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

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Basic information

Entry
Database: PDB / ID: 8fmw
TitleThe structure of a hibernating ribosome in the Lyme disease pathogen
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 33
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • E-site t-RNA
  • Ribosomal subunit interface protein
KeywordsRIBOSOME / hibernating ribosome / bacterial / pathogen / 70S / translation
Function / homology
Function and homology information


large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / transferase activity / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding ...large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / transferase activity / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / 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 L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / : / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal 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 L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / 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 L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L28 / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L19, conserved site
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Uncharacterized protein ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 B31 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 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 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S ribosomal RNA
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14 type Z
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: 30S ribosomal protein S21
V: 30S ribosomal protein bS22
W: Ribosomal subunit interface protein
X: E-site t-RNA
AA: 23S ribosomal RNA
AB: 5S ribosomal RNA
AC: 50S ribosomal protein L1
AD: 50S ribosomal protein L2
AE: 50S ribosomal protein L3
AF: 50S ribosomal protein L4
AG: 50S ribosomal protein L5
AH: 50S ribosomal protein L6
AI: 50S ribosomal protein L9
AJ: 50S ribosomal protein L10
AK: 50S ribosomal protein L11
AL: 50S ribosomal protein L13
AM: 50S ribosomal protein L14
AN: 50S ribosomal protein L15
AO: 50S ribosomal protein L16
AP: 50S ribosomal protein L17
AQ: 50S ribosomal protein L18
AR: 50S ribosomal protein L19
AS: 50S ribosomal protein L20
AT: 50S ribosomal protein L21
AU: 50S ribosomal protein L22
AV: 50S ribosomal protein L23
AW: 50S ribosomal protein L24
AX: 50S ribosomal protein L25
AY: 50S ribosomal protein L27
AZ: 50S ribosomal protein L28
Aa: 50S ribosomal protein L29
Ab: 50S ribosomal protein uL30
Ac: 50S ribosomal protein L31 type B
Ad: 50S ribosomal protein L32
Ae: 50S ribosomal protein L33
Af: 50S ribosomal protein L34
Ag: 50S ribosomal protein L35
Ah: 50S ribosomal protein L36
Ai: 50S ribosomal protein bL38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,227,79762
Polymers2,227,53558
Non-polymers2624
Water00
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 , 4 types, 4 molecules AXAAAB

#1: RNA chain 16S ribosomal RNA


Mass: 495137.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: GenBank: AE000783
#23: RNA chain E-site t-RNA


Mass: 24417.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: GenBank: AE000783.1
#24: 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
#25: 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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30S ribosomal protein ... , 20 types, 20 molecules CDEFGHIJKLMNOPQRSTUV

#2: Protein 30S ribosomal protein S3


Mass: 23361.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: P94273
#3: Protein 30S ribosomal protein S4


Mass: 24003.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51560
#4: Protein 30S ribosomal protein S5


Mass: 17030.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51448
#5: Protein 30S ribosomal protein S6


Mass: 11595.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51142
#6: Protein 30S ribosomal protein S7


Mass: 18289.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51347
#7: Protein 30S ribosomal protein S8


Mass: 14838.454 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51445
#8: Protein 30S ribosomal protein S9


Mass: 14855.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51313
#9: Protein 30S ribosomal protein S10


Mass: 11657.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: P94266
#10: Protein 30S ribosomal protein S11


Mass: 12480.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51454
#11: Protein 30S ribosomal protein S12


Mass: 13823.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51348
#12: Protein 30S ribosomal protein S13


Mass: 12936.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51453
#13: Protein 30S ribosomal protein S14 type Z


Mass: 7088.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51444
#14: Protein 30S ribosomal protein S15


Mass: 10241.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51744
#15: Protein 30S ribosomal protein S16


Mass: 9700.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51638
#16: Protein 30S ribosomal protein S17


Mass: 9675.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51440
#17: Protein 30S ribosomal protein S18


Mass: 7417.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51140
#18: Protein 30S ribosomal protein S19


Mass: 9495.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: P94271
#19: Protein 30S ribosomal protein S20


Mass: 9977.187 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: P49394
#20: Protein 30S ribosomal protein S21


Mass: 8605.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51271
#21: Protein/peptide 30S ribosomal protein bS22


Mass: 3575.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria)

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50S ribosomal protein ... , 33 types, 33 molecules ACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZAaAbAcAdAeAf...

#26: Protein 50S ribosomal protein L1


Mass: 25177.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51353
#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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
#34: 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
#35: 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
#36: 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
#37: 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
#38: 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
#39: 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
#40: 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
#41: 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
#42: 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
#43: 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
#44: 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
#45: 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
#46: 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
#47: 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
#48: 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
#49: 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
#50: 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
#51: 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)
#52: Protein 50S ribosomal protein L31 type B


Mass: 9318.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51247
#53: 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
#54: 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
#55: 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
#56: 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
#57: 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
#58: 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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Protein / Non-polymers , 2 types, 5 molecules W

#22: Protein Ribosomal subunit interface protein


Mass: 11617.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Borreliella burgdorferi B31 (bacteria) / References: UniProt: O51405
#59: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: Hibernating 70S ribosome bound to E-tRNA and hibernation promoting factor protein
Type: RIBOSOME / Entity ID: #1-#58 / Source: NATURAL
Molecular weightValue: 2.082918 MDa / Experimental 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 FIELD / 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: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 288776 / Symmetry type: POINT
Atomic model buildingB value: 57.2 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 113.24 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0053160372
ELECTRON MICROSCOPYf_angle_d0.8467238881
ELECTRON MICROSCOPYf_chiral_restr0.084230092
ELECTRON MICROSCOPYf_plane_restr0.003613004
ELECTRON MICROSCOPYf_dihedral_angle_d15.316374756

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