8IFE image
Deposition Date 2023-02-17
Release Date 2024-02-14
Last Version Date 2024-06-19
Entry Detail
PDB ID:
8IFE
Keywords:
RIBOSOME
Title:
Arbekacin-added human 80S ribosome
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.57 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8IFE validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:28S ribosomal RNA
Chain IDs:A (auth: 1A)
Chain Length:5070
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: 1B)
Chain Length:121
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:C (auth: 1C)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8
Gene (Uniprot):RPL8
Chain IDs:D (auth: 1D)
Chain Length:257
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62917 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:E (auth: 1E)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P39023 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Gene (Uniprot):RPL4
Chain IDs:F (auth: 1F)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P36578 Pfam ID:PF00573, PF14374
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:G (auth: 1G)
Chain Length:297
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46777 Pfam ID:PF17144, PF14204
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):RPL6
Chain IDs:H (auth: 1H)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q02878 Pfam ID:PF03868, PF01159
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19
Gene (Uniprot):RPS19
Chain IDs:IB (auth: 20)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P39019 Pfam ID:PF01090
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Gene (Uniprot):RPS20
Chain IDs:JB (auth: 21)
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P60866 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7
Gene (Uniprot):RPL7
Chain IDs:I (auth: 2A)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P18124 Pfam ID:PF08079, PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Gene (Uniprot):RPL7A
Chain IDs:J (auth: 2B)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62424 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Gene (Uniprot):RPL9, RPL9P7, RPL9P8, RPL9P9
Chain IDs:K (auth: 2C)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P32969 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10-like
Gene (Uniprot):RPL10L
Chain IDs:L (auth: 2D)
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96L21 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11
Gene (Uniprot):RPL11
Chain IDs:M (auth: 2E)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62913 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Gene (Uniprot):RPL13
Chain IDs:N (auth: 2F)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P26373 Pfam ID:PF01294
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Gene (Uniprot):RPL14
Chain IDs:O (auth: 2G)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P50914 Pfam ID:PF01929
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15
Gene (Uniprot):RPL15
Chain IDs:P (auth: 2H)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61313 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13a
Gene (Uniprot):RPL13A
Chain IDs:Q (auth: 2I)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P40429 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17
Gene (Uniprot):RPL17
Chain IDs:R (auth: 2J)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P18621 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Gene (Uniprot):RPL18
Chain IDs:S (auth: 2K)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q07020 Pfam ID:PF17135
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19
Gene (Uniprot):RPL19
Chain IDs:T (auth: 2L)
Chain Length:217
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P84098 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Gene (Uniprot):RPL18A
Chain IDs:U (auth: 2M)
Chain Length:176
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q02543 Pfam ID:PF01775
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21
Gene (Uniprot):RPL21
Chain IDs:V (auth: 2N)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46778 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22
Gene (Uniprot):RPL22
Chain IDs:W (auth: 2O)
Chain Length:264
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P35268 Pfam ID:PF01776
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Gene (Uniprot):RPL23
Chain IDs:X (auth: 2P)
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62829 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24
Gene (Uniprot):RPL24
Chain IDs:Y (auth: 2Q)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P83731 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23a
Gene (Uniprot):RPL23A
Chain IDs:Z (auth: 2R)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62750 Pfam ID:PF03939, PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26
Gene (Uniprot):RPL26
Chain IDs:AA (auth: 2S)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61254 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Gene (Uniprot):RPL27
Chain IDs:BA (auth: 2T)
Chain Length:208
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61353 Pfam ID:PF00467, PF01777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27a
Gene (Uniprot):RPL27A
Chain IDs:CA (auth: 2U)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46776 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):RPL29
Chain IDs:DA (auth: 2V)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P47914 Pfam ID:PF01779
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:EA (auth: 2W)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62888 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Gene (Uniprot):RPL31
Chain IDs:FA (auth: 2X)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62899 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:GA (auth: 2Y)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62910 Pfam ID:PF01655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35a
Gene (Uniprot):RPL35A
Chain IDs:HA (auth: 2Z)
Chain Length:152
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P18077 Pfam ID:PF01247
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34
Gene (Uniprot):RPL34
Chain IDs:IA (auth: 2a)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P49207 Pfam ID:PF01199
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Gene (Uniprot):RPL35
Chain IDs:JA (auth: 2b)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P42766 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):RPL36
Chain IDs:KA (auth: 2c)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3U8 Pfam ID:PF01158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37
Gene (Uniprot):RPL37
Chain IDs:LA (auth: 2d)
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61927 Pfam ID:PF01907
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:MA (auth: 2e)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P63173 Pfam ID:PF01781
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:NA (auth: 2f)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62891 Pfam ID:PF00832
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal protein L40
Gene (Uniprot):UBA52
Chain IDs:OA (auth: 2g)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62987 Pfam ID:PF00240, PF01020
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41
Gene (Uniprot):RPL41
Chain IDs:PA (auth: 2h)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62945 Pfam ID:PF05162
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36a
Gene (Uniprot):RPL36A
Chain IDs:QA (auth: 2i)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P83881 Pfam ID:PF00935
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37a
Gene (Uniprot):RPL37A
Chain IDs:RA (auth: 2j)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61513 Pfam ID:PF01780
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:SA (auth: 2k)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46779 Pfam ID:PF01778
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10a
Gene (Uniprot):RPL10A
Chain IDs:TA (auth: 2l)
Chain Length:217
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62906 Pfam ID:PF00687
Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:UA (auth: 2m)
Chain Length:176
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Gene (Uniprot):RPSA
Chain IDs:VA (auth: 2n)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P08865 Pfam ID:PF00318, PF16122
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):RPS3A
Chain IDs:WA (auth: 2o)
Chain Length:264
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61247 Pfam ID:PF01015
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:XA (auth: 2p)
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P23396 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4, X isoform
Gene (Uniprot):RPS4X
Chain IDs:YA (auth: 2q)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62701 Pfam ID:PF08071, PF00900, PF00467, PF16121
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:ZA (auth: 2r)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46782 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):RPS7
Chain IDs:AB (auth: 2s)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62081 Pfam ID:PF01251
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):RPS8
Chain IDs:BB (auth: 2t)
Chain Length:208
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62241 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10
Gene (Uniprot):RPS10
Chain IDs:CB (auth: 2u)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46783 Pfam ID:PF03501
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Gene (Uniprot):RPS11
Chain IDs:DB (auth: 2v)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62280 Pfam ID:PF16205, PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:EB (auth: 2w)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62841 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Gene (Uniprot):RPS16
Chain IDs:FB (auth: 2x)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62249 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17
Gene (Uniprot):RPS17
Chain IDs:GB (auth: 2y)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P08708 Pfam ID:PF00833
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Gene (Uniprot):RPS18
Chain IDs:HB (auth: 2z)
Chain Length:152
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62269 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Gene (Uniprot):RPS21
Chain IDs:KB (auth: 3A)
Chain Length:83
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P63220 Pfam ID:PF01249
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Gene (Uniprot):RPS23
Chain IDs:LB (auth: 3B)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62266 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Gene (Uniprot):RPS26
Chain IDs:MB (auth: 3C)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62854 Pfam ID:PF01283
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:NB (auth: 3D)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62857 Pfam ID:PF01200
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29
Gene (Uniprot):RPS29
Chain IDs:OB (auth: 3E)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62273 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Receptor of activated protein C kinase 1
Gene (Uniprot):RACK1
Chain IDs:PB (auth: 3F)
Chain Length:317
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P63244 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Gene (Uniprot):RPS2
Chain IDs:QB (auth: 3G)
Chain Length:293
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P15880 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:RB (auth: 3H)
Chain Length:249
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62753 Pfam ID:PF01092
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9
Gene (Uniprot):RPS9
Chain IDs:SB (auth: 3I)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46781 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:TB (auth: 3J)
Chain Length:132
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P25398 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:UB (auth: 3K)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62277 Pfam ID:PF08069, PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Gene (Uniprot):RPS14
Chain IDs:VB (auth: 3L)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62263 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:WB (auth: 3M)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62244 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):RPS24
Chain IDs:XB (auth: 3N)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62847 Pfam ID:PF01282
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Gene (Uniprot):RPS25
Chain IDs:YB (auth: 3O)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62851 Pfam ID:PF03297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:ZB (auth: 3P)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P42677 Pfam ID:PF01667
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):FAU
Chain IDs:AC (auth: 3Q)
Chain Length:59
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62861 Pfam ID:PF04758
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S27a
Gene (Uniprot):RPS27A
Chain IDs:BC (auth: 3R)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62979 Pfam ID:PF00240, PF01599
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MLZ OA LYS modified residue
Ligand Molecules
84G
MG
ZN
Primary Citation
Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside.
J.Biochem. 175 587 598 (2024)
PMID: 38227611 DOI: 10.1093/jb/mvae002

Abstact

The rapid emergence of multi-drug-resistant bacteria has raised a serious public health concern. Therefore, new antibiotic developments have been highly desired. Here, we propose a new method to visualize antibiotic actions on translating ribosomes in the cell-free system under macromolecular crowding conditions by cryo-electron microscopy, designated as the DARC method: the Direct visualization of Antibiotic binding on Ribosomes in the Cell-free translation system. This new method allows for acquiring a more comprehensive understanding of the mode of action of antibiotics on the translation inhibition without ribosome purification. Furthermore, with the direct link to biochemical analysis at the same condition as cryo-EM observation, we revealed the evolution of 2-DOS aminoglycosides from dibekacin (DBK) to arbekacin (ABK) by acquiring the synthetic tailored anchoring motif to lead to stronger binding affinity to ribosomes. Our cryo-EM structures of DBK and ABK bound ribosomes in the cell-free environment clearly depicted a synthetic tailored γ-amino-α-hydroxybutyryl (HABA) motif formed additional interactions with the ribosome enhancing antibiotic bindings. This new approach would be valuable for understanding the function of antibiotics for more efficient drug development.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
8IFE