8K2B image
Deposition Date 2023-07-12
Release Date 2024-07-10
Last Version Date 2024-07-10
Entry Detail
PDB ID:
8K2B
Keywords:
RIBOSOME
Title:
Cryo-EM structure of the human 39S mitoribosome with Tigecycline
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8K2B validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16s rRNA
Chain IDs:A (auth: L1)
Chain Length:1559
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:Val tRNA
Chain IDs:B (auth: L2)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL53
Gene (Uniprot):MRPL53
Chain IDs:SA (auth: L3)
Chain Length:112
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96EL3 Pfam ID:PF10780
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL54
Gene (Uniprot):MRPL54
Chain IDs:TA (auth: L4)
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P161 Pfam ID:PF08561
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL55
Gene (Uniprot):MRPL55
Chain IDs:UA (auth: L5)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z7F7 Pfam ID:PF09776
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL63
Gene (Uniprot):MRPL57
Chain IDs:VA (auth: L6)
Chain Length:102
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BQC6 Pfam ID:PF14978
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL62
Gene (Uniprot):MRPL58
Chain IDs:WA (auth: L7)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q14197 Pfam ID:PF00472 EC:3.1.1.29
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL64
Gene (Uniprot):GADD45GIP1
Chain IDs:XA (auth: L8)
Chain Length:222
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8TAE8 Pfam ID:PF10147
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2m
Gene (Uniprot):MRPL2
Chain IDs:C (auth: LB)
Chain Length:256
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q5T653 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3m
Gene (Uniprot):MRPL3
Chain IDs:D (auth: LC)
Chain Length:348
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P09001 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4m
Gene (Uniprot):MRPL4
Chain IDs:E (auth: LD)
Chain Length:161
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYD3 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL9m
Gene (Uniprot):MRPL9
Chain IDs:F (auth: LI)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYD2 Pfam ID:PF01281, PF22078
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL10m
Gene (Uniprot):MRPL10
Chain IDs:G (auth: LJ)
Chain Length:103
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z7H8 Pfam ID:PF00466
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL11m
Gene (Uniprot):MRPL11
Chain IDs:H (auth: LK)
Chain Length:423
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3B7 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13m
Gene (Uniprot):MRPL13
Chain IDs:I (auth: LM)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYD1 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14m
Gene (Uniprot):MRPL14
Chain IDs:J (auth: LN)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P1L8 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15m
Gene (Uniprot):MRPL15
Chain IDs:K (auth: LO)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9P015 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16m
Gene (Uniprot):MRPL16
Chain IDs:L (auth: LP)
Chain Length:251
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NX20 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL17m
Gene (Uniprot):MRPL17
Chain IDs:M (auth: LQ)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NRX2 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L18, isoform CRA_b
Chain IDs:N (auth: LR)
Chain Length:179
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H0U6 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL19m
Gene (Uniprot):MRPL19
Chain IDs:O (auth: LS)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P49406 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL20m
Gene (Uniprot):MRPL20
Chain IDs:P (auth: LT)
Chain Length:149
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYC9 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL21m
Gene (Uniprot):MRPL21
Chain IDs:Q (auth: LU)
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7Z2W9 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L22, mitochondrial
Chain IDs:R (auth: LV)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NWU5 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23m
Gene (Uniprot):MRPL23
Chain IDs:S (auth: LW)
Chain Length:153
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q16540 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24m
Gene (Uniprot):MRPL24
Chain IDs:T (auth: LX)
Chain Length:216
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96A35 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27m
Gene (Uniprot):MRPL27
Chain IDs:U (auth: La)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9P0M9 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL28m
Gene (Uniprot):MRPL28
Chain IDs:V (auth: Lb)
Chain Length:256
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13084 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30m
Gene (Uniprot):MRPL30
Chain IDs:X (auth: Ld)
Chain Length:161
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8TCC3 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL32m
Gene (Uniprot):MRPL32
Chain IDs:Y (auth: Lf)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYC8 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33m
Gene (Uniprot):MRPL33
Chain IDs:Z (auth: Lg)
Chain Length:65
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75394 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34m
Gene (Uniprot):MRPL34
Chain IDs:AA (auth: Lh)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BQ48 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL35m
Gene (Uniprot):MRPL35
Chain IDs:BA (auth: Li)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NZE8 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL36m
Gene (Uniprot):MRPL36
Chain IDs:CA (auth: Lj)
Chain Length:103
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9P0J6 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL37
Gene (Uniprot):MRPL37
Chain IDs:DA (auth: Lk)
Chain Length:423
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BZE1 Pfam ID:PF07147
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL38
Gene (Uniprot):MRPL38
Chain IDs:EA (auth: Ll)
Chain Length:380
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96DV4 Pfam ID:PF01161
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL39
Gene (Uniprot):MRPL39
Chain IDs:FA (auth: Lm)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NYK5
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL40
Gene (Uniprot):MRPL40
Chain IDs:GA (auth: Ln)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NQ50 Pfam ID:PF09812
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL41
Gene (Uniprot):MRPL41
Chain IDs:HA (auth: Lo)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8IXM3 Pfam ID:PF09809
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL42
Gene (Uniprot):MRPL42
Chain IDs:IA (auth: Lp)
Chain Length:251
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y6G3 Pfam ID:PF10210
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL43
Gene (Uniprot):MRPL43
Chain IDs:JA (auth: Lq)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N983 Pfam ID:PF05047
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL44
Gene (Uniprot):MRPL44
Chain IDs:KA (auth: Lr)
Chain Length:179
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H9J2 Pfam ID:PF22935, PF22892
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL45
Gene (Uniprot):MRPL45
Chain IDs:LA (auth: Ls)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BRJ2 Pfam ID:PF04280
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL46
Gene (Uniprot):MRPL46
Chain IDs:MA (auth: Lt)
Chain Length:149
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H2W6 Pfam ID:PF11788
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29m
Gene (Uniprot):MRPL47
Chain IDs:W (auth: Lu)
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9HD33 Pfam ID:PF06984
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL48
Gene (Uniprot):MRPL48
Chain IDs:NA (auth: Lv)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96GC5 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL49
Gene (Uniprot):MRPL49
Chain IDs:OA (auth: Lw)
Chain Length:153
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13405 Pfam ID:PF05046
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL50
Gene (Uniprot):MRPL50
Chain IDs:PA (auth: Lx)
Chain Length:216
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N5N7 Pfam ID:PF10501
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL51
Gene (Uniprot):MRPL51
Chain IDs:QA (auth: Ly)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q4U2R6 Pfam ID:PF10244
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L52, mitochondrial
Chain IDs:RA (auth: Lz)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:A8K7J6 Pfam ID:PF18699
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL66
Gene (Uniprot):MRPS18A
Chain IDs:YA (auth: SR)
Chain Length:196
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NVS2 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL65
Gene (Uniprot):MRPS30
Chain IDs:ZA (auth: Sf)
Chain Length:439
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NP92 Pfam ID:PF07147
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial assembly of ribosomal large subunit protein 1
Gene (Uniprot):MALSU1
Chain IDs:AB (auth: u)
Chain Length:234
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96EH3 Pfam ID:PF02410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosome and complex I assembly factor AltMIEF1
Gene (Uniprot):MIEF1
Chain IDs:BB (auth: v)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:L0R8F8 Pfam ID:PF05347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein, mitochondrial
Gene (Uniprot):NDUFAB1
Chain IDs:CB (auth: w)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O14561 Pfam ID:PF00550
Ligand Molecules
MG
PNS
T1C
ZN
Primary Citation
Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
Nat Commun 15 5481 5481 (2024)
PMID: 38942792 DOI: 10.1038/s41467-024-49797-7

Abstact

Tigecycline is widely used for treating complicated bacterial infections for which there are no effective drugs. It inhibits bacterial protein translation by blocking the ribosomal A-site. However, even though it is also cytotoxic for human cells, the molecular mechanism of its inhibition remains unclear. Here, we present cryo-EM structures of tigecycline-bound human mitochondrial 55S, 39S, cytoplasmic 80S and yeast cytoplasmic 80S ribosomes. We find that at clinically relevant concentrations, tigecycline effectively targets human 55S mitoribosomes, potentially, by hindering A-site tRNA accommodation and by blocking the peptidyl transfer center. In contrast, tigecycline does not bind to human 80S ribosomes under physiological concentrations. However, at high tigecycline concentrations, in addition to blocking the A-site, both human and yeast 80S ribosomes bind tigecycline at another conserved binding site restricting the movement of the L1 stalk. In conclusion, the observed distinct binding properties of tigecycline may guide new pathways for drug design and therapy.

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Protein

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Primary Citation of related structures
8K2B
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