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- PDB-8fn2: The structure of a 50S ribosomal subunit in the Lyme disease path... -

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Basic information

Entry
Database: PDB / ID: 8fn2
TitleThe structure of a 50S ribosomal subunit in the Lyme disease pathogen Borreliella burgdorferi
Components
  • (50S ribosomal protein ...) x 32
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / hibernating ribosome / bacterial / pathogen / 50S / translation
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation ...large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L31 type B / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / : / Ribosomal protein L11, bacterial-type ...Ribosomal protein L31 type B / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / : / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L10-like domain superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 signature. / 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 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, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / 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 L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL9 / Uncharacterized protein / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL31B ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL9 / Uncharacterized protein / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL33 / 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 uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / 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 uL2 / Large ribosomal subunit protein uL22
Similarity search - Component
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSharma, M.R. / Manjari, S.R. / Agrawal, E.K. / Keshavan, P. / Koripella, R.K. / Majumdar, S. / Marcinkiewicz, A.L. / Lin, Y.P. / Agrawal, R.K. / Banavali, N.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM61576 United States
CitationJournal: Nat Commun / Year: 2023
Title: The structure of a hibernating ribosome in a Lyme disease pathogen.
Authors: Manjuli R Sharma / Swati R Manjari / Ekansh K Agrawal / Pooja Keshavan / Ravi K Koripella / Soneya Majumdar / Ashley L Marcinkiewicz / Yi-Pin Lin / Rajendra K Agrawal / Nilesh K Banavali /
Abstract: The spirochete bacterial pathogen Borrelia (Borreliella) burgdorferi (Bbu) affects more than 10% of the world population and causes Lyme disease in about half a million people in the US annually. ...The spirochete bacterial pathogen Borrelia (Borreliella) burgdorferi (Bbu) affects more than 10% of the world population and causes Lyme disease in about half a million people in the US annually. Therapy for Lyme disease includes antibiotics that target the Bbu ribosome. Here we present the structure of the Bbu 70S ribosome obtained by single particle cryo-electron microscopy at 2.9 Å resolution, revealing a bound hibernation promotion factor protein and two genetically non-annotated ribosomal proteins bS22 and bL38. The ribosomal protein uL30 in Bbu has an N-terminal α-helical extension, partly resembling the mycobacterial bL37 protein, suggesting evolution of bL37 and a shorter uL30 from a longer uL30 protein. Its analogy to proteins uL30m and mL63 in mammalian mitochondrial ribosomes also suggests a plausible evolutionary pathway for expansion of protein content in mammalian mitochondrial ribosomes. Computational binding free energy predictions for antibiotics reflect subtle distinctions in antibiotic-binding sites in the Bbu ribosome. Discovery of these features in the Bbu ribosome may enable better ribosome-targeted antibiotic design for Lyme disease treatment.
History
DepositionDec 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 23S ribosomal RNA
B: 5S ribosomal RNA
D: 50S ribosomal protein L2
E: 50S ribosomal protein L3
F: 50S ribosomal protein L4
G: 50S ribosomal protein L5
H: 50S ribosomal protein L6
I: 50S ribosomal protein L9
J: 50S ribosomal protein L10
K: 50S ribosomal protein L11
L: 50S ribosomal protein L13
M: 50S ribosomal protein L14
N: 50S ribosomal protein L15
O: 50S ribosomal protein L16
P: 50S ribosomal protein L17
Q: 50S ribosomal protein L18
R: 50S ribosomal protein L19
S: 50S ribosomal protein L20
T: 50S ribosomal protein L21
U: 50S ribosomal protein L22
V: 50S ribosomal protein L23
W: 50S ribosomal protein L24
X: 50S ribosomal protein L25
Y: 50S ribosomal protein L27
Z: 50S ribosomal protein L28
a: 50S ribosomal protein L29
b: 50S ribosomal protein uL30
c: 50S ribosomal protein L31 type B
d: 50S ribosomal protein L32
e: 50S ribosomal protein L33
f: 50S ribosomal protein L34
g: 50S ribosomal protein L35
h: 50S ribosomal protein L36
i: 50S ribosomal protein bL38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,420,66936
Polymers1,420,53834
Non-polymers1312
Water0
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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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 23S ribosomal RNA /


Mass: 948648.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: GenBank: AE000783
#2: RNA chain 5S ribosomal RNA /


Mass: 36188.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: GenBank: AE000783

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50S ribosomal protein ... , 32 types, 32 molecules DEFGHIJKLMNOPQRSTUVWXYZabcdefghi

#3: Protein 50S ribosomal protein L2 /


Mass: 30655.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: P94270
#4: Protein 50S ribosomal protein L3 /


Mass: 22265.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: P94267
#5: Protein 50S ribosomal protein L4 /


Mass: 23535.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: P94268
#6: Protein 50S ribosomal protein L5 /


Mass: 20445.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51443
#7: Protein 50S ribosomal protein L6 /


Mass: 19972.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51446
#8: Protein 50S ribosomal protein L9 /


Mass: 17121.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51139
#9: Protein 50S ribosomal protein L10 /


Mass: 18086.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51352
#10: Protein 50S ribosomal protein L11 /


Mass: 14731.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51354
#11: Protein 50S ribosomal protein L13 /


Mass: 16594.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51314
#12: Protein 50S ribosomal protein L14 /


Mass: 13465.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51441
#13: Protein 50S ribosomal protein L15 /


Mass: 16072.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51450
#14: Protein 50S ribosomal protein L16 /


Mass: 15598.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51438
#15: Protein 50S ribosomal protein L17 /


Mass: 14308.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51456
#16: Protein 50S ribosomal protein L18 /


Mass: 13753.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51447
#17: Protein 50S ribosomal protein L19 /


Mass: 13544.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51642
#18: Protein 50S ribosomal protein L20 /


Mass: 13415.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51206
#19: Protein 50S ribosomal protein L21 /


Mass: 12204.228 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51719
#20: Protein 50S ribosomal protein L22 /


Mass: 13150.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: P94272
#21: Protein 50S ribosomal protein L23 /


Mass: 11164.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: P94269
#22: Protein 50S ribosomal protein L24 /


Mass: 11467.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51442
#23: Protein 50S ribosomal protein L25 / / General stress protein CTC


Mass: 20347.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51727
#24: Protein 50S ribosomal protein L27 /


Mass: 8104.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51721
#25: Protein 50S ribosomal protein L28 /


Mass: 10069.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51325
#26: Protein 50S ribosomal protein L29 /


Mass: 7915.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51439
#27: Protein 50S ribosomal protein uL30 /


Mass: 11661.239 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria)
#28: Protein 50S ribosomal protein L31 type B / Ribosome


Mass: 9318.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51247
#29: Protein 50S ribosomal protein L32 /


Mass: 6960.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51646
#30: Protein 50S ribosomal protein L33 /


Mass: 6100.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51357
#31: Protein/peptide 50S ribosomal protein L34 /


Mass: 6059.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: P29220
#32: Protein 50S ribosomal protein L35 /


Mass: 7840.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51207
#33: Protein/peptide 50S ribosomal protein L36 /


Mass: 4418.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51452
#34: Protein/peptide 50S ribosomal protein bL38 /


Mass: 5351.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51184

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Non-polymers , 1 types, 2 molecules

#35: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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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: 50S ribosomal subunitProkaryotic large ribosomal subunit
Type: RIBOSOME / Entity ID: #1-#34 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Borreliella burgdorferi (Lyme disease spirochete) / Strain: B31
Buffer solutionpH: 7.5 / Details: HMA-10 buffer
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
230 mMAmmonium chlorideNH4Cl1
310 mMMagnesium chlorideMgCl21
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 820 nm / Cs: 0.001 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 67.527 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4661
EM imaging opticsEnergyfilter slit width: 30 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 50 / Used frames/image: 1-50

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Processing

EM software
IDNameVersionCategory
1cryoSPARC2.15particle selection
2Leginonimage acquisition
4cryoSPARC2.15CTF correction
7UCSF Chimeramodel fitting
10cryoSPARC2.15final Euler assignment
11cryoSPARC2.15classification
12cryoSPARC2.153D reconstruction
13PHENIX1.18model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 541319
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12449 / Symmetry type: POINT
Atomic model buildingB value: 2 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient

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