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- PDB-9j1m: KU13-bond Mycobacterium tuberculosis 70S ribosome -

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Basic information

Entry
Database: PDB / ID: 9j1m
TitleKU13-bond Mycobacterium tuberculosis 70S ribosome
Components
  • (Large ribosomal subunit protein ...) x 28
  • (Small ribosomal subunit protein ...) x 18
  • 16S rRNA
  • 23S rRNA
  • 30S ribosomal protein THX
  • 5S rRNA
  • Mitochondrial domain of uncharacterised function (DUF1713)
  • tRNA
KeywordsRIBOSOME/ANTIBIOTIC / ribosome / macrolide / ANTIBIOTIC / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9 signature. / : / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L27 / Ribosomal protein S6 superfamily / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L21
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein bL25 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL13 / : / : / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18A / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL33A / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein bL36
Similarity search - Component
Biological speciesMycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.33 Å
AuthorsNishihara, D. / Fujino, M. / Tanaka, Y. / Yokoyama, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other private Japan
CitationJournal: Sci Adv / Year: 2025
Title: Creation of a macrolide antibiotic against non-tuberculous using late-stage boron-mediated aglycon delivery.
Authors: Yuka Isozaki / Takumi Makikawa / Kosuke Kimura / Daiki Nishihara / Maho Fujino / Yoshikazu Tanaka / Chigusa Hayashi / Yoshimasa Ishizaki / Masayuki Igarashi / Takeshi Yokoyama / Kazunobu ...Authors: Yuka Isozaki / Takumi Makikawa / Kosuke Kimura / Daiki Nishihara / Maho Fujino / Yoshikazu Tanaka / Chigusa Hayashi / Yoshimasa Ishizaki / Masayuki Igarashi / Takeshi Yokoyama / Kazunobu Toshima / Daisuke Takahashi /
Abstract: Non-tuberculous mycobacteria (NTM) is gaining clinical recognition as a recently emerging pulmonary pathogen. complex (MAC), the most common NTM, is the cause of pulmonary MAC disease. Currently, ...Non-tuberculous mycobacteria (NTM) is gaining clinical recognition as a recently emerging pulmonary pathogen. complex (MAC), the most common NTM, is the cause of pulmonary MAC disease. Currently, the macrolide azithromycin (AZM) is the standard first-line antibiotic for treatment of the disease. However, the rise of drug-resistant MAC necessitates the development of alternative therapeutics. Here, we present a late-stage boron-mediated aglycon delivery strategy for selective modification of AZM, generating a library of potential anti-MAC drugs designated to . Screening of to revealed that exhibited enhanced antimicrobial activity against wild-type and macrolide-resistant MAC compared to AZM. Cryo-electron microscopy analysis indicated that the inserted tercyclic moiety of formed a robust anchor on the bacterial ribosome, creating a binding pocket with base flipping of U2847, potentially bypassing the standard mechanism of macrolide resistance. These results position as a promising lead for therapeutics against macrolide-resistant MAC.
History
DepositionAug 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: Large ribosomal subunit protein bL32
1: Large ribosomal subunit protein bL33A
2: Large ribosomal subunit protein bL34
3: Large ribosomal subunit protein bL35
4: Large ribosomal subunit protein bL36
7: 30S ribosomal protein THX
A: 23S rRNA
B: 5S rRNA
C: Large ribosomal subunit protein uL2
D: Large ribosomal subunit protein uL3
E: Large ribosomal subunit protein uL4
F: Large ribosomal subunit protein uL5
G: Large ribosomal subunit protein uL6
H: Large ribosomal subunit protein bL9
J: Large ribosomal subunit protein uL13
K: Large ribosomal subunit protein uL14
L: Large ribosomal subunit protein uL15
M: Large ribosomal subunit protein uL16
N: Large ribosomal subunit protein bL17
O: Large ribosomal subunit protein uL18
P: Large ribosomal subunit protein bL19
Q: Large ribosomal subunit protein bL20
R: Large ribosomal subunit protein bL21
S: Large ribosomal subunit protein uL22
T: Large ribosomal subunit protein uL23
U: Large ribosomal subunit protein uL24
V: Large ribosomal subunit protein bL25
W: Large ribosomal subunit protein bL27
X: Large ribosomal subunit protein bL28
Y: Large ribosomal subunit protein uL29
Z: Large ribosomal subunit protein uL30
a: 16S rRNA
c: Small ribosomal subunit protein uS3
d: Small ribosomal subunit protein uS4
e: Small ribosomal subunit protein uS5
f: Small ribosomal subunit protein bS6
g: Small ribosomal subunit protein uS7
h: Small ribosomal subunit protein uS8
i: Small ribosomal subunit protein uS9
j: Small ribosomal subunit protein uS10
k: Small ribosomal subunit protein uS11
l: Small ribosomal subunit protein uS12
m: Small ribosomal subunit protein uS13
n: Small ribosomal subunit protein uS14B
o: Small ribosomal subunit protein uS15
p: Small ribosomal subunit protein bS16
q: Small ribosomal subunit protein uS17
r: Small ribosomal subunit protein bS18A
s: Small ribosomal subunit protein uS19
t: Small ribosomal subunit protein bS20
x: Mitochondrial domain of uncharacterised function (DUF1713)
u: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,247,404499
Polymers2,235,21352
Non-polymers12,191447
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Large ribosomal subunit protein ... , 28 types, 28 molecules 01234CDEFGHJKLMNOPQRSTUVWXYZ

#1: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6525.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KHB5
#2: Protein Large ribosomal subunit protein bL33A / 50S ribosomal protein L33 1


Mass: 6512.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGB4
#3: Protein/peptide Large ribosomal subunit protein bL34


Mass: 5643.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A0A0G2Q9F3
#4: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7241.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KJ59
#5: Protein/peptide Large ribosomal subunit protein bL36 / 50S ribosomal protein L36


Mass: 4355.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KPE7
#9: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 30644.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGI5
#10: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 23127.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGI2
#11: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 23779.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGI3
#12: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 21052.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGJ7
#13: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19408.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGK0
#14: Protein Large ribosomal subunit protein bL9 / 50S ribosomal protein L9


Mass: 16196.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KEM4
#15: Protein Large ribosomal subunit protein uL13


Mass: 21646.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A0A0T9D5H2
#16: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13451.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGJ5
#17: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15554.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGK4
#18: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 15724.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGI9
#19: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 19512.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KPE2
#20: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 13211.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGK1
#21: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 13041.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KMP8
#22: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 14557.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KJ60
#23: Protein Large ribosomal subunit protein bL21


Mass: 11173.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A0A0H3MFJ0
#24: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 20424.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGI7
#25: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 10976.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGI4
#26: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11500.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGJ6
#27: Protein Large ribosomal subunit protein bL25 / General stress protein CTC


Mass: 22466.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A0A0H3M3R5
#28: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 8987.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KLD7
#29: Protein Large ribosomal subunit protein bL28


Mass: 6920.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A0AAE8WTM0
#30: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 8872.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGJ0
#31: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 7361.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGK3

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RNA chain , 4 types, 4 molecules ABau

#7: RNA chain 23S rRNA


Mass: 1017834.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: GenBank: 1500175159
#8: RNA chain 5S rRNA


Mass: 37097.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: GenBank: 1500175159
#32: RNA chain 16S rRNA


Mass: 498401.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: GenBank: 1500179159
#52: RNA chain tRNA


Mass: 894.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)

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Small ribosomal subunit protein ... , 18 types, 18 molecules cdefghijklmnopqrst

#33: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 30071.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGI8
#34: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23515.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KPE4
#35: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 22925.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGK2
#36: Protein Small ribosomal subunit protein bS6 / 30S ribosomal protein S6


Mass: 10952.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KEM1
#37: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 17633.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGG3
#38: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14432.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGJ9
#39: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 16465.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KPC9
#40: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11452.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGI1
#41: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 14800.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KPE5
#42: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13882.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGG2
#43: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 14383.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KPE6
#44: Protein Small ribosomal subunit protein uS14B / 30S ribosomal protein S14 type Z


Mass: 6841.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGJ8
#45: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10500.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KMC8
#46: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 17466.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KMQ3
#47: Protein Small ribosomal subunit protein uS17


Mass: 14776.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A0A0H3M2V9
#48: Protein Small ribosomal subunit protein bS18A / 30S ribosomal protein S18 1


Mass: 9565.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KEM3
#49: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10830.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KGI6
#50: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9428.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A1KLA4

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Protein/peptide / Protein , 2 types, 2 molecules 7x

#51: Protein Mitochondrial domain of uncharacterised function (DUF1713)


Mass: 8310.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
#6: Protein/peptide 30S ribosomal protein THX


Mass: 2882.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Strain: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2
References: UniProt: A0AAE8WR80

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Non-polymers , 3 types, 447 molecules

#53: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#54: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 441 / Source method: obtained synthetically / Formula: Mg
#55: Chemical ChemComp-A1L32 / (2~{R},3~{R},4~{R},5~{R},8~{R},10~{R},11~{R},12~{S},13~{S},14~{R})-11-[(2~{S},3~{R},4~{S},6~{R})-4-(dimethylamino)-6-methyl-3-oxidanyl-oxan-2-yl]oxy-2-ethyl-4-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4-bis(oxidanyl)-5-[[4-(4-pyridin-4-yl-1,2,3-triazol-1-yl)phenyl]methoxy]oxan-2-yl]oxy-13-[(2~{R},4~{R},5~{S},6~{S})-4-methoxy-4,6-dimethyl-5-oxidanyl-oxan-2-yl]oxy-3,5,6,8,10,12,14-heptamethyl-3,10-bis(oxidanyl)-1-oxa-6-azacyclopentadecan-15-one / KU-13, chemically modified azithromycin


Mass: 1145.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C58H92N6O17 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: KU13-bond Mycobacterium tuberculosis 70S ribosome / Type: RIBOSOME / Entity ID: #1-#52 / Source: NATURAL
Source (natural)Organism: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
EM embeddingMaterial: vitrified ice
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4.0.1particle selection
2SerialEMimage acquisition
4CTFFIND4.1.14CTF correction
7Cootmodel fitting
9RELION4.0.1initial Euler assignment
10RELION4.0.1final Euler assignment
11RELION4.0.1classification
12RELION4.0.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 515051
3D reconstructionResolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205461 / Symmetry type: POINT

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