9G30 image
Deposition Date 2024-07-11
Release Date 2025-04-23
Last Version Date 2025-05-07
Entry Detail
PDB ID:
9G30
Keywords:
RIBOSOME
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:
Candida albicans (Taxon ID: 5476)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.35 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9G30 validation report
Macromolecular Entities
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
UniProt ID:A0A1D8PLC9
Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:B (auth: 1)
Chain Length:3359
Number of Molecules:1
Biological Source:Candida albicans
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
UniProt ID:A0A1D8PGY0
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
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
UniProt ID:A0A1D8PPT5
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
UniProt ID:Q5A6A1
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
UniProt ID:A0A1D8PPS1
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
UniProt ID:A0A1D8PCQ5
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:J (auth: A)
Chain Length:105
Number of Molecules:1
Biological Source:Candida albicans
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
UniProt ID:A0A1D8PFG4
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
UniProt ID:A0A1D8PSC5
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
UniProt ID:A0A1D8PF57
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
UniProt ID:A0A1D8PM75 Pfam ID:PF01248
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
UniProt ID:A0A1D8PHF5
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
UniProt ID:A0A1D8PPN6
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
UniProt ID:A0A1D8PHH4
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
UniProt ID:A0A1D8PDZ1
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
UniProt ID:A0A1D8PK30
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
UniProt ID:A0A1D8PH21
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
UniProt ID:A0A1D8PF45 Pfam ID:PF01907
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
UniProt ID:A0A1D8PG16 Pfam ID:PF01781
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
UniProt ID:A0A1D8PDT4
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
UniProt ID:A0A1D8PL68 Pfam ID:PF01020
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
UniProt ID:P9WER7 Pfam ID:PF05162
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
UniProt ID:A0A1D8PEV4
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
UniProt ID:A0A1D8PP14 Pfam ID:PF01780
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
UniProt ID:O42817
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
UniProt ID:P40910
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
UniProt ID:Q5A900
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
UniProt ID:A0A1D8PSV5
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
UniProt ID:A0A1D8PCI6 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121
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
UniProt ID:Q5AG43
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Chain IDs:Q (auth: H)
Chain Length:236
Number of Molecules:1
Biological Source:Candida albicans
UniProt ID:A0A1D8PL99
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
UniProt ID:Q5AJ93
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
UniProt ID:Q59T44
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
UniProt ID:A0A1D8PGY8
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
UniProt ID:A0A1D8PI15
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
UniProt ID:A0A1D8PN83 Pfam ID:PF16205, PF00366
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:AC (auth: MR)
Chain Length:39
Number of Molecules:1
Biological Source:Candida albicans
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
UniProt ID:Q5ADQ6
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
UniProt ID:A0A1D8PPE0
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
UniProt ID:A0A1D8PDT3
Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:ZB (auth: PT), BC (auth: AT)
Chain Length:77
Number of Molecules:2
Biological Source:Candida albicans
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:Z (auth: Q)
Chain Length:142
Number of Molecules:1
Biological Source:Candida albicans
UniProt ID:A0A1D8PK22 Pfam ID:PF00203
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
UniProt ID:A0A1D8PCW6
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
UniProt ID:A0A1D8PEY9
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
UniProt ID:A0A1D8PQQ5
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
UniProt ID:A0A1D8PK61
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
UniProt ID:Q5A389
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
UniProt ID:A0A1D8PCG7
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22-A
Chain IDs:GA (auth: X)
Chain Length:130
Number of Molecules:1
Biological Source:Candida albicans
UniProt ID:Q96W54
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
UniProt ID:A0A1D8PDU3
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
UniProt ID:Q5A7K0
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Chain IDs:JA (auth: a)
Chain Length:105
Number of Molecules:1
Biological Source:Candida albicans
UniProt ID:A0A1D8PNQ6
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
UniProt ID:Q5ALV6
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
UniProt ID:A0A1D8PTI7
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
UniProt ID:A0A1D8PQN0
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
UniProt ID:A0A1D8PTR4 Pfam ID:PF00253
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
UniProt ID:A0A1D8PSK2 Pfam ID:PF04758
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
UniProt ID:Q5A109 Pfam ID:PF00240, PF01599
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:236
Number of Molecules:1
Biological Source:Candida albicans
UniProt ID:P83774 Pfam ID:PF00400
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
UniProt ID:A0A1D8PF08
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
UniProt ID:Q59LS1 Pfam ID:PF00297
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
UniProt ID:A0A1D8PFV1
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
UniProt ID:Q5AGZ7 Pfam ID:PF17144, PF14204
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
UniProt ID:A0A1D8PCX8
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
UniProt ID:A0A1D8PDL6
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
UniProt ID:Q5ANA1
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-B
Chain IDs:YA (auth: q)
Chain Length:142
Number of Molecules:1
Biological Source:Candida albicans
UniProt ID:Q5AEN2
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
UniProt ID:Q5AIB8 Pfam ID:PF00252
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
UniProt ID:A0A1D8PHW1
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
UniProt ID:O59931
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
UniProt ID:A0A1D8PFL9
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
UniProt ID:Q5A6R1 Pfam ID:PF00827
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
UniProt ID:Q5AB87
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L22
Chain IDs:FB (auth: x)
Chain Length:130
Number of Molecules:1
Biological Source:Candida albicans
UniProt ID:Q59TE0
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
UniProt ID:A0A1D8PK43
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
UniProt ID:A0A1D8PK40 Pfam ID:PF01280
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
Ligand Molecules
GET
SPK
ZN
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
8CQ7
8CQW
8CRE
8OEQ
9G1Z