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- PDB-6hma: Improved model derived from cryo-EM map of Staphylococcus aureus ... -

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Basic information

Entry
Database: PDB / ID: 6hma
TitleImproved model derived from cryo-EM map of Staphylococcus aureus large ribosomal subunit
Components
  • (50S ribosomal protein ...) x 27
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / ribosomal RNA / pathogen / ribosomal protein / cryo-EM
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 / RNA binding / cytoplasm
Similarity search - Function
: / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal Protein L25; Chain P / Ribosomal protein L30/L7 ...: / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal Protein L25; Chain P / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal protein L6 / Ribosomal protein L22/L17 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L30; Chain: A, / Ribosomal Protein L22; Chain A / Outer Surface Protein A; domain 3 / Aldehyde Oxidoreductase; domain 3 / Rubrerythrin, 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 / Nucleic acid-binding proteins / 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 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 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 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 / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL25 / 50S ribosomal protein L32 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL25 / 50S ribosomal protein L32 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL22 / 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 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL18
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsEyal, Z. / Cimicata, G. / Matzov, D. / Fox, T. / de Val, N. / Zimmerman, E. / Bashan, A. / Yonath, A.
Citation
Journal: mBio / Year: 2022
Title: Structural Studies Reveal the Role of Helix 68 in the Elongation Step of Protein Biosynthesis.
Authors: Giuseppe Cimicata / Gil Fridkin / Tanaya Bose / Zohar Eyal / Yehuda Halfon / Elinor Breiner-Goldstein / Tara Fox / Ella Zimmerman / Anat Bashan / Natalia de Val / Alexander Wlodawer / Ada Yonath /
Abstract: The ribosome, a multicomponent assembly consisting of RNA and proteins, is a pivotal macromolecular machine that translates the genetic code into proteins. The large ribosomal subunit rRNA helix 68 ...The ribosome, a multicomponent assembly consisting of RNA and proteins, is a pivotal macromolecular machine that translates the genetic code into proteins. The large ribosomal subunit rRNA helix 68 (H68) is a key element in the protein synthesis process, as it coordinates the coupled movements of the actors involved in translocation, including the tRNAs and L1 stalk. Examination of cryo-electron microscopy (cryo-EM) structures of ribosomes incubated for various time durations at physiological temperatures led to the identification of functionally relevant H68 movements. These movements assist the transition of the L1 stalk between its open and closed states. H68 spatial flexibility and its significance to the protein synthesis process were confirmed through its effective targeting with antisense PNA oligomers. Our results suggest that H68 is actively involved in ribosome movements that are central to the elongation process. The mechanism that regulates the translocation step in ribosomes during protein synthesis is not fully understood. In this work, cryo-EM techniques used to image ribosomes from Staphylococcus aureus after incubation at physiological temperature allowed the identification of a conformation of the helix 68 that has never been observed so far. We then propose a mechanism in which such helix, switching between two different conformations, actively coordinates the translocation step, shedding light on the dynamics of ribosomal components. In addition, the relevance of helix 68 to ribosome function and its potential as an antibiotic target was proved by inhibiting Staphylococcus aureus ribosomes activity using oligomers with sequence complementarity.
#1: Journal: Proc Natl Acad Sci U S A / Year: 2015
Title: Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus.
Authors: Zohar Eyal / Donna Matzov / Miri Krupkin / Itai Wekselman / Susanne Paukner / Ella Zimmerman / Haim Rozenberg / Anat Bashan / Ada Yonath /
Abstract: The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from ...The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus.
History
DepositionSep 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.0Nov 14, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 14, 2018Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 14, 2018Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 14, 2018Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 14, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 14, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 14, 2018Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 14, 2018Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 14, 2018Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 14, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 14, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
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Revision 1.0Nov 14, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Nov 13, 2024Group: 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 / pdbx_modification_feature
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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 L13
I: 50S ribosomal protein L14
J: 50S ribosomal protein L15
K: 50S ribosomal protein L16
L: 50S ribosomal protein L17
M: 50S ribosomal protein L18
N: 50S ribosomal protein L19
O: 50S ribosomal protein L20
P: 50S ribosomal protein L21
Q: 50S ribosomal protein L22
R: 50S ribosomal protein L23
S: 50S ribosomal protein L24
T: 50S ribosomal protein L25
U: 50S ribosomal protein L27
V: 50S ribosomal protein L28
W: 50S ribosomal protein L29
X: 50S ribosomal protein L30
Z: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,328,827266
Polymers1,323,06729
Non-polymers5,760237
Water00
1


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

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 23S ribosomal RNA


Mass: 946738.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1418434134
#2: RNA chain 5S ribosomal RNA


Mass: 36974.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1434110260

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50S ribosomal protein ... , 27 types, 27 molecules CDEFGHIJKLMNOPQRSTUVWXZ1234

#3: Protein 50S ribosomal protein L2


Mass: 29827.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YYP9, UniProt: P60430*PLUS
#4: Protein 50S ribosomal protein L3


Mass: 23199.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YYP6, UniProt: Q2FW06*PLUS
#5: Protein 50S ribosomal protein L4


Mass: 22364.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YYP7, UniProt: Q2FW07*PLUS
#6: Protein 50S ribosomal protein L5


Mass: 17651.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A2S6D0C0, UniProt: Q2FW18*PLUS
#7: Protein 50S ribosomal protein L6


Mass: 19501.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YYL2, UniProt: Q2FW21*PLUS
#8: Protein 50S ribosomal protein L13


Mass: 16359.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YYM8, UniProt: Q2FW38*PLUS
#9: Protein 50S ribosomal protein L14


Mass: 13157.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YYK7, UniProt: Q2FW16*PLUS
#10: Protein 50S ribosomal protein L15


Mass: 15628.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YYL6, UniProt: P0A0F8*PLUS
#11: Protein 50S ribosomal protein L16


Mass: 15599.435 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YYQ3, UniProt: Q2FW13*PLUS
#12: Protein 50S ribosomal protein L17


Mass: 13583.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YYM3, UniProt: Q2FW33*PLUS
#13: Protein 50S ribosomal protein L18


Mass: 13124.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRE0, UniProt: Q2FW22*PLUS
#14: Protein 50S ribosomal protein L19


Mass: 13392.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YXM4, UniProt: Q2FZ42*PLUS
#15: Protein 50S ribosomal protein L20


Mass: 13459.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YTB1, UniProt: Q2FXQ1*PLUS
#16: Protein 50S ribosomal protein L21


Mass: 11354.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YT83, UniProt: Q2FXS8*PLUS
#17: Protein 50S ribosomal protein L22


Mass: 12328.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YYQ1, UniProt: Q2FW11*PLUS
#18: Protein 50S ribosomal protein L23


Mass: 10380.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YYP8, UniProt: Q2FW08*PLUS
#19: Protein 50S ribosomal protein L24


Mass: 11316.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YYK8, UniProt: Q2FW17*PLUS
#20: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 10462.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A133Q8Z9, UniProt: Q2FJE0*PLUS
#21: Protein 50S ribosomal protein L27


Mass: 8595.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YT85, UniProt: Q2FXT0*PLUS
#22: Protein/peptide 50S ribosomal protein L28


Mass: 5499.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YXJ2, UniProt: Q2FZ60*PLUS
#23: Protein 50S ribosomal protein L29


Mass: 7845.942 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YYN0, UniProt: Q2FW14*PLUS
#24: Protein 50S ribosomal protein L30


Mass: 6434.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YYL5, UniProt: P0A0G2*PLUS
#25: Protein/peptide 50S ribosomal protein L32


Mass: 5569.565 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A1Q8DAT0, UniProt: Q2FZF1*PLUS
#26: Protein/peptide 50S ribosomal protein L33


Mass: 5684.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077V2P0, UniProt: Q2FYU6*PLUS
#27: Protein/peptide 50S ribosomal protein L34


Mass: 5252.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YZB6, UniProt: Q2FUQ0*PLUS
#28: Protein 50S ribosomal protein L35


Mass: 7461.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YTB0, UniProt: Q2FXQ0*PLUS
#29: Protein/peptide 50S ribosomal protein L36


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UGV8, UniProt: Q2FW29*PLUS

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Non-polymers , 1 types, 237 molecules

#30: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 237 / Source method: obtained synthetically / Formula: Mg

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Details

Has protein modificationY

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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: Staphylococcus aureus large ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#29 / Source: NATURAL
Source (natural)Organism: Staphylococcus aureus (bacteria)
Buffer solutionpH: 7.6
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 211046 / Symmetry type: POINT

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