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- EMDB-29304: The structure of a 50S ribosomal subunit in the Lyme disease path... -

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Basic information

Entry
Database: EMDB / ID: EMD-29304
TitleThe structure of a 50S ribosomal subunit in the Lyme disease pathogen Borreliella burgdorferi
Map dataBorreliella burgdorferi 50S ribosomal subunit
Sample
  • Complex: 50S ribosomal subunit
    • RNA: x 2 types
    • Protein or peptide: x 32 types
  • Ligand: x 1 types
Keywordshibernating ribosome / bacterial / pathogen / 50S / translation / RIBOSOME
Function / homology
Function and homology information


ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit ...ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L31 type B / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein L1, bacterial-type / Ribosomal protein L25, long-form / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal ...Ribosomal protein L31 type B / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein L1, bacterial-type / Ribosomal protein L25, long-form / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / : / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L16 signature 1. / Ribosomal protein L10P / Ribosomal protein L10 / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / 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 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, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / 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 L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L20 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L27, conserved site
Similarity search - Domain/homology
Large ribosomal subunit protein bL9 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Uncharacterized protein / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL31B / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 ...Large ribosomal subunit protein bL9 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Uncharacterized protein / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL31B / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL33 / Ribosomal subunit interface protein / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein bS16 / 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 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3
Similarity search - Component
Biological speciesBorreliella burgdorferi (Lyme disease spirochete) / Borreliella burgdorferi B31 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSharma MR / Manjari SR / Agrawal EK / Keshavan P / Koripella RK / Majumdar S / Marcinkiewicz AL / Lin YP / Agrawal RK / Banavali NK
Funding support United States, 1 items
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, 2022-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29304.png

Downloads & links

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Map

FileDownload / File: emd_29304.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBorreliella burgdorferi 50S ribosomal subunit
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 450 pix.
= 493.245 Å		1.1 Å/pix.
x 450 pix.
= 493.245 Å		1.1 Å/pix.
x 450 pix.
= 493.245 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0961 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.30854878 - 0.78340226
Average (Standard dev.)-0.0021739956 (±0.038717087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 493.245 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29304_msk_1.map
Projections & Slices
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Half map: Borreliella burgdorferi 50S ribosomal subunit half map B

Fileemd_29304_half_map_1.map
AnnotationBorreliella burgdorferi 50S ribosomal subunit half map B
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Half map: Borreliella burgdorferi 50S ribosomal subunit half map A

Fileemd_29304_half_map_2.map
AnnotationBorreliella burgdorferi 50S ribosomal subunit half map A
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Sample components

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Entire : 50S ribosomal subunit

EntireName: 50S ribosomal subunit
Components
  • Complex: 50S ribosomal subunit
    • RNA: 23S ribosomal RNA
    • RNA: 5S ribosomal RNA
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L9
    • Protein or peptide: 50S ribosomal protein L10
    • Protein or peptide: 50S ribosomal protein L11
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L16
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L25
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein uL30
    • Protein or peptide: 50S ribosomal protein L31 type B
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L36
    • Protein or peptide: 50S ribosomal protein bL38
  • Ligand: ZINC ION

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Supramolecule #1: 50S ribosomal subunit

SupramoleculeName: 50S ribosomal subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#34
Source (natural)Organism: Borreliella burgdorferi (Lyme disease spirochete) / Strain: B31

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Macromolecule #1: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 948.648188 KDa
SequenceString: UGGUCAAAGU AAUAAGAGUC UAUGGUGAAU GCCUAGGAGC UUUAAGGCGA AGAAGGUCGU GGUAAGCUGC GAAAAGCUUG GGGGAGAAG CAAACAUUUA UUGAUCCCAA GAUUACCGAA UGGAGUAAUC CAGCUAGCAA GAUGCUAGCU AUCUAUUAUU U AAAUAAUA ...String:
UGGUCAAAGU AAUAAGAGUC UAUGGUGAAU GCCUAGGAGC UUUAAGGCGA AGAAGGUCGU GGUAAGCUGC GAAAAGCUUG GGGGAGAAG CAAACAUUUA UUGAUCCCAA GAUUACCGAA UGGAGUAAUC CAGCUAGCAA GAUGCUAGCU AUCUAUUAUU U AAAUAAUA GAGGCGAUAC CAGGGGAAGU GAACCAUCUA AGUACCCUGA GGAAAAGAAA UCAAAGAGAU UCCCUUAGUA GU GGCGAGC GAAAAGGGAG UAGCCCAAAC UUUAAAUGUG UCAAGCUGCA GAGCGUUGCA UUUAUGGGGU UGUAGGACGU UUA GGCUUA GUCUGUAAUA AGCAAAAAAG UUACAAAAUA UUUAUAUAGA AGAAUAAUCU GGAAAGUUUA ACCAAAGAAG GUGA UAGUC CUGUAAUUUA AAUGUAAAUA UCUUUUUAAA AUGUUCCUGA GUAGGACGAG GCACGAGAAA CCUUGUUUGA AGCUG GGGA GACCACUCUC CAAGGCUAAA UACUAGAAAG CUACCGAUAG AGAAGAGUAC CGUGAGGGAA AGGUGAAAAG AACCCC GGG AGGGGAGUGA AAUAGAACUG AAACCGUAGA CUUACAAGCA GUCAAAGCCG UAAUUUAUUG CGGUGAUGGC GUGCCUU UU GCAUAAUGAA CCUGCGAGUU AUCAUGUCUA GCAAGAUUAA AGCAUAGAAG UGCUGGAGUC GAAGCGAAAG CGAGUCUU A AAAGGGCGAU UUAGUUAGAU GUGGUAGACC CGAAGCCGAG UGAUCUAUUU AUGGCCAGGC UGAAGCUUGG GUAAAACCA AGUGGAGGGC CGAACUCUAG UCUGUUUAAA AAGGCAGGGA UGAGCUGUGA AUAGGAGUGA AAGGCUAAAC AAACUCGGAG AUAGCUGGU UCUCCCCGAA AUGGAUUUAA GUUCAGCCUU AUUUUAGUUU AAUAGAGGUA GAGCACUAAU UGAGCUAGGG C CUGUCAAA GGGUACCAAA CUCAGUUAAA CUCCGAAUGC UAUUAAAUGA UGAAUAGGAG UGAGACUAUG GGCGAUAAGG UU CAUAGUC GAGAGGGAAA CAACCCAGAC CAACAGCUAA GGUCUCAAAA AUGUGUUAAG UGGAAAAGGA GGUUUAGGUA CGU AAACAG CCAGGAGGUU GGCUUAGAAG CAGCCAUACC UUUAAAGAGU GCGUAAUAGC UCACUGGUCG AGUACUUAAG CGCC GAUAA UGUAACGGGG CUAAACACAU UACCGAAGCU UUGGAUCUUA ACGAAAGUUA AGAUGGUAGG GGAGCGUUCU GUAAG CCAG AGAAGUUAAG CUGGAAAGUU UGAUGGAGGU AUCAGAAGUG AGAAUGCAGG UAUGAGUAAC GAAAAAAUGG GUGAGA UUC CCAUUCGCCG AAAACCUAAG GUUUCCUGGG UAAAGGUCGU CUUCCCAGGG UUAGUCGGCC CCUAAGGCAA AGCUGAA AA GUGUAGUCGA UGGGAAACGG GUUAAUAUUC CCGUACCUCU UAUAGUUUCG AUGGAGUGAC GCAUGAGGUU AACUACUG C UAGGCGAUGG UUGUCCUAGU UUAAGCAUUA AGGCGAUGAU CUUAAUAGGA AAAUCCGUUA AGAGAGCUAA GAUGUGAUG AUGAGUGCUA UUUAGGUAGC AUGAAAUGUA GGUAGUCAAG GUGCCAAGAA AUAGCUUCUA AGGUUAGGCU AUAAGGGACC GUACCGCAA ACCGACACAG GUAGGUGGGA UGAAAAUUCU AAGGCGCGCG AGAGAAUCCA CGUUAAGGAA CUCUGCAAAA U ACGUACGU AACUUCGGGA UAAGUACGAC CUAAGCAAUU AGGUAGCAUA AAAAUGGUCC AAACGACUGU UUACCAAAAA CA CAGGUCU CUGCAAAUCU GUAAAGAGAA GUAUAGGGAC UGACACCUGC CCGGUGCUGG AAGGUUAAGA GGAGAUGUUA GUU UAUGCG AAGCAUUGAA UUUAAGCCCC AGUAAACGGC GGCCGUAACU AUAACGGUCC UAAGGUAGCG AAAUUCCUUG UCGG GUAAG UUCCGACCCG CACGAAUGGU GUAACGAUUU GGACGCUGUC UCAACGUGGA GCUCGGUGAA AUUGAAGUAU CGGUG AAGA UGCCGAUUAC UUGUGGUUAG ACGGAAAGAC CCCGUGAACC UUUACUAUAG CUUGGUAUUG AGAUUUGAUU AAAUAU GUG UAGGAUAGGU GGGAGACUUU GAAGCUAUCU CGUCAGGGGU AGUGGAGUCA AUCUUGAAAU ACCACCCUUG UUUAAUU AG GUUUCUAACU UAUAGAAAUA UGAGGAGAGU GCCAGGUGGG UAGUUUGACU GGGGCGGUCG CCUCCUAAAG AGUAACGG A GGUGCGCAAA GGUUACCUUA GAGUGGUUGG AAAUCACUCU GUAAGUGUAA AGGCAUAAGG UAGCUUAACU GUAAGACUG ACAAGUCGAA CAGAUACGAA AGUAGGUCUU AGUGAUCUGG CGGUGGCAAG UGGAAGCGCC GUCACUUAAC GAAUAAAAGG UACUCCGGG GAUAACAGGC UUAUCCUUCC CAAGAGUUCA CAUCGACGGA AGGGUUUGGC ACCUCGAUGU CGGCUCAUCG C AUCCUAGG GCUGGAGCAG GUCCUAAGGG UAUGGCUGUU CGCCAUUUAA AGCGGUACGC GAGCUGGGUU CAGAACGUCG UG AGACAGU UUGGUCCCUA UCUGCCACAA GCGUUGGAUA UUUGAGAGGA GCUAUCUUUA GUACGAGAGG ACCGAGAUGG ACG AACCUC UAGUGUGCCA GUUAUCCUGC CAAGGGUAAG UGCUGGGUAG CUACGUUCGG AAAGGAUAAC CGCUGAAAGC AUCU AAGUG GGAAGCCUUC CUCAAGAUGA GAUAUCCUUU AAGGGUCCUG GAAGAAUACC AGGUUGAUAG GUUAGAAGUG UAAGU AUAG CAAUAUAUUA AGCUGACUAA UACUAAUUAC CCGUAUCUUU GGCCA

GENBANK: GENBANK: AE000783.1

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Macromolecule #2: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 36.188477 KDa
SequenceString:
CCCUGGUGGU UAAAGAAAAG AGGAAACACC UGUUAUCAUU CCGAACACAG AAGUUAAGCU CUUAUUCGCU GAUGGUACUG CGAGUUCGC GGGAGAGUAG GUUAUUGCCA GGG

GENBANK: GENBANK: AE000783.1

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Macromolecule #3: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 30.65557 KDa
SequenceString: MGIKTYKPKT SSLRYKTTLS FDDLSKGNDP LKSLTKGKKF KSGRDSSGRI SIRRRGGGHK RKYRLIDFNR RDKFSIPARV ASIEYDPNR SANIALLVYK DGEKRYIISP KGIKVGDVLE SGPNAPIKIG NALPLENIPI GRTVHNIELN VGKGGQLIRS A GGYAMILA ...String:
MGIKTYKPKT SSLRYKTTLS FDDLSKGNDP LKSLTKGKKF KSGRDSSGRI SIRRRGGGHK RKYRLIDFNR RDKFSIPARV ASIEYDPNR SANIALLVYK DGEKRYIISP KGIKVGDVLE SGPNAPIKIG NALPLENIPI GRTVHNIELN VGKGGQLIRS A GGYAMILA SDGNYVTVKL SSGEMRLIFK KCIATIGEIG NEDYANISIG KAGKSRWLGR RPKVRGVAMN PVDHPHGGGE GK TSGGRHP VSPWGQPTKG YKTRKKKRYS DKFIIKRRNK

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #4: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 22.265965 KDa
SequenceString: MLGLIGKKVG MTQIFQKNGI VVPVTVIEFQ PNYIIGKKTV DRDGYSALIA GSVDLKSSKV SKPIKGQYKS LKDIEPKRYV IELKGLDGY DAGDEIKVDV FKSVKYVDVT GTTKGKGFQG AMKRHNFSGG PSSHGSKFHR HLGGTGQATT PARTFKGTKM A GRMAGNQQ ...String:
MLGLIGKKVG MTQIFQKNGI VVPVTVIEFQ PNYIIGKKTV DRDGYSALIA GSVDLKSSKV SKPIKGQYKS LKDIEPKRYV IELKGLDGY DAGDEIKVDV FKSVKYVDVT GTTKGKGFQG AMKRHNFSGG PSSHGSKFHR HLGGTGQATT PARTFKGTKM A GRMAGNQQ TIQNLEVVLI DEEKRALLVK GAVPGAKGSF VVVKKSKK

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #5: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 23.535393 KDa
SequenceString: MERKVFSKDG KEIGTINLDD RVFNIEISHG SIYNAIKNEL SNLRVGTSST KTRSEVRGSS KKPWKQKGTG RARVGTKRNP VWIGGGIAL GPKPRDYSYR LPKKVKKLAF KSVLSLRAAD ENSFKVIENF NVESGKTKDL ALIIKNFASF NGKVVILLGN D DQMIKRAG ...String:
MERKVFSKDG KEIGTINLDD RVFNIEISHG SIYNAIKNEL SNLRVGTSST KTRSEVRGSS KKPWKQKGTG RARVGTKRNP VWIGGGIAL GPKPRDYSYR LPKKVKKLAF KSVLSLRAAD ENSFKVIENF NVESGKTKDL ALIIKNFASF NGKVVILLGN D DQMIKRAG KNIRDLKILS FDKLRVVDLF YAKNLIALES AVNKLNEFYI K

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #6: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 20.445861 KDa
SequenceString:
MNYVPELKKY YKDSVIKELV KEFEYKSIMQ VPKLEKIVIS VGVGEAVRNK KLLDSAVLEL AQITGQKAVK TKAKKAIAGF KIRQGQEIG AKVTLRGNAM YEFLYKLIHL ALPRVKDFRG INGDAFDGNG NYSFGITEQI IFSEIDYDKI ERISGLNITI V TTASNDKE SKALLLKFGM PFSN

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #7: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 19.972275 KDa
SequenceString:
MSRIGRLPIK IPDAVKVDVK DNLVIVEGIR GRLVQDIKDS INVKVENGSV IVDRVLNDKK AKAYHGLYRS LIFNMVKGVT EGFSKSLTI NGIGYRVEQQ GNSLFLSLGY STQFEYVIPD GISVKLDGNT KISVEGIDKF KVGQVAAEIR SLKKPEPYKG K GIKYDNEV IRRKVGKSGV KK

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #8: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 17.121998 KDa
SequenceString:
MKVILKEDFI NLGKEGDTVE VRDGFARNYL LPKGFAVFSN KHNIEIFNQK RRSILKKQEA KKQMANDLKS KLDLVKLEFF MKSNDSGKL FHSINSLNIA DELLKLGFDI ERKKIDIHHG TLKTFGTYDV TIKLYEGISS IIKVEIKKE

UniProtKB: Large ribosomal subunit protein bL9

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Macromolecule #9: 50S ribosomal protein L10

MacromoleculeName: 50S ribosomal protein L10 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 18.086355 KDa
SequenceString:
MSAKINAKKL EMFDLLKQFI DSKQNLFFLD YRGLNVAQLT ELRNKIEGEH GSLKVVKNNI MKMVLKEKNI NVVDSCLVGP TVVVTALEE ANVIAKIFYD FVKSSTLKVK GGFVLGEFYD EAKVQAYSKL PTKKESISLF ASVLKAPVSK LARTLKALAD V KN

UniProtKB: Large ribosomal subunit protein uL10

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Macromolecule #10: 50S ribosomal protein L11

MacromoleculeName: 50S ribosomal protein L11 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 14.731271 KDa
SequenceString:
KAISWIKLQV PAAQAAPGAK IGQALGPHGV SGPQFVKEFN ERTAKMDPGI VVPVIITVYS DKSFSFIVKT PPASILIKKA IGIESGSKK SNTDKVGTIS KEKLMEIARI KMSDLNAKSE SAAFKIIAGS ARSMGVEVEK

UniProtKB: Large ribosomal subunit protein uL11

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Macromolecule #11: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 16.594471 KDa
SequenceString:
NKITNNDTIW IKPKTVEKKW YVIDAADRIL GKVAVDVVKI LRGKHKAYYT PHQDLGDNVI IINASKVKLT GKKYQQKLYY RHSRYPGGL YSDTFRTLSE RKPCAPLEIA IKGMLPKGPL GRNLFRNLKV FSGSEHTLKA QNPIKL

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #12: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 13.465821 KDa
SequenceString:
MIQMQTYLTI ADNTGGKVAQ CIKVLGGSKR RYAKIGDIIT IVVKQAIPNS SVKKGDVYKA VIVRTSKEVR RKNGTYVRFD DNACVILDA NLSPRGKRVF GPVARELRDA NFMKVVSLAS EVI

UniProtKB: Large ribosomal subunit protein uL14

+
Macromolecule #13: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 16.072958 KDa
SequenceString:
MFNLLKPKGA SKRRKIVGRG PGSGLGKTSG RGQKGQKARN TSPRLGFEGG QTPLYRRLPR KGFSNSDYKL EYAIVNLGDI DKKFKDGQV VNYDTLLENK LIKKKNKKIK ILSNGKLTKK VSFEVSKISK SAESLVIKIG CTIQLV

UniProtKB: Large ribosomal subunit protein uL15

+
Macromolecule #14: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 15.598465 KDa
SequenceString:
MLSPKKVKYR KKQRGRLSGE AQKGNKISFG EYGLVSLETN FITARQIEAA RIAMTRKIKR GGRVWIRIFP DIPYTKKPAE TRMGKGKGG VDHWNAPVKL GTVMFEMSGV VEELAQEAMS LASSKLPVKT MFVVRRDLR

UniProtKB: Large ribosomal subunit protein uL16

+
Macromolecule #15: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 14.308107 KDa
SequenceString:
MKTKLGFNRL SRKSSHRRAL LKNMVISFFK HEKISSTKTK LFEVKRFAER LITRAKVDTV HNRRELSKFI HDKHILNKLF TKISPVFRQ RSGGYTRMIK LGKRYGDAAE MAILELVEKP LK

UniProtKB: Large ribosomal subunit protein bL17

+
Macromolecule #16: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 13.753123 KDa
SequenceString:
MKKIKEAEQR KLRRKKRIKD KIGRGVASRP RITVFKSNRY FYAQVIDDSK GHTIASISTI EKSLNLGKNI DDVKKLGEVL AKRLKEKNI NNLIFDRNGY KYHGLIASFA TSLREFGINI

UniProtKB: Large ribosomal subunit protein uL18

+
Macromolecule #17: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 13.544148 KDa
SequenceString:
MDLIRKIEAQ NKKNEAFVFN VGDTVRVVYK IIEGSNERLQ SFEGIVISFQ NKGIGKTFLI RKISSGIGVE KIFPVYSPII EKVEVLRRG KVRRAKLYYM RNRIGKAAMK IKERLTIK

UniProtKB: Large ribosomal subunit protein bL19

+
Macromolecule #18: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 13.415998 KDa
SequenceString:
ARAKNGTVHV ARRKRILKKT KGFWGTKKSN YKKAKDTLRK GMMYATRDRK VRKRDFRRLW ISRISAALSD TGVTYSRFIE GLLKSNIKI NRKILSNLAI EDVEAFKKIV LEIRR

UniProtKB: Large ribosomal subunit protein bL20

+
Macromolecule #19: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 12.204228 KDa
SequenceString:
MYALVEINGK QYKAIEGEFL KIDKISPVEK DKLEFNSVLL INKDGEVKIG KPYVVNSLIR CTYKEDKKDK KVVSYRYRRR KSSERKVGH RQTYSYILVD EIVF

UniProtKB: Large ribosomal subunit protein bL21

+
Macromolecule #20: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 13.150511 KDa
SequenceString:
LVNRRYTAKG KNLPSSPKKV RPIADNIRGE SYIKAIAVLC SMPNKGAKLL EKVVKSAASN AMYHNKNLSE DMIFVKTVMV DDGRRRKKI WPRARGRADR LVNRNCHIFV EVDEKK

UniProtKB: Large ribosomal subunit protein uL22

+
Macromolecule #21: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 11.164223 KDa
SequenceString:
MKAYDIIVSP MLTEKTNTQR ESINVYVFKV NKRANKKEVG AAIKELFNVT PVSCNLLNIK SKAKVVVSRK GYPIGKGKTS SWKKAYVYL KKEDKIDIF

UniProtKB: Large ribosomal subunit protein uL23

+
Macromolecule #22: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 11.467756 KDa
SequenceString:
MKTKLKIGDS VKILSGKDRG RIGKIASINR KKNKVIVESC NMVKKVIKAR TPQEKGRIID KEAAIDISNV MIFVKGTSSR LGIRFENNE KIRYLKKNGQ RI

UniProtKB: Large ribosomal subunit protein uL24

+
Macromolecule #23: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 20.347449 KDa
SequenceString:
ENSRVLSCQY RSSFGSSNAR RIRAKSEIPA VVYGQGKDVS HLRIKSSEFN KKFAKFTDNT VLILDDGKLE RCVFVKDAAE NIASKLIYH IDFYEVDRNV ELEKYVPIKL IGASIGVKEG GILTVLKEQV KVRSLPLDLP EFIELDLTPV NKGDSVLLKD L VLPSNVRL AENDENLEVV IIK

UniProtKB: Large ribosomal subunit protein bL25

+
Macromolecule #24: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 8.104452 KDa
SequenceString:
GSSKNGRDSI SKRLGVKRSG GQFVKAGEII VRQRGTKFHK GKNVGLGRDY TIFALSSGKV EFKTLKGRKY VSIV

UniProtKB: Large ribosomal subunit protein bL27

+
Macromolecule #25: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 10.069145 KDa
SequenceString:
ARKCEITGKK TMFGNNVPRK GLAKKKGGAG QHIGVKTKRT FKVNLINKKF FIPNLGRSVS IKVSANALRS ISKIGLDAFL KKNCKKIEN FL

UniProtKB: Large ribosomal subunit protein bL28

+
Macromolecule #26: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 7.915463 KDa
SequenceString:
MKNFKNFTLE DMKAKRLELK KEYLDLRFKS VVGHVENPLK KREIRRDIAR LNTMICEYEL GIRKV

UniProtKB: Large ribosomal subunit protein uL29

+
Macromolecule #27: 50S ribosomal protein uL30

MacromoleculeName: 50S ribosomal protein uL30 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 11.661239 KDa
SequenceString:
IKRKLRLQLK KARFNASRSR SKNKCFIKRM ENNRKIISKN NINVQVFLVR SLIGKLNKKV KVLKALGLNK IGDKKVHFLN ESIKGMLNE TINMILLSEV M

+
Macromolecule #28: 50S ribosomal protein L31 type B

MacromoleculeName: 50S ribosomal protein L31 type B / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 9.318736 KDa
SequenceString:
MRKDIHPKNN LVVFKDGSNG AMFLTKSTLN SKETIKYIDG KEYPLVTVEI TSKSHPFYTG QQKFVDAAGR IDKFNKRYKK S

UniProtKB: Large ribosomal subunit protein bL31B

+
Macromolecule #29: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 6.960201 KDa
SequenceString:
AVPKFKPSKS RSRTRRSINM RKKIPQFQEC SNCGNLGVRH RICLKCGYYR NNQYLEIGL

UniProtKB: Large ribosomal subunit protein bL32

+
Macromolecule #30: 50S ribosomal protein L33

MacromoleculeName: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 6.100251 KDa
SequenceString:
AVELISLICE ETGIRNYTTT KNRRNKQEKL ELMKYCPKLR KHTLHKEGKI K

UniProtKB: Large ribosomal subunit protein bL33

+
Macromolecule #31: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 6.0594 KDa
SequenceString:
MKRTYQPSRV KRNRKFGFRA RMKTKGGRLI LSRRRAKGRM KLTVSDEKKK

UniProtKB: Large ribosomal subunit protein bL34

+
Macromolecule #32: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 7.840516 KDa
SequenceString:
MANKMKTRKS AKKRYSFTVN GKVKYKKQNL RHILTKKSSK RKRNLRKSGN LSCFEVKRIK TLLPYG

UniProtKB: Large ribosomal subunit protein bL35

+
Macromolecule #33: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 4.418586 KDa
SequenceString:
MKVRVSVKPI CEKCKVIKRK GVLRIICDNL KHKQRQK

UniProtKB: Large ribosomal subunit protein bL36

+
Macromolecule #34: 50S ribosomal protein bL38

MacromoleculeName: 50S ribosomal protein bL38 / type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 5.351283 KDa
SequenceString:
RVGSKELISR WGGKIIMKSK FENGKIKHYA ECQTSKNTAR KPRDLF

UniProtKB: Uncharacterized protein

+
Macromolecule #35: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 35 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.25 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
30.0 mMNH4ClAmmonium chloride
10.0 mMMgCl2Magnesium chloride

Details: HMA-10 buffer
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 4661 / Average exposure time: 10.0 sec. / Average electron dose: 67.527 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8200000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 541319
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 12449
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.15)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.15)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 2 / Target criteria: Cross-correlation coefficient
Output model

PDB-8fmw:
The structure of a hibernating ribosome in the Lyme disease pathogen

PDB-8fn2:
The structure of a 50S ribosomal subunit in the Lyme disease pathogen Borreliella burgdorferi

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