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Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in complex with protein Y, hygromycin A, and azithromycin at 2.65A resolution

Source organisms:
Biochemical function: structural constituent of ribosome
Biological process: translation
Cellular component: ribonucleoprotein complex

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Biochemical function:
Biological process:
Cellular component:

Sequence families

Pfam Protein families (Pfam)
PF00347
Domain description: Ribosomal protein L6
Occurring in:
  1. Large ribosomal subunit protein uL6
The deposited structure of PDB entry 8fc5 contains 4 copies of Pfam domain PF00347 (Ribosomal protein L6) in Large ribosomal subunit protein uL6. Showing 2 copies in chain G [auth 1H].

PF02482
Domain description: Sigma 54 modulation protein / S30EA ribosomal protein
Occurring in:
  1. Ribosome-associated inhibitor A
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF02482 (Sigma 54 modulation protein / S30EA ribosomal protein) in Ribosome-associated inhibitor A. Showing 1 copy in chain AB [auth 1y].

PF17070
Domain description: 30S ribosomal protein Thx
Occurring in:
  1. Small ribosomal subunit protein bTHX
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF17070 (30S ribosomal protein Thx) in Small ribosomal subunit protein bTHX. Showing 1 copy in chain ZA [auth 1u].

PF01649
Domain description: Ribosomal protein S20
Occurring in:
  1. Small ribosomal subunit protein bS20
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF01649 (Ribosomal protein S20) in Small ribosomal subunit protein bS20. Showing 1 copy in chain ZC [auth 2t].

PF00203
Domain description: Ribosomal protein S19
Occurring in:
  1. Small ribosomal subunit protein uS19
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00203 (Ribosomal protein S19) in Small ribosomal subunit protein uS19. Showing 1 copy in chain XA [auth 1s].

PF01084
Domain description: Ribosomal protein S18
Occurring in:
  1. Small ribosomal subunit protein bS18
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF01084 (Ribosomal protein S18) in Small ribosomal subunit protein bS18. Showing 1 copy in chain WA [auth 1r].

PF00366
Domain description: Ribosomal protein S17
Occurring in:
  1. Small ribosomal subunit protein uS17
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00366 (Ribosomal protein S17) in Small ribosomal subunit protein uS17. Showing 1 copy in chain VA [auth 1q].

PF00886
Domain description: Ribosomal protein S16
Occurring in:
  1. Small ribosomal subunit protein bS16
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00886 (Ribosomal protein S16) in Small ribosomal subunit protein bS16. Showing 1 copy in chain UA [auth 1p].

PF00312
Domain description: Ribosomal protein S15
Occurring in:
  1. Small ribosomal subunit protein uS15
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00312 (Ribosomal protein S15) in Small ribosomal subunit protein uS15. Showing 1 copy in chain TA [auth 1o].

PF00253
Domain description: Ribosomal protein S14p/S29e
Occurring in:
  1. Small ribosomal subunit protein uS14
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00253 (Ribosomal protein S14p/S29e) in Small ribosomal subunit protein uS14. Showing 1 copy in chain SA [auth 1n].

PF00416
Domain description: Ribosomal protein S13/S18
Occurring in:
  1. Small ribosomal subunit protein uS13
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00416 (Ribosomal protein S13/S18) in Small ribosomal subunit protein uS13. Showing 1 copy in chain RA [auth 1m].

PF00164
Domain description: Ribosomal protein S12/S23
Occurring in:
  1. Small ribosomal subunit protein uS12
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00164 (Ribosomal protein S12/S23) in Small ribosomal subunit protein uS12. Showing 1 copy in chain QA [auth 1l].

PF00411
Domain description: Ribosomal protein S11
Occurring in:
  1. Small ribosomal subunit protein uS11
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00411 (Ribosomal protein S11) in Small ribosomal subunit protein uS11. Showing 1 copy in chain PA [auth 1k].

PF00338
Domain description: Ribosomal protein S10p/S20e
Occurring in:
  1. Small ribosomal subunit protein uS10
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00338 (Ribosomal protein S10p/S20e) in Small ribosomal subunit protein uS10. Showing 1 copy in chain OA [auth 1j].

PF00380
Domain description: Ribosomal protein S9/S16
Occurring in:
  1. Small ribosomal subunit protein uS9
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00380 (Ribosomal protein S9/S16) in Small ribosomal subunit protein uS9. Showing 1 copy in chain NA [auth 1i].

PF00410
Domain description: Ribosomal protein S8
Occurring in:
  1. Small ribosomal subunit protein uS8
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00410 (Ribosomal protein S8) in Small ribosomal subunit protein uS8. Showing 1 copy in chain MA [auth 1h].

PF00177
Domain description: Ribosomal protein S7p/S5e
Occurring in:
  1. Small ribosomal subunit protein uS7
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00177 (Ribosomal protein S7p/S5e) in Small ribosomal subunit protein uS7. Showing 1 copy in chain LA [auth 1g].

PF01250
Domain description: Ribosomal protein S6
Occurring in:
  1. Small ribosomal subunit protein bS6
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF01250 (Ribosomal protein S6) in Small ribosomal subunit protein bS6. Showing 1 copy in chain KA [auth 1f].

PF03719
Domain description: Ribosomal protein S5, C-terminal domain
Occurring in:
  1. Small ribosomal subunit protein uS5
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF03719 (Ribosomal protein S5, C-terminal domain) in Small ribosomal subunit protein uS5. Showing 1 copy in chain JA [auth 1e].

PF00333
Domain description: Ribosomal protein S5, N-terminal domain
Occurring in:
  1. Small ribosomal subunit protein uS5
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00333 (Ribosomal protein S5, N-terminal domain) in Small ribosomal subunit protein uS5. Showing 1 copy in chain JA [auth 1e].

PF01479
Domain description: S4 domain
Occurring in:
  1. Small ribosomal subunit protein uS4
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF01479 (S4 domain) in Small ribosomal subunit protein uS4. Showing 1 copy in chain IA [auth 1d].

PF00163
Domain description: Ribosomal protein S4/S9 N-terminal domain
Occurring in:
  1. Small ribosomal subunit protein uS4
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00163 (Ribosomal protein S4/S9 N-terminal domain) in Small ribosomal subunit protein uS4. Showing 1 copy in chain IA [auth 1d].

PF00189
Domain description: Ribosomal protein S3, C-terminal domain
Occurring in:
  1. Small ribosomal subunit protein uS3
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00189 (Ribosomal protein S3, C-terminal domain) in Small ribosomal subunit protein uS3. Showing 1 copy in chain HA [auth 1c].

PF07650
Domain description: KH domain
Occurring in:
  1. Small ribosomal subunit protein uS3
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF07650 (KH domain) in Small ribosomal subunit protein uS3. Showing 1 copy in chain HA [auth 1c].

PF00318
Domain description: Ribosomal protein S2
Occurring in:
  1. Small ribosomal subunit protein uS2
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00318 (Ribosomal protein S2) in Small ribosomal subunit protein uS2. Showing 1 copy in chain GA [auth 1b].

PF14693
Domain description: Ribosomal protein TL5, C-terminal domain
Occurring in:
  1. Large ribosomal subunit protein bL25
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF14693 (Ribosomal protein TL5, C-terminal domain) in Large ribosomal subunit protein bL25. Showing 1 copy in chain U [auth 1Z].

PF01386
Domain description: Ribosomal L25p family
Occurring in:
  1. Large ribosomal subunit protein bL25
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF01386 (Ribosomal L25p family) in Large ribosomal subunit protein bL25. Showing 1 copy in chain U [auth 1Z].

PF17136
Domain description: Ribosomal proteins 50S L24/mitochondrial 39S L24
Occurring in:
  1. Large ribosomal subunit protein uL24
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF17136 (Ribosomal proteins 50S L24/mitochondrial 39S L24) in Large ribosomal subunit protein uL24. Showing 1 copy in chain T [auth 1Y].

PF00467
Domain description: KOW motif
Occurring in:
  1. Large ribosomal subunit protein uL24
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00467 (KOW motif) in Large ribosomal subunit protein uL24. Showing 1 copy in chain T [auth 1Y].

PF00276
Domain description: Ribosomal protein L23
Occurring in:
  1. Large ribosomal subunit protein uL23
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00276 (Ribosomal protein L23) in Large ribosomal subunit protein uL23. Showing 1 copy in chain S [auth 1X].

PF00237
Domain description: Ribosomal protein L22p/L17e
Occurring in:
  1. Large ribosomal subunit protein uL22
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00237 (Ribosomal protein L22p/L17e) in Large ribosomal subunit protein uL22. Showing 1 copy in chain R [auth 1W].

PF00829
Domain description: Ribosomal prokaryotic L21 protein
Occurring in:
  1. Large ribosomal subunit protein bL21
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00829 (Ribosomal prokaryotic L21 protein) in Large ribosomal subunit protein bL21. Showing 1 copy in chain Q [auth 1V].

PF00453
Domain description: Ribosomal protein L20
Occurring in:
  1. Large ribosomal subunit protein bL20
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00453 (Ribosomal protein L20) in Large ribosomal subunit protein bL20. Showing 1 copy in chain P [auth 1U].

PF01245
Domain description: Ribosomal protein L19
Occurring in:
  1. Large ribosomal subunit protein bL19
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF01245 (Ribosomal protein L19) in Large ribosomal subunit protein bL19. Showing 1 copy in chain O [auth 1T].

PF00861
Domain description: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Occurring in:
  1. Large ribosomal subunit protein uL18
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00861 (Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast) in Large ribosomal subunit protein uL18. Showing 1 copy in chain N [auth 1S].

PF01196
Domain description: Ribosomal protein L17
Occurring in:
  1. Large ribosomal subunit protein bL17
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF01196 (Ribosomal protein L17) in Large ribosomal subunit protein bL17. Showing 1 copy in chain M [auth 1R].

PF00252
Domain description: Ribosomal protein L16p/L10e
Occurring in:
  1. Large ribosomal subunit protein uL16
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00252 (Ribosomal protein L16p/L10e) in Large ribosomal subunit protein uL16. Showing 1 copy in chain L [auth 1Q].

PF00828
Domain description: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Occurring in:
  1. Large ribosomal subunit protein uL15
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00828 (Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A) in Large ribosomal subunit protein uL15. Showing 1 copy in chain K [auth 1P].

PF00238
Domain description: Ribosomal protein L14p/L23e
Occurring in:
  1. Large ribosomal subunit protein uL14
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00238 (Ribosomal protein L14p/L23e) in Large ribosomal subunit protein uL14. Showing 1 copy in chain J [auth 1O].

PF00572
Domain description: Ribosomal protein L13
Occurring in:
  1. Large ribosomal subunit protein uL13
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00572 (Ribosomal protein L13) in Large ribosomal subunit protein uL13. Showing 1 copy in chain I [auth 1N].

PF03948
Domain description: Ribosomal protein L9, C-terminal domain
Occurring in:
  1. Large ribosomal subunit protein bL9
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF03948 (Ribosomal protein L9, C-terminal domain) in Large ribosomal subunit protein bL9. Showing 1 copy in chain H [auth 1I].

PF01281
Domain description: Ribosomal protein L9, N-terminal domain
Occurring in:
  1. Large ribosomal subunit protein bL9
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF01281 (Ribosomal protein L9, N-terminal domain) in Large ribosomal subunit protein bL9. Showing 1 copy in chain H [auth 1I].

PF00673
Domain description: ribosomal L5P family C-terminus
Occurring in:
  1. Large ribosomal subunit protein uL5
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00673 (ribosomal L5P family C-terminus) in Large ribosomal subunit protein uL5. Showing 1 copy in chain F [auth 1G].

PF00281
Domain description: Ribosomal protein L5
Occurring in:
  1. Large ribosomal subunit protein uL5
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00281 (Ribosomal protein L5) in Large ribosomal subunit protein uL5. Showing 1 copy in chain F [auth 1G].

PF00573
Domain description: Ribosomal protein L4/L1 family
Occurring in:
  1. Large ribosomal subunit protein uL4
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00573 (Ribosomal protein L4/L1 family) in Large ribosomal subunit protein uL4. Showing 1 copy in chain E [auth 1F].

PF00297
Domain description: Ribosomal protein L3
Occurring in:
  1. Large ribosomal subunit protein uL3
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00297 (Ribosomal protein L3) in Large ribosomal subunit protein uL3. Showing 1 copy in chain D [auth 1E].

PF03947
Domain description: Ribosomal Proteins L2, C-terminal domain
Occurring in:
  1. Large ribosomal subunit protein uL2
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF03947 (Ribosomal Proteins L2, C-terminal domain) in Large ribosomal subunit protein uL2. Showing 1 copy in chain C [auth 1D].

PF00181
Domain description: Ribosomal Proteins L2, RNA binding domain
Occurring in:
  1. Large ribosomal subunit protein uL2
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00181 (Ribosomal Proteins L2, RNA binding domain) in Large ribosomal subunit protein uL2. Showing 1 copy in chain C [auth 1D].

PF00444
Domain description: Ribosomal protein L36
Occurring in:
  1. Large ribosomal subunit protein bL36
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00444 (Ribosomal protein L36) in Large ribosomal subunit protein bL36. Showing 1 copy in chain EA [auth 19].

PF01632
Domain description: Ribosomal protein L35
Occurring in:
  1. Large ribosomal subunit protein bL35
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF01632 (Ribosomal protein L35) in Large ribosomal subunit protein bL35. Showing 1 copy in chain DA [auth 18].

PF00468
Domain description: Ribosomal protein L34
Occurring in:
  1. Large ribosomal subunit protein bL34
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00468 (Ribosomal protein L34) in Large ribosomal subunit protein bL34. Showing 1 copy in chain CA [auth 17].

PF00471
Domain description: Ribosomal protein L33
Occurring in:
  1. Large ribosomal subunit protein bL33
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00471 (Ribosomal protein L33) in Large ribosomal subunit protein bL33. Showing 1 copy in chain BA [auth 16].

PF01783
Domain description: Ribosomal L32p protein family
Occurring in:
  1. Large ribosomal subunit protein bL32
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF01783 (Ribosomal L32p protein family) in Large ribosomal subunit protein bL32. Showing 1 copy in chain AA [auth 15].

PF01197
Domain description: Ribosomal protein L31
Occurring in:
  1. Large ribosomal subunit protein bL31
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF01197 (Ribosomal protein L31) in Large ribosomal subunit protein bL31. Showing 1 copy in chain Z [auth 14].

PF00327
Domain description: Ribosomal protein L30p/L7e
Occurring in:
  1. Large ribosomal subunit protein uL30
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00327 (Ribosomal protein L30p/L7e) in Large ribosomal subunit protein uL30. Showing 1 copy in chain Y [auth 13].

PF00831
Domain description: Ribosomal L29 protein
Occurring in:
  1. Large ribosomal subunit protein uL29
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00831 (Ribosomal L29 protein) in Large ribosomal subunit protein uL29. Showing 1 copy in chain X [auth 12].

PF00830
Domain description: Ribosomal L28 family
Occurring in:
  1. Large ribosomal subunit protein bL28
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF00830 (Ribosomal L28 family) in Large ribosomal subunit protein bL28. Showing 1 copy in chain W [auth 11].

PF01016
Domain description: Ribosomal L27 protein
Occurring in:
  1. Large ribosomal subunit protein bL27
The deposited structure of PDB entry 8fc5 contains 2 copies of Pfam domain PF01016 (Ribosomal L27 protein) in Large ribosomal subunit protein bL27. Showing 1 copy in chain V [auth 10].

Rfam RNA families (Rfam)
RF02541
Domain description: Bacterial large subunit ribosomal RNA
Occurring in:
  1. 23S ribosomal RNA
The deposited structure of PDB entry 8fc5 contains 2 copies of Rfam domain RF02541 (Bacterial large subunit ribosomal RNA) in 23S ribosomal RNA. Showing 1 copy in chain A [auth 1A].

RF00001
Domain description: 5S ribosomal RNA
Occurring in:
  1. 5S ribosomal RNA
The deposited structure of PDB entry 8fc5 contains 2 copies of Rfam domain RF00001 (5S ribosomal RNA) in 5S ribosomal RNA. Showing 1 copy in chain B [auth 1B].

RF00177
Domain description: Bacterial small subunit ribosomal RNA
Occurring in:
  1. 16S ribosomal RNA
The deposited structure of PDB entry 8fc5 contains 2 copies of Rfam domain RF00177 (Bacterial small subunit ribosomal RNA) in 16S ribosomal RNA. Showing 1 copy in chain GC [auth 2a].

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