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- PDB-5myj: Structure of 70S ribosome from Lactococcus lactis -

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Basic information

Entry
Database: PDB / ID: 5myj
TitleStructure of 70S ribosome from Lactococcus lactis
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 27
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Ribosome hibernation promotion factor
KeywordsRIBOSOME / 70S / lactoccocus lactis / Cryo-EM
Function / homology
Function and homology information


primary metabolic process / ribosomal large subunit assembly / large ribosomal subunit / regulation of translation / small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome ...primary metabolic process / ribosomal large subunit assembly / large ribosomal subunit / regulation of translation / small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosomal protein L31 type B / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein S21, conserved site ...Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosomal protein L31 type B / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / 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 L17 signature. / Ribosomal protein S14/S29 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 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 L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L14P, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein S16 domain superfamily / 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 S15, bacterial-type / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L32 / 50S ribosomal protein L34 / 50S ribosomal protein L28 / 30S ribosomal protein S21 / 30S ribosomal protein S4 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L32 / 50S ribosomal protein L34 / 50S ribosomal protein L28 / 30S ribosomal protein S21 / 30S ribosomal protein S4 / Ribosome hibernation promotion factor / 50S ribosomal protein L31 type B / 30S ribosomal protein S16 / 50S ribosomal protein L27 / 50S ribosomal protein L21 / 50S ribosomal protein L19 / 30S ribosomal protein S20 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 30S ribosomal protein S15 / 50S ribosomal protein L17 / 30S ribosomal protein S11 / 30S ribosomal protein S13 / 50S ribosomal protein L36 / 50S ribosomal protein L15 / 50S ribosomal protein L30 / 30S ribosomal protein S5 / 50S ribosomal protein L18 / 50S ribosomal protein L6 / 30S ribosomal protein S8 / 30S ribosomal protein S14 type Z / 50S ribosomal protein L5 / 50S ribosomal protein L24 / 50S ribosomal protein L14 / 30S ribosomal protein S17 / 50S ribosomal protein L29 / 50S ribosomal protein L16 / 30S ribosomal protein S3 / 50S ribosomal protein L22 / 30S ribosomal protein S19 / 50S ribosomal protein L2 / 50S ribosomal protein L23 / 50S ribosomal protein L4 / 50S ribosomal protein L3 / 30S ribosomal protein S10 / 50S ribosomal protein L33 3 / 30S ribosomal protein S2 / 30S ribosomal protein S18 / 30S ribosomal protein S6 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 30S ribosomal protein S7 / 30S ribosomal protein S12
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris MG1363 (lactic acid bacteria)
Lactococcus lactis subsp. cremoris (lactic acid bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsFranken, L.E. / Oostergetel, G.T. / Pijning, T. / Puri, P. / Boekema, E.J. / Poolman, B. / Guskov, A.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
NWOTOPGO L.10.060 Netherlands
European Research CouncilERC-2014-ADG Netherlands
CitationJournal: Nat Commun / Year: 2017
Title: A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy.
Authors: Linda E Franken / Gert T Oostergetel / Tjaard Pijning / Pranav Puri / Valentina Arkhipova / Egbert J Boekema / Bert Poolman / Albert Guskov /
Abstract: Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion ...Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion factor (HPF) and ribosome modulation factor. Here we report the cryo-electron microscopy study on 100S ribosomes from Lactococcus lactis and a dimerization mechanism involving a single protein: HPF. The N-terminal domain of HPF binds at the same site as HPF in Escherichia coli 100S ribosomes. Contrary to ribosome modulation factor, the C-terminal domain of HPF binds exactly at the dimer interface. Furthermore, ribosomes from Lactococcus lactis do not undergo conformational changes in the 30S head domains upon binding of HPF, and the Shine-Dalgarno sequence and mRNA entrance tunnel remain accessible. Ribosome activity is blocked by HPF due to the inhibition of mRNA recognition by the platform binding center. Phylogenetic analysis of HPF proteins suggests that HPF-mediated dimerization is a widespread mechanism of ribosome hibernation in bacteria.When bacteria enter the stationary growth phase, protein translation is suppressed via the dimerization of 70S ribosomes into inactive complexes. Here the authors provide a structural basis for how the dual domain hibernation promotion factor promotes ribosome dimerization and hibernation in bacteria.
History
DepositionJan 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release

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Assembly

Deposited unit
AA: 16S ribosomal RNA
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14 type Z
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein S21
B0: 50S ribosomal protein L28
B1: 50S ribosomal protein L29
B2: 50S ribosomal protein L30
B3: 50S ribosomal protein L31 type B
B4: 50S ribosomal protein L32
B5: 50S ribosomal protein L33 3
B6: 50S ribosomal protein L34
B7: 50S ribosomal protein L35
B8: 50S ribosomal protein L36
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BD: 50S ribosomal protein L2
BE: 50S ribosomal protein L3
BF: 50S ribosomal protein L4
BG: 50S ribosomal protein L5
BH: 50S ribosomal protein L6
BM: 50S ribosomal protein L13
BN: 50S ribosomal protein L14
BO: 50S ribosomal protein L15
BP: 50S ribosomal protein L16
BQ: 50S ribosomal protein L17
BR: 50S ribosomal protein L18
BS: 50S ribosomal protein L19
BT: 50S ribosomal protein L20
BU: 50S ribosomal protein L21
BV: 50S ribosomal protein L22
BW: 50S ribosomal protein L23
BX: 50S ribosomal protein L24
BZ: 50S ribosomal protein L27
A: Ribosome hibernation promotion factor


Theoretical massNumber of molelcules
Total (without water)2,115,46251
Polymers2,115,46251
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area240680 Å2
ΔGint-1878 kcal/mol
Surface area742030 Å2
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules AABABB

#1: RNA chain 16S ribosomal RNA /


Mass: 497142.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris MG1363 (lactic acid bacteria)
References: GenBank: 124491690
#31: RNA chain 23S ribosomal RNA /


Mass: 938591.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris MG1363 (lactic acid bacteria)
References: GenBank: 124491690
#32: RNA chain 5S ribosomal RNA /


Mass: 37065.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris MG1363 (lactic acid bacteria)
References: GenBank: 124491690

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30S ribosomal protein ... , 20 types, 20 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAU

#2: Protein 30S ribosomal protein S2 /


Mass: 28589.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNV0
#3: Protein 30S ribosomal protein S3 /


Mass: 24058.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNP9
#4: Protein 30S ribosomal protein S4 /


Mass: 23232.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RI10
#5: Protein 30S ribosomal protein S5 /


Mass: 17609.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNN6
#6: Protein 30S ribosomal protein S6 /


Mass: 11321.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNZ4
#7: Protein 30S ribosomal protein S7 /


Mass: 17713.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RP73
#8: Protein 30S ribosomal protein S8 /


Mass: 14692.106 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNN9
#9: Protein 30S ribosomal protein S9 /


Mass: 14124.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RP61
#10: Protein 30S ribosomal protein S10 /


Mass: 11764.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNQ6
#11: Protein 30S ribosomal protein S11 /


Mass: 13310.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNM8
#12: Protein 30S ribosomal protein S12 /


Mass: 15157.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RP74
#13: Protein 30S ribosomal protein S13 /


Mass: 13519.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNM9
#14: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7151.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNP2
#15: Protein 30S ribosomal protein S15 /


Mass: 10367.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RMV9
#16: Protein 30S ribosomal protein S16 /


Mass: 10270.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RJS1
#17: Protein 30S ribosomal protein S17 /


Mass: 10166.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNP6
#18: Protein 30S ribosomal protein S18 /


Mass: 9392.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNZ2
#19: Protein 30S ribosomal protein S19 /


Mass: 10595.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNQ1
#20: Protein 30S ribosomal protein S20 /


Mass: 8384.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RMG0
#21: Protein 30S ribosomal protein S21 /


Mass: 7041.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RHW9

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50S ribosomal protein ... , 27 types, 27 molecules B0B1B2B3B4B5B6B7B8BDBEBFBGBHBMBNBOBPBQBRBSBTBUBVBWBXBZ

#22: Protein 50S ribosomal protein L28 /


Mass: 7187.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RHS3
#23: Protein 50S ribosomal protein L29 /


Mass: 7874.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNP7
#24: Protein 50S ribosomal protein L30 /


Mass: 6202.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNN5
#25: Protein 50S ribosomal protein L31 type B / Ribosome


Mass: 9366.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RJP7
#26: Protein 50S ribosomal protein L32 /


Mass: 6681.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RHH0
#27: Protein/peptide 50S ribosomal protein L33 3 / Ribosome


Mass: 5567.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNR2
#28: Protein/peptide 50S ribosomal protein L34 /


Mass: 5200.206 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RHL6
#29: Protein 50S ribosomal protein L35 /


Mass: 7844.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RMR2
#30: Protein/peptide 50S ribosomal protein L36 /


Mass: 4432.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNN0
#33: Protein 50S ribosomal protein L2 /


Mass: 29641.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNQ2
#34: Protein 50S ribosomal protein L3 /


Mass: 21956.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNQ5
#35: Protein 50S ribosomal protein L4 /


Mass: 22393.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNQ4
#36: Protein 50S ribosomal protein L5 /


Mass: 20034.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNP3
#37: Protein 50S ribosomal protein L6 /


Mass: 19313.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNN8
#38: Protein 50S ribosomal protein L13 /


Mass: 16192.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RP62
#39: Protein 50S ribosomal protein L14 /


Mass: 12944.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNP5
#40: Protein 50S ribosomal protein L15 /


Mass: 15376.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNN4
#41: Protein 50S ribosomal protein L16 /


Mass: 15375.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNP8
#42: Protein 50S ribosomal protein L17 /


Mass: 14280.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNM6
#43: Protein 50S ribosomal protein L18 /


Mass: 12426.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNN7
#44: Protein 50S ribosomal protein L19 /


Mass: 13129.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RLS5
#45: Protein 50S ribosomal protein L20 /


Mass: 13726.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RMR1
#46: Protein 50S ribosomal protein L21 /


Mass: 11444.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RLA4
#47: Protein 50S ribosomal protein L22 /


Mass: 12490.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNQ0
#48: Protein 50S ribosomal protein L23 /


Mass: 10819.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNQ3
#49: Protein 50S ribosomal protein L24 /


Mass: 10897.782 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RNP4
#50: Protein 50S ribosomal protein L27 /


Mass: 10053.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RLA2

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Protein , 1 types, 1 molecules A

#51: Protein Ribosome hibernation promotion factor / HPF / Lactococcus lactis hibernation promotion factor / LIHPF


Mass: 21345.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / References: UniProt: A2RIX0

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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: 70S ribosomeRibosome / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Lactococcus lactis (lactic acid bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 291.15 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
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
EM imaging opticsSpherical aberration corrector: Cs-corrector (CEOS, Heidelberg, Germany)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9PHENIX1.11.1model refinement
10Xmippinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43530 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementHighest resolution: 5.6 Å

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