[English] 日本語
Yorodumi
- PDB-9j1m: KU13-bond Mycobacterium tuberculosis 70S ribosome -

+
Open data


ID or keywords:

Loading...

-
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 / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
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 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, N-terminal domain superfamily / Ribosomal protein L9 / 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 L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / 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 S14/S29 / 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 L33 / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / Ribosomal protein S15, bacterial-type / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal protein S12, bacterial-type / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

+
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

-
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)

-
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

-
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

-
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

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more