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- PDB-6spd: Pseudomonas aeruginosa 50s ribosome from a clinical isolate -

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Basic information

Entry
Database: PDB / ID: 6spd
TitlePseudomonas aeruginosa 50s ribosome from a clinical isolate
Components
  • (50S ribosomal protein ...) x 29
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Ribosomal protein uL29
KeywordsRIBOSOME / Pseudomonas aeruginosa
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L28/L24 / Ribosomal protein L25, C-terminal domain / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L24e; Chain: T; / Ribosomal protein L30/L7 / Ribosomal protein L16/L10 / Ribosomal Protein L14 ...Ribosomal protein L28/L24 / Ribosomal protein L25, C-terminal domain / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L24e; Chain: T; / Ribosomal protein L30/L7 / Ribosomal protein L16/L10 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal protein L6 / Ribosomal protein L22/L17 / Ribosomal Protein L30; Chain: A, / Ribosomal Protein L22; Chain A / Outer Surface Protein A; domain 3 / Aldehyde Oxidoreductase; domain 3 / Rubrerythrin, domain 2 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / RRM (RNA recognition motif) domain / Single Sheet / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 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 / Beta Complex / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / 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 L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL20 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL36
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsHalfon, Y. / Jimenez-Fernande, A. / La Ros, R. / Espinos, R. / Krogh Johansen, H. / Matzov, D. / Eyal, Z. / Bashan, A. / Zimmerman, E. / Belousoff, M. ...Halfon, Y. / Jimenez-Fernande, A. / La Ros, R. / Espinos, R. / Krogh Johansen, H. / Matzov, D. / Eyal, Z. / Bashan, A. / Zimmerman, E. / Belousoff, M. / Molin, S. / Yonath, A.
Funding support Denmark, 4items
OrganizationGrant numberCountry
Danish Council for Independent ResearchDFF-4181-00115 Denmark
Novo Nordisk Foundation Denmark
European Research Council322581
European UnioniNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Structure of ribosomes from an aminoglycoside-resistant clinical isolate.
Authors: Yehuda Halfon / Alicia Jimenez-Fernandez / Ruggero La Rosa / Rocio Espinosa Portero / Helle Krogh Johansen / Donna Matzov / Zohar Eyal / Anat Bashan / Ella Zimmerman / Matthew Belousoff / ...Authors: Yehuda Halfon / Alicia Jimenez-Fernandez / Ruggero La Rosa / Rocio Espinosa Portero / Helle Krogh Johansen / Donna Matzov / Zohar Eyal / Anat Bashan / Ella Zimmerman / Matthew Belousoff / Søren Molin / Ada Yonath /
Abstract: Resistance to antibiotics has become a major threat to modern medicine. The ribosome plays a fundamental role in cell vitality by the translation of the genetic code into proteins; hence, it is a ...Resistance to antibiotics has become a major threat to modern medicine. The ribosome plays a fundamental role in cell vitality by the translation of the genetic code into proteins; hence, it is a major target for clinically useful antibiotics. We report here the cryo-electron microscopy structures of the ribosome of a pathogenic aminoglycoside (AG)-resistant strain, as well as of a nonresistance strain isolated from a cystic fibrosis patient. The structural studies disclosed defective ribosome complex formation due to a conformational change of rRNA helix H69, an essential intersubunit bridge, and a secondary binding site of the AGs. In addition, a stable conformation of nucleotides A1486 and A1487, pointing into helix h44, is created compared to a non-AG-bound ribosome. We suggest that altering the conformations of ribosomal protein uL6 and rRNA helix H69, which interact with initiation-factor IF2, interferes with proper protein synthesis initiation.
History
DepositionSep 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2019Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2019Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2019Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / struct_ref / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _struct_ref.db_name / _struct_ref_seq_dif.pdbx_seq_db_name
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary
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Structure visualization

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Assembly

Deposited unit
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 L11
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: Ribosomal protein uL29
Z: 50S ribosomal protein L30
1: 50S ribosomal protein L31
2: 50S ribosomal protein L32
3: 50S ribosomal protein L33
4: 50S ribosomal protein L34
5: 50S ribosomal protein L35
6: 50S ribosomal protein L36


Theoretical massNumber of molelcules
Total (without water)1,354,51432
Polymers1,354,51432
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area152010 Å2
ΔGint-1294 kcal/mol
Surface area512490 Å2
MethodPISA

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 23S ribosomal RNA


Mass: 935951.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: GenBank: 470469287
#2: RNA chain 5S ribosomal RNA


Mass: 37335.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: GenBank: 1384417243

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50S ribosomal protein ... , 29 types, 29 molecules CDEFGHIJKLMNOPQRSTUVWXZ123456

#3: Protein 50S ribosomal protein L2


Mass: 29438.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A241XHA2
#4: Protein 50S ribosomal protein L3


Mass: 22179.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A072ZBZ2
#5: Protein 50S ribosomal protein L4


Mass: 21542.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A241XH26
#6: Protein 50S ribosomal protein L5


Mass: 19951.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A072ZMU2
#7: Protein 50S ribosomal protein L6


Mass: 18610.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A2V3F3S9
#8: Protein 50S ribosomal protein L9


Mass: 15420.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A072ZKF0
#9: Protein 50S ribosomal protein L11


Mass: 14623.716 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A2V3GYK0
#10: Protein 50S ribosomal protein L13


Mass: 15927.382 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A071L356
#11: Protein 50S ribosomal protein L14


Mass: 13223.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: E2RXT6
#12: Protein 50S ribosomal protein L15


Mass: 15073.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A2V3D5Z8
#13: Protein 50S ribosomal protein L16


Mass: 15203.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A069QEB6
#14: Protein 50S ribosomal protein L17


Mass: 13495.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A072ZCA1
#15: Protein 50S ribosomal protein L18


Mass: 12556.470 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: E2RXU0
#16: Protein 50S ribosomal protein L19


Mass: 12708.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A263PZC6
#17: Protein 50S ribosomal protein L20


Mass: 13266.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A069QEE3
#18: Protein 50S ribosomal protein L21


Mass: 11678.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A072ZDZ0
#19: Protein 50S ribosomal protein L22


Mass: 11804.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A1C7BCP0
#20: Protein 50S ribosomal protein L23


Mass: 10231.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: E2RXT1
#21: Protein 50S ribosomal protein L24


Mass: 11423.413 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: E2RXT7
#22: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 20346.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A072ZBM5
#23: Protein 50S ribosomal protein L27


Mass: 8124.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A071LFT4
#24: Protein 50S ribosomal protein L28


Mass: 8956.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A072ZIQ9
#26: Protein 50S ribosomal protein L30


Mass: 6358.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: E2RXU1
#27: Protein/peptide 50S ribosomal protein L31


Mass: 3368.921 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A072ZJG4
#28: Protein 50S ribosomal protein L32


Mass: 6043.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A069QB25
#29: Protein/peptide 50S ribosomal protein L33


Mass: 5928.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A140SG33
#30: Protein/peptide 50S ribosomal protein L34


Mass: 5226.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A087L9L7
#31: Protein 50S ribosomal protein L35


Mass: 7256.800 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A069QC44
#32: Protein/peptide 50S ribosomal protein L36


Mass: 4447.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: E2RXU2

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Protein , 1 types, 1 molecules Y

#25: Protein Ribosomal protein uL29


Mass: 6807.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria)

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Details

Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Pseudomonas aeruginosa 70s ribosome from a clinical isolate
Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pseudomonas aeruginos (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128795 / Symmetry type: POINT

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