:A (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:B (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:C (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:D (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:E (auth: A)
Chain Length:1554
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:F (auth: B)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:G (auth: C)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:H (auth: D)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:I (auth: E)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:J (auth: F)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:K (auth: G)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:L (auth: H)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:M (auth: I)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:N (auth: J)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:O (auth: K)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:P (auth: L)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:Q (auth: M)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:R (auth: N)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:S (auth: O)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:T (auth: P)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:U (auth: Q)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:V (auth: R)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:W (auth: S)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:X (auth: T)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:Y (auth: U)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:Z (auth: X)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:AA (auth: Z)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:BA (auth: a)
Chain Length:1554
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:CA (auth: b)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:DA (auth: c)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:EA (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:FA (auth: e)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:GA (auth: f)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:HA (auth: g)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:IA (auth: h)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:JA (auth: i)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:KA (auth: j)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:LA (auth: k)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:MA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:NA (auth: m)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:OA (auth: n)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:PA (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:QA (auth: p)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:RA (auth: q)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:SA (auth: r)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:TA (auth: s)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:UA (auth: t)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:VA (auth: u)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:WA (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:XA (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:YA (auth: x)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:ZA (auth: y)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:AB (auth: z)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli B
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG E G modified residue
4D4 MA ARG modified residue
4OC E C modified residue
5MC E C modified residue
D2T P ASP modified residue
G7M E G modified residue
MA6 E A modified residue
MEQ EA GLN modified residue
PSU E U modified residue
UR3 E U modified residue
Primary Citation
The translating bacterial ribosome at 1.55 angstrom resolution generated by cryo-EM imaging services.
Nat Commun 14 1095 1095 (2023)
PMID: 36841832 DOI: 10.1038/s41467-023-36742-3

Abstact

Our understanding of protein synthesis has been conceptualised around the structure and function of the bacterial ribosome. This complex macromolecular machine is the target of important antimicrobial drugs, an integral line of defence against infectious diseases. Here, we describe how open access to cryo-electron microscopy facilities combined with bespoke user support enabled structural determination of the translating ribosome from Escherichia coli at 1.55 Å resolution. The obtained structures allow for direct determination of the rRNA sequence to identify ribosome polymorphism sites in the E. coli strain used in this study and enable interpretation of the ribosomal active and peripheral sites at unprecedented resolution. This includes scarcely populated chimeric hybrid states of the ribosome engaged in several tRNA translocation steps resolved at ~2 Å resolution. The current map not only improves our understanding of protein synthesis but also allows for more precise structure-based drug design of antibiotics to tackle rising bacterial resistance.

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Primary Citation of related structures