9G30 image
Deposition Date 2024-07-11
Release Date 2025-04-23
Last Version Date 2025-05-07
Entry Detail
PDB ID:
9G30
Keywords:
Title:
The structure of the Candida albicans ribosome with tRNA-fMet, mRNA, and compounds (GEN and MFQ) shows strong density for the A site tRNA
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.35 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20
Chain IDs:A (auth: 0)
Chain Length:172
Number of Molecules:1
Biological Source:Candida albicans
Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:B (auth: 1)
Chain Length:3359
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Chain IDs:C (auth: 2)
Chain Length:160
Number of Molecules:1
Biological Source:Candida albicans
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:D (auth: 3)
Chain Length:121
Number of Molecules:1
Biological Source:Candida albicans
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:E (auth: 4)
Chain Length:158
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Chain IDs:F (auth: 6)
Chain Length:137
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24-A
Chain IDs:G (auth: 7)
Chain Length:155
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Chain IDs:H (auth: 8)
Chain Length:142
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L24
Chain IDs:I (auth: 9)
Chain Length:127
Number of Molecules:1
Biological Source:Candida albicans
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:J (auth: A)
Chain Length:1787
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Chain IDs:IB (auth: AA)
Chain Length:136
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Chain IDs:JB (auth: AB)
Chain Length:149
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Chain IDs:KB (auth: AC)
Chain Length:63
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:LB (auth: AD)
Chain Length:106
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-B
Chain IDs:MB (auth: AE)
Chain Length:112
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Chain IDs:NB (auth: AF)
Chain Length:131
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Chain IDs:OB (auth: AG)
Chain Length:107
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-B
Chain IDs:PB (auth: AH)
Chain Length:122
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L29
Chain IDs:QB (auth: AI)
Chain Length:120
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Chain IDs:RB (auth: AJ)
Chain Length:99
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-B
Gene (Uniprot):RPL37B
Chain IDs:SB (auth: AK)
Chain Length:90
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:TB (auth: AL)
Chain Length:78
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Chain IDs:UB (auth: AM)
Chain Length:51
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L40-B
Gene (Uniprot):RPL40B
Chain IDs:VB (auth: AN)
Chain Length:52
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41
Gene (Uniprot):RPL41
Chain IDs:WB (auth: AO)
Chain Length:25
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42-B
Chain IDs:XB (auth: AP)
Chain Length:106
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:YB (auth: AQ)
Chain Length:92
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S0
Chain IDs:K (auth: B)
Chain Length:119
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S1
Chain IDs:L (auth: C)
Chain Length:82
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S5
Chain IDs:M (auth: D)
Chain Length:249
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S3
Chain IDs:N (auth: E)
Chain Length:251
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4
Gene (Uniprot):RPS42
Chain IDs:O (auth: F)
Chain Length:262
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S7
Chain IDs:P (auth: G)
Chain Length:225
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Chain IDs:Q (auth: H)
Chain Length:317
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Chain IDs:R (auth: I)
Chain Length:186
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Chain IDs:S (auth: J)
Chain Length:254
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S4
Chain IDs:T (auth: K)
Chain Length:389
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10-A
Chain IDs:U (auth: L)
Chain Length:363
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11A
Gene (Uniprot):CAALFM_C501540WA
Chain IDs:V (auth: M)
Chain Length:155
Number of Molecules:1
Biological Source:Candida albicans
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:AC (auth: MR)
Chain Length:39
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Chain IDs:W (auth: N)
Chain Length:176
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Chain IDs:X (auth: O)
Chain Length:241
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-A
Chain IDs:Y (auth: P)
Chain Length:132
Number of Molecules:1
Biological Source:Candida albicans
Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:ZB (auth: PT), BC (auth: AT)
Chain Length:77
Number of Molecules:2
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:Z (auth: Q)
Chain Length:191
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Chain IDs:BA (auth: R)
Chain Length:220
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17-B
Chain IDs:CA (auth: S)
Chain Length:137
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18-B
Chain IDs:AA (auth: T)
Chain Length:145
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19-A
Chain IDs:DA (auth: U)
Chain Length:131
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S10
Chain IDs:EA (auth: V)
Chain Length:204
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Chain IDs:FA (auth: W)
Chain Length:87
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22-A
Chain IDs:GA (auth: X)
Chain Length:185
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S23 (S12)
Chain IDs:HA (auth: Y)
Chain Length:145
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Chain IDs:IA (auth: Z)
Chain Length:135
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Chain IDs:JA (auth: a)
Chain Length:1787
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Chain IDs:KA (auth: b)
Chain Length:119
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Chain IDs:LA (auth: c)
Chain Length:82
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28-B
Chain IDs:MA (auth: d)
Chain Length:249
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29A
Gene (Uniprot):CAALFM_CR08480CA, orf19.6415.1
Chain IDs:NA (auth: e)
Chain Length:251
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):RPS30
Chain IDs:OA (auth: f)
Chain Length:262
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S31 fusion protein
Gene (Uniprot):UBI3
Chain IDs:PA (auth: g)
Chain Length:225
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein subunit beta-like protein
Gene (Uniprot):ASC1
Chain IDs:QA (auth: h)
Chain Length:317
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-B
Chain IDs:RA (auth: j)
Chain Length:254
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:SA (auth: k)
Chain Length:389
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-B
Chain IDs:TA (auth: l)
Chain Length:363
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:UA (auth: m)
Chain Length:155
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Chain IDs:VA (auth: n)
Chain Length:176
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Chain IDs:WA (auth: o)
Chain Length:241
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8
Chain IDs:XA (auth: p)
Chain Length:132
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-B
Chain IDs:YA (auth: q)
Chain Length:191
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:ZA (auth: r)
Chain Length:220
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11-B
Chain IDs:AB (auth: s)
Chain Length:137
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Chain IDs:BB (auth: t)
Chain Length:145
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-B
Chain IDs:CB (auth: u)
Chain Length:131
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:DB (auth: v)
Chain Length:204
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L13
Chain IDs:EB (auth: w)
Chain Length:87
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L22
Chain IDs:FB (auth: x)
Chain Length:185
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Chain IDs:GB (auth: y)
Chain Length:145
Number of Molecules:1
Biological Source:Candida albicans
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:HB (auth: z)
Chain Length:135
Number of Molecules:1
Biological Source:Candida albicans
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MLZ F LYS modified residue
OMC B C modified residue
OMG B G modified residue
Primary Citation
Mechanism of read-through enhancement by aminoglycosides and mefloquine.
Proc.Natl.Acad.Sci.USA 122 e2420261122 e2420261122 (2025)
PMID: 40273100 DOI: 10.1073/pnas.2420261122

Abstact

Nonsense mutations are associated with numerous and diverse pathologies, yet effective treatment strategies remain elusive. A promising approach to combat these conditions involves the use of aminoglycosides, particularly in combination with stop-codon read-through enhancers, for developing drugs that can rescue the production of full-length proteins. Using X-ray crystallography and single-particle cryo-EM, we obtained structures of the eukaryotic ribosome in complexes with several aminoglycosides (geneticin G418, paromomycin, and hygromycin B) and the antimalarial drug mefloquine (MFQ), which has also been identified as a read-through enhancer. Our study reveals a binding site of MFQ, which holds significant promise for the development of therapies targeting premature termination codon-related genetic and oncological diseases. The results underscore the crucial role of the bridge B7b/c in mediating the effects of MFQ on subunit rotation dynamics. Through a comprehensive analysis of the interactions between the drugs and the eukaryotic ribosome, we propose a unifying hypothesis for read-through enhancement by small molecules, highlighting the role of decoding center rearrangements and intersubunit rotation dynamics.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
Feedback Form
Name
Email
Institute
Feedback