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- PDB-5njt: Structure of the Bacillus subtilis hibernating 100S ribosome reve... -

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Basic information

Entry
Database: PDB / ID: 5njt
TitleStructure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 28
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Ribosome hibernation promotion factor
KeywordsTRANSLATION / 100S / Bacillus subtilis / cryo-EM / Hibernation / HPF / RMF / rRNA / YvyD
Function / homology
Function and homology information


negative regulation of translational elongation / primary metabolic process / positive regulation of rRNA processing / nucleoid / ribosomal small subunit binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / rRNA processing / ribosomal small subunit assembly / cytosolic small ribosomal subunit ...negative regulation of translational elongation / primary metabolic process / positive regulation of rRNA processing / nucleoid / ribosomal small subunit binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / rRNA processing / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / DNA binding / RNA binding / zinc ion binding / metal ion binding / cytosol / 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 / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 ...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 / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L10-like domain superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10P / Ribosomal protein L10 / 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 L32p, bacterial type / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 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
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS11 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL21 / Ribosome hibernation promotion factor / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBeckert, B. / Abdelshahid, M. / Schaefer, H. / Steinchen, W. / Arenz, S. / Berninghausen, O. / Beckmann, R. / Bange, G. / Turgay, K. / Wilson, D.N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSPP-1879 Germany
CitationJournal: EMBO J / Year: 2017
Title: Structure of the hibernating 100S ribosome reveals the basis for 70S dimerization.
Authors: Bertrand Beckert / Maha Abdelshahid / Heinrich Schäfer / Wieland Steinchen / Stefan Arenz / Otto Berninghausen / Roland Beckmann / Gert Bange / Kürşad Turgay / Daniel N Wilson /
Abstract: Under stress conditions, such as nutrient deprivation, bacteria enter into a hibernation stage, which is characterized by the appearance of 100S ribosomal particles. In , dimerization of 70S ...Under stress conditions, such as nutrient deprivation, bacteria enter into a hibernation stage, which is characterized by the appearance of 100S ribosomal particles. In , dimerization of 70S ribosomes into 100S requires the action of the ribosome modulation factor (RMF) and the hibernation-promoting factor (HPF). Most other bacteria lack RMF and instead contain a long form HPF (LHPF), which is necessary and sufficient for 100S formation. While some structural information exists as to how RMF and HPF mediate formation of 100S (100S), structural insight into 100S formation by LHPF has so far been lacking. Here we present a cryo-EM structure of the hibernating 100S (100S), revealing that the C-terminal domain (CTD) of the LHPF occupies a site on the 30S platform distinct from RMF Moreover, unlike RMF, the HPF-CTD is directly involved in forming the dimer interface, thereby illustrating the divergent mechanisms by which 100S formation is mediated in the majority of bacteria that contain LHPF, compared to some γ-proteobacteria, such as .
History
DepositionMar 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.2Jul 26, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Aug 2, 2017Group: Data collection / Experimental preparation / Category: em_sample_support / em_software
Item: _em_sample_support.grid_type / _em_software.name / _em_software.version
Revision 1.4Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: em_admin / pdbx_data_processing_status ...em_admin / pdbx_data_processing_status / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-3656
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: 16S ribosomal RNA
B: 30S ribosomal protein S2
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
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: 23S ribosomal RNA
V: 5S ribosomal RNA
W: 50S ribosomal protein L2
X: 50S ribosomal protein L3
Y: 50S ribosomal protein L4
Z: 50S ribosomal protein L5
a: 50S ribosomal protein L6
b: 50S ribosomal protein L10
c: 50S ribosomal protein L13
d: 50S ribosomal protein L14
e: 50S ribosomal protein L15
f: 50S ribosomal protein L16
g: 50S ribosomal protein L17
h: 50S ribosomal protein L18
i: 50S ribosomal protein L19
j: 50S ribosomal protein L20
k: 50S ribosomal protein L21
l: 50S ribosomal protein L22
m: 50S ribosomal protein L23
n: 50S ribosomal protein L24
o: 50S ribosomal protein L27
p: 50S ribosomal protein L32
q: 50S ribosomal protein L33 1
r: 50S ribosomal protein L34
s: 50S ribosomal protein L35
t: 50S ribosomal protein L36
u: 50S ribosomal protein L28
v: 50S ribosomal protein L29
w: 50S ribosomal protein L30
y: 50S ribosomal protein L31
x: Ribosome hibernation promotion factor


Theoretical massNumber of molelcules
Total (without water)2,111,70051
Polymers2,111,70051
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area162980 Å2
ΔGint-1401 kcal/mol
Surface area699130 Å2
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules AUV

#1: RNA chain 16S ribosomal RNA /


Mass: 500263.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Plasmid details: Bacillus Genetic Stock Center, Columbus, Ohio, USA -1A1
Variant: trpC2 / References: GenBank: 225184640
#21: RNA chain 23S ribosomal RNA /


Mass: 947975.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 467326
#22: RNA chain 5S ribosomal RNA /


Mass: 36157.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 728882887

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30S ribosomal protein ... , 19 types, 19 molecules BCDEFGHIJKLMNOPQRST

#2: Protein 30S ribosomal protein S2 / / BS1 / Vegetative protein 209 / VEG209


Mass: 25730.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21464
#3: Protein 30S ribosomal protein S3 / / BS3 / BS2


Mass: 23488.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21465
#4: Protein 30S ribosomal protein S4 / / BS4


Mass: 22743.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21466
#5: Protein 30S ribosomal protein S5 / / BS5


Mass: 17519.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21467
#6: Protein 30S ribosomal protein S6 / / BS9


Mass: 11140.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21468
#7: Protein 30S ribosomal protein S7 / / BS7


Mass: 17530.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21469
#8: Protein 30S ribosomal protein S8 / / BS8


Mass: 14770.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12879
#9: Protein 30S ribosomal protein S9 / / BS10


Mass: 14335.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21470
#10: Protein 30S ribosomal protein S10 / / BS13


Mass: 11687.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21471
#11: Protein 30S ribosomal protein S11 / / BS11


Mass: 12476.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P04969
#12: Protein 30S ribosomal protein S12 / / BS12


Mass: 15117.538 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21472
#13: Protein 30S ribosomal protein S13 / / BS14


Mass: 12599.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20282
#14: Protein 30S ribosomal protein S14 / / 30S ribosomal protein S14 type Z / 30S ribosomal protein S14-1 / BS-A


Mass: 7132.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12878
#15: Protein 30S ribosomal protein S15 / / BS18


Mass: 10466.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21473
#16: Protein 30S ribosomal protein S16 / / BS17


Mass: 10022.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21474
#17: Protein 30S ribosomal protein S17 / / BS16


Mass: 10089.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12874
#18: Protein 30S ribosomal protein S18 / / BS21


Mass: 8245.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21475
#19: Protein 30S ribosomal protein S19 / / BS19


Mass: 9185.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21476
#20: Protein 30S ribosomal protein S20 / / BS20


Mass: 9393.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21477

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50S ribosomal protein ... , 28 types, 28 molecules WXYZabcdefghijklmnopqrstuvwy

#23: Protein 50S ribosomal protein L2 / / BL2


Mass: 30074.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42919
#24: Protein 50S ribosomal protein L3 / / BL3


Mass: 22462.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42920
#25: Protein 50S ribosomal protein L4 /


Mass: 22222.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42921
#26: Protein 50S ribosomal protein L5 / / BL6


Mass: 20046.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12877
#27: Protein 50S ribosomal protein L6 / / BL10


Mass: 19124.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46898
#28: Protein 50S ribosomal protein L10 / / BL5 / Cold acclimatization protein / CAP / Vegetative protein 300 / VEG300


Mass: 13607.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42923
#29: Protein 50S ribosomal protein L13 /


Mass: 16017.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P70974
#30: Protein 50S ribosomal protein L14 /


Mass: 13175.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12875
#31: Protein 50S ribosomal protein L15 /


Mass: 15410.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19946
#32: Protein 50S ribosomal protein L16 /


Mass: 15619.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P14577
#33: Protein 50S ribosomal protein L17 / / BL15 / BL21


Mass: 13643.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20277
#34: Protein 50S ribosomal protein L18 / / BL16


Mass: 12993.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46899
#35: Protein 50S ribosomal protein L19 /


Mass: 13285.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O31742
#36: Protein 50S ribosomal protein L20 /


Mass: 13408.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55873
#37: Protein 50S ribosomal protein L21 / / BL20


Mass: 11164.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P26908
#38: Protein 50S ribosomal protein L22 /


Mass: 12035.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42060
#39: Protein 50S ribosomal protein L23 /


Mass: 10778.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42924
#40: Protein 50S ribosomal protein L24 / / 12 kDa DNA-binding protein / BL23 / HPB12


Mass: 10790.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P0CI78
#41: Protein 50S ribosomal protein L27 / / BL24 / BL30


Mass: 8956.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05657
#42: Protein 50S ribosomal protein L32 /


Mass: 6184.386 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O34687
#43: Protein/peptide 50S ribosomal protein L33 1 / Ribosome


Mass: 5786.696 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P56849
#44: Protein/peptide 50S ribosomal protein L34 /


Mass: 5271.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05647
#45: Protein 50S ribosomal protein L35 /


Mass: 7320.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55874
#46: Protein/peptide 50S ribosomal protein L36 / / BL38 / Ribosomal protein B / Ribosomal protein II


Mass: 4187.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20278
#47: Protein 50S ribosomal protein L28 /


Mass: 6367.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P37807
#48: Protein 50S ribosomal protein L29 /


Mass: 7598.849 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12873
#49: Protein 50S ribosomal protein L30 / / BL27


Mass: 6519.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19947
#50: Protein 50S ribosomal protein L31 /


Mass: 7216.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: Q03223

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Protein , 1 types, 1 molecules x

#51: Protein Ribosome hibernation promotion factor / HPF / Hst23 / Putative sigma-54 modulation protein / SigL modulation protein


Mass: 12355.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P28368

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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: Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization
Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHepes-KOH1
2100 mMKOAc1
325 mMMg(OAc)21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 4 OD260/ml ml Bs100S sample were applied to 2 nm pre-coated Quantifoil R3/3 holey carbon supported grids and vitrified using Vitrobot Mark IV (FEI Company)
Specimen supportGrid type: Quantifoil R3/3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2.5 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: REFMAC / Classification: refinement
EM software
IDNameVersionCategory
1Signature2particle selection
4CTFFIND4CTF correction
7UCSF Chimera1.11.2model fitting
9PHENIXmodel refinement
10FREALIGN9.11initial Euler assignment
11FREALIGN9.11final Euler assignment
12FREALIGN9.11classification
13FREALIGN9.113D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 253905
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24546
Details: 30S-70S_subcomplex primary map: 70S-30S_Masked_embf41.mrc
Symmetry type: POINT
Displacement parametersBiso max: 276.67 Å2 / Biso mean: 96.7637 Å2 / Biso min: 0 Å2

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