[English] 日本語
Yorodumi
- PDB-7uvy: A. baumannii ribosome-Streptothricin-D complex: 70S with P-site tRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7uvy
TitleA. baumannii ribosome-Streptothricin-D complex: 70S with P-site tRNA
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 28
  • 16s Ribosomal RNA
  • 23s ribosomal RNA
  • 5s ribosomal RNA
  • mRNA
  • tRNA-met
KeywordsRibosome/RNA / Streptothricin / Nourseothricin / Antibiotic / Ribosome / Ribosome-RNA complex
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit assembly / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding ...large ribosomal subunit / transferase activity / ribosomal small subunit assembly / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large 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 / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / : ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / 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 L32p, bacterial type / 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 L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / 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 S2, bacteria/mitochondria/plastid / 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 L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / 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 S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein L27 / Ribosomal L27 protein
Similarity search - Domain/homology
Streptothricin D / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / 30S ribosomal protein S10 ...Streptothricin D / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / 30S ribosomal protein S10 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL20
Similarity search - Component
Biological speciesAcinetobacter baumannii AB0057 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsMorgan, C.E. / Yu, E.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: PLoS Biol / Year: 2023
Title: Streptothricin F is a bactericidal antibiotic effective against highly drug-resistant gram-negative bacteria that interacts with the 30S subunit of the 70S ribosome.
Authors: Christopher E Morgan / Yoon-Suk Kang / Alex B Green / Kenneth P Smith / Matthew G Dowgiallo / Brandon C Miller / Lucius Chiaraviglio / Katherine A Truelson / Katelyn E Zulauf / Shade ...Authors: Christopher E Morgan / Yoon-Suk Kang / Alex B Green / Kenneth P Smith / Matthew G Dowgiallo / Brandon C Miller / Lucius Chiaraviglio / Katherine A Truelson / Katelyn E Zulauf / Shade Rodriguez / Anthony D Kang / Roman Manetsch / Edward W Yu / James E Kirby /
Abstract: The streptothricin natural product mixture (also known as nourseothricin) was discovered in the early 1940s, generating intense initial interest because of excellent gram-negative activity. Here, we ...The streptothricin natural product mixture (also known as nourseothricin) was discovered in the early 1940s, generating intense initial interest because of excellent gram-negative activity. Here, we establish the activity spectrum of nourseothricin and its main components, streptothricin F (S-F, 1 lysine) and streptothricin D (S-D, 3 lysines), purified to homogeneity, against highly drug-resistant, carbapenem-resistant Enterobacterales (CRE) and Acinetobacter baumannii. For CRE, the MIC50 and MIC90 for S-F and S-D were 2 and 4 μM, and 0.25 and 0.5 μM, respectively. S-F and nourseothricin showed rapid, bactericidal activity. S-F and S-D both showed approximately 40-fold greater selectivity for prokaryotic than eukaryotic ribosomes in in vitro translation assays. In vivo, delayed renal toxicity occurred at >10-fold higher doses of S-F compared with S-D. Substantial treatment effect of S-F in the murine thigh model was observed against the otherwise pandrug-resistant, NDM-1-expressing Klebsiella pneumoniae Nevada strain with minimal or no toxicity. Cryo-EM characterization of S-F bound to the A. baumannii 70S ribosome defines extensive hydrogen bonding of the S-F steptolidine moiety, as a guanine mimetic, to the 16S rRNA C1054 nucleobase (Escherichia coli numbering) in helix 34, and the carbamoylated gulosamine moiety of S-F with A1196, explaining the high-level resistance conferred by corresponding mutations at the residues identified in single rrn operon E. coli. Structural analysis suggests that S-F probes the A-decoding site, which potentially may account for its miscoding activity. Based on unique and promising activity, we suggest that the streptothricin scaffold deserves further preclinical exploration as a potential therapeutic for drug-resistant, gram-negative pathogens.
History
DepositionMay 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.0Apr 19, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 19, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 19, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 19, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 19, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 19, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 19, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Mar 19, 2025Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details
Item: _chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag ..._chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: 50S ribosomal protein L33
1: 50S ribosomal protein L34
2: 50S ribosomal protein L35
3: 50S ribosomal protein L36
A: 23s ribosomal RNA
B: 5s ribosomal RNA
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
I: 50S ribosomal protein L13
J: 50S ribosomal protein L14
K: 50S ribosomal protein L15
L: 50S ribosomal protein L16
M: 50S ribosomal protein L17
N: 50S ribosomal protein L18
O: 50S ribosomal protein L19
P: 50S ribosomal protein L20
Q: 50S ribosomal protein L21
R: 50S ribosomal protein L22
S: 50S ribosomal protein L23
T: 50S ribosomal protein L24
U: 50S ribosomal protein L25
V: 50S ribosomal protein L27
W: 50S ribosomal protein L28
X: 50S ribosomal protein L29
Y: 50S ribosomal protein L30
Z: 50S ribosomal protein L32
a: 16s Ribosomal RNA
b: 30S ribosomal protein S2
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
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
u: 30S ribosomal protein S21
v: tRNA-met
w: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,169,99167
Polymers2,160,79553
Non-polymers9,19614
Water905
1


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

-
Components

+
50S ribosomal protein ... , 28 types, 28 molecules 0123CDEFGHIJKLMNOPQRSTUVWXYZ

#1: Protein 50S ribosomal protein L33


Mass: 6105.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: A0A7U4DFF9
#2: Protein/peptide 50S ribosomal protein L34


Mass: 5192.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: A0A1J6Y3G0
#3: Protein 50S ribosomal protein L35


Mass: 7424.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I693
#4: Protein/peptide 50S ribosomal protein L36


Mass: 4276.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA18
#7: Protein 50S ribosomal protein L2


Mass: 30346.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA36
#8: Protein 50S ribosomal protein L3


Mass: 22512.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA39
#9: Protein 50S ribosomal protein L4


Mass: 21583.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA38
#10: Protein 50S ribosomal protein L5


Mass: 20051.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA27
#11: Protein 50S ribosomal protein L6


Mass: 19126.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA24
#12: Protein 50S ribosomal protein L9


Mass: 15800.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IBC3
#13: Protein 50S ribosomal protein L13


Mass: 15981.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I9B0
#14: Protein 50S ribosomal protein L14


Mass: 13523.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: N8SHC6
#15: Protein 50S ribosomal protein L15


Mass: 15509.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA20
#16: Protein 50S ribosomal protein L16


Mass: 15498.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA32
#17: Protein 50S ribosomal protein L17


Mass: 14022.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA13
#18: Protein 50S ribosomal protein L18


Mass: 12443.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA23
#19: Protein 50S ribosomal protein L19


Mass: 13619.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IAS9
#20: Protein 50S ribosomal protein L20


Mass: 13468.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: V5VGC9
#21: Protein 50S ribosomal protein L21


Mass: 11496.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I6V9
#22: Protein 50S ribosomal protein L22


Mass: 11828.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: A0A009I821
#23: Protein 50S ribosomal protein L23


Mass: 11607.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA37
#24: Protein 50S ribosomal protein L24


Mass: 11187.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA28
#25: Protein 50S ribosomal protein L25


Mass: 10942.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I7B6
#26: Protein 50S ribosomal protein L27


Mass: 9072.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I6V8
#27: Protein 50S ribosomal protein L28


Mass: 9125.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: N9N7A0
#28: Protein 50S ribosomal protein L29


Mass: 7449.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA31
#29: Protein 50S ribosomal protein L30


Mass: 6654.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA21
#30: Protein 50S ribosomal protein L32


Mass: 7096.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I7A4

-
RNA chain , 5 types, 5 molecules ABavw

#5: RNA chain 23s ribosomal RNA


Mass: 945315.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria)
#6: RNA chain 5s ribosomal RNA


Mass: 36996.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: GenBank: 1577037162
#31: RNA chain 16s Ribosomal RNA


Mass: 500297.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: GenBank: 1211343212
#52: RNA chain tRNA-met


Mass: 24760.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: GenBank: 1723902888
#53: RNA chain mRNA


Mass: 935.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria)

-
30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu

#32: Protein 30S ribosomal protein S2


Mass: 27680.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: V5VBC2
#33: Protein 30S ribosomal protein S3


Mass: 27972.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: V5V9N0
#34: Protein 30S ribosomal protein S4


Mass: 23311.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA15
#35: Protein 30S ribosomal protein S5


Mass: 17181.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA22
#36: Protein 30S ribosomal protein S6


Mass: 14986.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IBC1
#37: Protein 30S ribosomal protein S7


Mass: 17733.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I7S0
#38: Protein 30S ribosomal protein S8


Mass: 14250.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA25
#39: Protein 30S ribosomal protein S9


Mass: 14287.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: V5VBA5
#40: Protein 30S ribosomal protein S10


Mass: 11718.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: A0A009L7S8
#41: Protein 30S ribosomal protein S11


Mass: 13558.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: A0A4R0F9S8
#42: Protein 30S ribosomal protein S12


Mass: 13797.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I7R9
#43: Protein 30S ribosomal protein S13


Mass: 13295.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA17
#44: Protein 30S ribosomal protein S14


Mass: 11438.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA26
#45: Protein 30S ribosomal protein S15


Mass: 10145.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I3U0
#46: Protein 30S ribosomal protein S16


Mass: 11223.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: A0A1V3DIZ9
#47: Protein 30S ribosomal protein S17


Mass: 9543.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA30
#48: Protein 30S ribosomal protein S18


Mass: 9009.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: A0A372MP10
#49: Protein 30S ribosomal protein S19


Mass: 10206.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7IA35
#50: Protein 30S ribosomal protein S20


Mass: 9723.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: B7I5N9
#51: Protein 30S ribosomal protein S21


Mass: 8474.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / References: UniProt: A0A0Q7FMS9

-
Non-polymers , 4 types, 19 molecules

#54: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#55: Chemical
ChemComp-OIY / Streptothricin D


Mass: 758.867 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C31H58N12O10 / Feature type: SUBJECT OF INVESTIGATION
#56: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#57: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
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: SD-70S Ribosome Complex with P-site tRNA / Type: RIBOSOME / Entity ID: #1-#53 / Source: NATURAL
Source (natural)Organism: Acinetobacter baumannii AB0057 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 36 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.19_4080: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144189 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004150889
ELECTRON MICROSCOPYf_angle_d0.621225738
ELECTRON MICROSCOPYf_dihedral_angle_d14.57859467
ELECTRON MICROSCOPYf_chiral_restr0.03928914
ELECTRON MICROSCOPYf_plane_restr0.00612064

+
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