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- PDB-7sfr: Unmethylated Mtb Ribosome 50S with SEQ-9 -

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Basic information

Entry
Database: PDB / ID: 7sfr
TitleUnmethylated Mtb Ribosome 50S with SEQ-9
Components
  • (30S ribosomal protein ...) x 18
  • (50S ribosomal protein ...) x 29
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • peptide
KeywordsRIBOSOME/ANTIBIOTIC / unmethylated / Mtb ribosome / drug discovery / SEQ-9 / Structural Genomics / TB Structural Genomics Consortium / TBSGC / 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 / metal 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 L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 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 L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L16 signature 1. / 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 L28/L24 superfamily / 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 L28 / 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 S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L9/RNase H1, N-terminal / 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 S4, bacterial-type / 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 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 L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein S15, bacterial-type / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type
Similarity search - Domain/homology
Sequanamycin 9 / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 ...Sequanamycin 9 / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL13 / 30S ribosomal protein THX / 50S ribosomal protein L36 / 50S ribosomal protein L34 / : / Small ribosomal subunit protein uS12
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsXing, Z. / Cui, Z. / Zhang, J. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01AI095208 United States
Welch FoundationA1863 United States
CitationJournal: Cell / Year: 2023
Title: Discovery of natural-product-derived sequanamycins as potent oral anti-tuberculosis agents.
Authors: Jidong Zhang / Christine Lair / Christine Roubert / Kwame Amaning / María Belén Barrio / Yannick Benedetti / Zhicheng Cui / Zhongliang Xing / Xiaojun Li / Scott G Franzblau / Nicolas ...Authors: Jidong Zhang / Christine Lair / Christine Roubert / Kwame Amaning / María Belén Barrio / Yannick Benedetti / Zhicheng Cui / Zhongliang Xing / Xiaojun Li / Scott G Franzblau / Nicolas Baurin / Florence Bordon-Pallier / Cathy Cantalloube / Stephanie Sans / Sandra Silve / Isabelle Blanc / Laurent Fraisse / Alexey Rak / Lasse B Jenner / Gulnara Yusupova / Marat Yusupov / Junjie Zhang / Takushi Kaneko / T J Yang / Nader Fotouhi / Eric Nuermberger / Sandeep Tyagi / Fabrice Betoudji / Anna Upton / James C Sacchettini / Sophie Lagrange /
Abstract: The emergence of drug-resistant tuberculosis has created an urgent need for new anti-tubercular agents. Here, we report the discovery of a series of macrolides called sequanamycins with outstanding ...The emergence of drug-resistant tuberculosis has created an urgent need for new anti-tubercular agents. Here, we report the discovery of a series of macrolides called sequanamycins with outstanding in vitro and in vivo activity against Mycobacterium tuberculosis (Mtb). Sequanamycins are bacterial ribosome inhibitors that interact with the ribosome in a similar manner to classic macrolides like erythromycin and clarithromycin, but with binding characteristics that allow them to overcome the inherent macrolide resistance of Mtb. Structures of the ribosome with bound inhibitors were used to optimize sequanamycin to produce the advanced lead compound SEQ-9. SEQ-9 was efficacious in mouse models of acute and chronic TB as a single agent, and it demonstrated bactericidal activity in a murine TB infection model in combination with other TB drugs. These results support further investigation of this series as TB clinical candidates, with the potential for use in new regimens against drug-susceptible and drug-resistant TB.
History
DepositionOct 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Refinement description
Category: citation / citation_author / pdbx_initial_refinement_model
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jun 5, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
6: 50S ribosomal protein L31
A: 23S rRNA
B: 5S rRNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
a: 16S rRNA
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14 type Z
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
v: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,243,571505
Polymers2,231,07151
Non-polymers12,500454
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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50S ribosomal protein ... , 29 types, 29 molecules 012346CDEFGHJKLMNOPQRSTUVWXYZ

#1: Protein 50S ribosomal protein L32


Mass: 6525.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IMI5
#2: Protein 50S ribosomal protein L33


Mass: 6512.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HU86
#3: Protein/peptide 50S ribosomal protein L34


Mass: 5643.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A3E0V610
#4: Protein 50S ribosomal protein L35


Mass: 7241.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045KKY9
#5: Protein/peptide 50S ribosomal protein L36


Mass: 4323.239 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A3E0V5U0
#6: Protein 50S ribosomal protein L31


Mass: 8770.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HLX7
#9: Protein 50S ribosomal protein L2


Mass: 30512.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H5T7
#10: Protein 50S ribosomal protein L3


Mass: 22680.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HU18
#11: Protein 50S ribosomal protein L4


Mass: 22086.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045J9H1
#12: Protein 50S ribosomal protein L5


Mass: 20048.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HUU0
#13: Protein 50S ribosomal protein L6


Mass: 19190.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JJU1
#14: Protein 50S ribosomal protein L9


Mass: 16196.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JW48
#15: Protein 50S ribosomal protein L13


Mass: 21646.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A0T9D5H2
#16: Protein 50S ribosomal protein L14


Mass: 13419.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HTP7
#17: Protein 50S ribosomal protein L15


Mass: 15566.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IWY0
#18: Protein 50S ribosomal protein L16


Mass: 15724.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IWV9
#19: Protein 50S ribosomal protein L17


Mass: 19512.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IVA2
#20: Protein 50S ribosomal protein L18


Mass: 13211.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JK28
#21: Protein 50S ribosomal protein L19


Mass: 13041.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IDD2
#22: Protein 50S ribosomal protein L20


Mass: 14557.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045KJ85
#23: Protein 50S ribosomal protein L21


Mass: 11173.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A7G7DRC6
#24: Protein 50S ribosomal protein L22


Mass: 20424.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H760
#25: Protein 50S ribosomal protein L23


Mass: 10976.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045J9M3
#26: Protein 50S ribosomal protein L24


Mass: 11500.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IXU4
#27: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 22466.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JAK4
#28: Protein 50S ribosomal protein L27


Mass: 8987.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045K0G1
#29: Protein 50S ribosomal protein L28


Mass: 6920.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IDB8
#30: Protein 50S ribosomal protein L29


Mass: 8872.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IQ64
#31: Protein 50S ribosomal protein L30


Mass: 7361.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H4J2

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RNA chain , 3 types, 3 molecules ABa

#7: RNA chain 23S rRNA


Mass: 1017862.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: GenBank: 1251771536
#8: RNA chain 5S rRNA


Mass: 37097.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: GenBank: 1251771551
#32: RNA chain 16S rRNA


Mass: 498415.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: GenBank: 1173866659

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30S ribosomal protein ... , 18 types, 18 molecules cdefghijklmnopqrst

#33: Protein 30S ribosomal protein S3


Mass: 30071.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H4H6
#34: Protein 30S ribosomal protein S4


Mass: 23515.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045GRS4
#35: Protein 30S ribosomal protein S5


Mass: 22925.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JKV0
#36: Protein 30S ribosomal protein S6


Mass: 10952.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JVY9
#37: Protein 30S ribosomal protein S7


Mass: 17633.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JMN7
#38: Protein 30S ribosomal protein S8


Mass: 14432.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IWX2
#39: Protein 30S ribosomal protein S9


Mass: 16465.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045I839
#40: Protein 30S ribosomal protein S10


Mass: 11452.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HTN2
#41: Protein 30S ribosomal protein S11


Mass: 14815.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045I821
#42: Protein 30S ribosomal protein S12


Mass: 13882.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: M9TET4
#43: Protein 30S ribosomal protein S13


Mass: 14383.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045GT82
#44: Protein 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 (bacteria) / References: UniProt: A0A045HUG3
#45: Protein 30S ribosomal protein S15


Mass: 10500.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JF49
#46: Protein 30S ribosomal protein S16


Mass: 17466.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JER3
#47: Protein 30S ribosomal protein S17


Mass: 14776.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A0E9AP91
#48: Protein 30S ribosomal protein S18


Mass: 9565.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JW21
#49: Protein 30S ribosomal protein S19


Mass: 10830.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IXT2
#50: Protein 30S ribosomal protein S20


Mass: 9428.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045GXQ2

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Protein/peptide , 1 types, 1 molecules v

#51: Protein/peptide peptide


Mass: 2664.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A3E0UTA6

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Non-polymers , 3 types, 454 molecules

#52: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#53: Chemical ChemComp-WDP / Sequanamycin 9


Mass: 1243.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C61H102N4O20S / Feature type: SUBJECT OF INVESTIGATION
#54: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 447 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestY

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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: Unmethylated Mth Ribosome with SEQ-9 / Type: RIBOSOME / Entity ID: #1-#51 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
250 mMPotassium ChlorideKCl1
310 mMAmmonium ChlorideNH4Cl1
410 mMMagnesium ChlorideMgCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodispersed unmethylated Mtb ribosome with SEQ-9
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Image recordingElectron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 35

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.2particle selection
4cryoSPARC3.2CTF correction
7UCSF Chimera1.15model fitting
13PHENIX1.19.1model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 719250 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 7KGB

7kgb


Accession code: 7KGB / Source name: PDB / Type: experimental model

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  • 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

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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

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