8K2D image
Deposition Date 2023-07-12
Release Date 2024-07-10
Last Version Date 2024-10-30
Entry Detail
PDB ID:
8K2D
Keywords:
RIBOSOME
Title:
Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A
Biological Source:
Source Organism:
Saccharomyces cerevisiae (Taxon ID: 4932)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8K2D validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:B (auth: C1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:A (auth: C2)
Chain Length:1800
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:D (auth: C3)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:C (auth: C4)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Elongation factor 2
Gene (Uniprot):EFT1, EFT2
Chain IDs:EC (auth: CD)
Chain Length:842
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32324 Pfam ID:PF00009, PF03144, PF14492, PF03764, PF00679
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 5A-1
Gene (Uniprot):HYP2
Chain IDs:BC (auth: CE)
Chain Length:157
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P23301 Pfam ID:PF21485, PF01287
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Suppressor protein STM1
Gene (Uniprot):STM1
Chain IDs:FC (auth: CS)
Chain Length:273
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P39015 Pfam ID:PF09598
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL1A
Gene (Uniprot):RPL1A
Chain IDs:CC (auth: L1)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX43 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2A
Gene (Uniprot):RPL2A
Chain IDs:LA
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX45 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3
Gene (Uniprot):RPL3
Chain IDs:MA (auth: LB)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14126 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4A
Gene (Uniprot):RPL4A
Chain IDs:NA (auth: LC)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P10664 Pfam ID:PF00573, PF14374
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):RPL5
Chain IDs:OA (auth: LD)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26321 Pfam ID:PF17144, PF14204
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL6A
Gene (Uniprot):RPL6A
Chain IDs:PA (auth: LE)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02326 Pfam ID:PF01159
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30A
Gene (Uniprot):RPL7A
Chain IDs:QA (auth: LF)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05737 Pfam ID:PF08079, PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL8A
Gene (Uniprot):RPL8A
Chain IDs:RA (auth: LG)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P17076 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6A
Gene (Uniprot):RPL9A
Chain IDs:SA (auth: LH)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05738 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16
Gene (Uniprot):RPL10
Chain IDs:TA (auth: LI)
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41805 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5A
Gene (Uniprot):RPL11A
Chain IDs:UA (auth: LJ)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C0W9 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL11A
Gene (Uniprot):RPL12A
Chain IDs:VA (auth: LK)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX53 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL13A
Gene (Uniprot):RPL13A
Chain IDs:WA (auth: LL)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12690 Pfam ID:PF01294
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL14A
Gene (Uniprot):RPL14A
Chain IDs:XA (auth: LM)
Chain Length:128
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36105 Pfam ID:PF00467, PF01929
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL15A
Gene (Uniprot):RPL15A
Chain IDs:YA (auth: LN)
Chain Length:25
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05748 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13A
Gene (Uniprot):RPL16A
Chain IDs:ZA (auth: LO)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26784 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22A
Gene (Uniprot):RPL17A
Chain IDs:AB (auth: LP)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05740 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL18A
Gene (Uniprot):RPL18A
Chain IDs:BB (auth: LQ)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX49 Pfam ID:PF17135
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL19A
Gene (Uniprot):RPL19A
Chain IDs:CB (auth: LR)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX82 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL20A
Gene (Uniprot):RPL20A
Chain IDs:DB (auth: LS)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX23 Pfam ID:PF01775
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL21A
Gene (Uniprot):RPL21A
Chain IDs:EB (auth: LT)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02753 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL22A
Gene (Uniprot):RPL22A
Chain IDs:FB (auth: LU)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05749 Pfam ID:PF01776
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14A
Gene (Uniprot):RPL23A
Chain IDs:GB (auth: LV)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX41 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL24A
Gene (Uniprot):RPL24A
Chain IDs:HB (auth: LW)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04449 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Gene (Uniprot):RPL25
Chain IDs:IB (auth: LX)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04456 Pfam ID:PF03939, PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24A
Gene (Uniprot):RPL26A
Chain IDs:JB (auth: LY)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05743 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL27A
Gene (Uniprot):RPL27A
Chain IDs:KB (auth: LZ)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C2H6 Pfam ID:PF01777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15
Gene (Uniprot):RPL28
Chain IDs:LB (auth: La)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P02406 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL29
Gene (Uniprot):RPL29
Chain IDs:MB (auth: Lb)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05747 Pfam ID:PF01779
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL30
Gene (Uniprot):RPL30
Chain IDs:NB (auth: Lc)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14120 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL31A
Gene (Uniprot):RPL31A
Chain IDs:OB (auth: Ld)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C2H8 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL32
Gene (Uniprot):RPL32
Chain IDs:PB (auth: Le)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38061 Pfam ID:PF01655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL33A
Gene (Uniprot):RPL33A
Chain IDs:QB (auth: Lf)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05744 Pfam ID:PF01247
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL34A
Gene (Uniprot):RPL34A
Chain IDs:RB (auth: Lg)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P87262 Pfam ID:PF01199
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29A
Gene (Uniprot):RPL35A
Chain IDs:SB (auth: Lh)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX84 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL36A
Gene (Uniprot):RPL36A
Chain IDs:TB (auth: Li)
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05745 Pfam ID:PF01158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL37A
Gene (Uniprot):RPL37A
Chain IDs:UB (auth: Lj)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P49166 Pfam ID:PF01907
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL38
Gene (Uniprot):RPL38
Chain IDs:VB (auth: Lk)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P49167 Pfam ID:PF01781
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL39
Gene (Uniprot):RPL39
Chain IDs:WB (auth: Ll)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04650 Pfam ID:PF00832
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-ribosomal protein eL40A fusion protein
Gene (Uniprot):RPL40A
Chain IDs:XB (auth: Lm)
Chain Length:128
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CH08 Pfam ID:PF00240, PF01020
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL41A
Gene (Uniprot):RPL41A
Chain IDs:YB (auth: Ln)
Chain Length:25
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX86 Pfam ID:PF05162
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL42A
Gene (Uniprot):RPL42A
Chain IDs:ZB (auth: Lo)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX27 Pfam ID:PF00935
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL43A
Gene (Uniprot):RPL43A
Chain IDs:AC (auth: Lp)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX25 Pfam ID:PF01780
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL10
Gene (Uniprot):RPP0
Chain IDs:DC (auth: P0)
Chain Length:312
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05317 Pfam ID:PF00466, PF17777, PF00428
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2A
Gene (Uniprot):RPS0A
Chain IDs:E (auth: SA)
Chain Length:119
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32905 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S1-A
Gene (Uniprot):RPS1A
Chain IDs:F (auth: SB)
Chain Length:82
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P33442 Pfam ID:PF01015
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Gene (Uniprot):RPS2
Chain IDs:G (auth: SC)
Chain Length:67
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25443 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):RPS3
Chain IDs:H (auth: SD)
Chain Length:240
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05750 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4-A
Gene (Uniprot):RPS4A
Chain IDs:I (auth: SE)
Chain Length:63
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX35 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Gene (Uniprot):RPS5
Chain IDs:J (auth: SF)
Chain Length:152
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26783 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6-A
Gene (Uniprot):RPS6A
Chain IDs:K (auth: SG)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX37 Pfam ID:PF01092
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7-A
Gene (Uniprot):RPS7A
Chain IDs:L (auth: SH)
Chain Length:190
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26786 Pfam ID:PF01251
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8-A
Gene (Uniprot):RPS8A
Chain IDs:M (auth: SI)
Chain Length:200
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX39 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9-A
Gene (Uniprot):RPS9A
Chain IDs:N (auth: SJ)
Chain Length:197
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:O13516 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS10A
Gene (Uniprot):RPS10A
Chain IDs:O (auth: SK)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q08745 Pfam ID:PF03501
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17A
Gene (Uniprot):RPS11A
Chain IDs:P (auth: SL)
Chain Length:156
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX47 Pfam ID:PF16205, PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS12
Gene (Uniprot):RPS12
Chain IDs:Q (auth: SM)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P48589 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:R (auth: SN)
Chain Length:151
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05756 Pfam ID:PF08069, PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-A
Gene (Uniprot):RPS14A
Chain IDs:S (auth: SO)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P06367 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
Gene (Uniprot):RPS15
Chain IDs:T (auth: SP)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q01855 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9A
Gene (Uniprot):RPS16A
Chain IDs:U (auth: SQ)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX51 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS17A
Gene (Uniprot):RPS17A
Chain IDs:V (auth: SR)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P02407 Pfam ID:PF00833
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13A
Gene (Uniprot):RPS18A
Chain IDs:W (auth: SS)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX55 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS19A
Gene (Uniprot):RPS19A
Chain IDs:X (auth: ST)
Chain Length:144
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P07280 Pfam ID:PF01090
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Gene (Uniprot):RPS20
Chain IDs:Y (auth: SU)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38701 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS21A
Gene (Uniprot):RPS21A
Chain IDs:Z (auth: SV)
Chain Length:87
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C0V8 Pfam ID:PF01249
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22-A
Gene (Uniprot):RPS22A
Chain IDs:AA (auth: SW)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C0W1 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23-A
Gene (Uniprot):RPS23A
Chain IDs:BA (auth: SX)
Chain Length:145
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX29 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24-A
Gene (Uniprot):RPS24A
Chain IDs:CA (auth: SY)
Chain Length:135
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX31 Pfam ID:PF01282
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS25A
Gene (Uniprot):RPS25A
Chain IDs:DA (auth: SZ)
Chain Length:108
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q3E792 Pfam ID:PF03297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS26B
Gene (Uniprot):RPS26B
Chain IDs:EA (auth: Sa)
Chain Length:119
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P39939 Pfam ID:PF01283
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27-A
Gene (Uniprot):RPS27A
Chain IDs:FA (auth: Sb)
Chain Length:82
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P35997 Pfam ID:PF01667
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS28A
Gene (Uniprot):RPS28A
Chain IDs:GA (auth: Sc)
Chain Length:67
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q3E7X9 Pfam ID:PF01200
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14A
Gene (Uniprot):RPS29A
Chain IDs:HA (auth: Sd)
Chain Length:240
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41057 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30-A
Gene (Uniprot):RPS30A
Chain IDs:IA (auth: Se)
Chain Length:63
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX33 Pfam ID:PF04758
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-ribosomal protein eS31 fusion protein
Gene (Uniprot):RPS31
Chain IDs:JA (auth: Sf)
Chain Length:152
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05759 Pfam ID:PF00240, PF01599
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein RACK1
Gene (Uniprot):ASC1
Chain IDs:KA (auth: Sg)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38011 Pfam ID:PF00400
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
5CT BC LYS modified residue
Ligand Molecules
GDP
MG
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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Primary Citation of related structures
8K2D