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- PDB-6dzi: Cryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosom... -

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Basic information

Entry
Database: PDB / ID: 6dzi
TitleCryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosome 70S-MPY complex
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 31
  • 16S rRNA
  • 23 S rRNA (3119-MER)
  • 5S RNA (118-MER)
  • CONSERVED PROTEIN DOMAINConservation
  • Ribosome hibernation promoting factor
  • Uncharacterized protein
KeywordsRIBOSOME / Hibernation factor complex
Function / homology
Function and homology information


primary metabolic process / large ribosomal subunit rRNA binding / regulation of translation / large ribosomal subunit / 5S rRNA binding / small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome ...primary metabolic process / large ribosomal subunit rRNA binding / regulation of translation / large ribosomal subunit / 5S rRNA binding / small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA 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 / 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 L25, long-form ...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 L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / : / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / 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 L11, conserved site / Ribosomal protein L10-like domain superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / 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 L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein 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
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S6 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S6 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / 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 / 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 uS8 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Ribosome hibernation promoting factor / Uncharacterized protein / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein bS18A / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein bL33B / 50S ribosomal protein L31 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL15
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
Mycobacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsSharma, M.R. / Li, Y. / Korripella, R. / Yang, Y. / Kaushal, P.S. / Lin, Q. / Wade, J.T. / Gray, A.G. / Derbyshire, K.M. / Agrawal, R.K. / Ojha, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM061576 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI107595 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI097191 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Zinc depletion induces ribosome hibernation in mycobacteria.
Authors: Yunlong Li / Manjuli R Sharma / Ravi K Koripella / Yong Yang / Prem S Kaushal / Qishan Lin / Joseph T Wade / Todd A Gray / Keith M Derbyshire / Rajendra K Agrawal / Anil K Ojha /
Abstract: Bacteria respond to zinc starvation by replacing ribosomal proteins that have the zinc-binding CXXC motif (C+) with their zinc-free (C-) paralogues. Consequences of this process beyond zinc ...Bacteria respond to zinc starvation by replacing ribosomal proteins that have the zinc-binding CXXC motif (C+) with their zinc-free (C-) paralogues. Consequences of this process beyond zinc homeostasis are unknown. Here, we show that the C- ribosome in is the exclusive target of a bacterial protein Y homolog, referred to as mycobacterial-specific protein Y (MPY), which binds to the decoding region of the 30S subunit, thereby inactivating the ribosome. MPY binding is dependent on another mycobacterial protein, MPY recruitment factor (MRF), which is induced on zinc depletion, and interacts with C- ribosomes. MPY binding confers structural stability to C- ribosomes, promoting survival of growth-arrested cells under zinc-limiting conditions. Binding of MPY also has direct influence on the dynamics of aminoglycoside-binding pockets of the C- ribosome to inhibit binding of these antibiotics. Together, our data suggest that zinc limitation leads to ribosome hibernation and aminoglycoside resistance in mycobacteria. Furthermore, our observation of the expression of the proteins of C- ribosomes in in a mouse model of infection suggests that ribosome hibernation could be relevant in our understanding of persistence and drug tolerance of the pathogen encountered during chemotherapy of TB.
History
DepositionJul 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

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Assembly

Deposited unit
h: 16S rRNA
j: CONSERVED PROTEIN DOMAIN
k: 30S ribosomal protein S3
l: 30S ribosomal protein S4
m: 30S ribosomal protein S5
n: 30S ribosomal protein S6
p: 30S ribosomal protein S7
q: 30S ribosomal protein S8
4: 30S ribosomal protein S9
s: 30S ribosomal protein S10
t: 30S ribosomal protein S11
u: 30S ribosomal protein S12
v: 30S ribosomal protein S13
x: 30S ribosomal protein S15
z: 30S ribosomal protein S16
5: 30S ribosomal protein S17
6: 30S ribosomal protein S19
7: 30S ribosomal protein S20
8: 30S ribosomal protein S2
r: 30S ribosomal protein S18 1
Y: Ribosome hibernation promoting factor
9: 30S ribosomal protein S14
A: 23 S rRNA (3119-MER)
B: 5S RNA (118-MER)
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
I: 50S ribosomal protein L10
J: 50S ribosomal protein L11
K: 50S ribosomal protein L13
L: 50S ribosomal protein L14
M: 50S ribosomal protein L15
N: 50S ribosomal protein L16
O: 50S ribosomal protein L17
P: 50S ribosomal protein L18
Q: 50S ribosomal protein L19
R: 50S ribosomal protein L20
S: 50S ribosomal protein L21
T: 50S ribosomal protein L22
U: 50S ribosomal protein L23
V: 50S ribosomal protein L24
W: 50S ribosomal protein L25
X: 50S ribosomal protein L27
Z: 50S ribosomal protein L29
a: 50S ribosomal protein L30
b: 50S ribosomal protein L32
c: 50S ribosomal protein L33 2
d: 50S ribosomal protein L34
e: 50S ribosomal protein L35
f: 50S ribosomal protein L36
g: 50S ribosomal protein L31
y: 50S ribosomal protein L28
3: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)2,238,24056
Polymers2,238,24056
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area267250 Å2
ΔGint-2156 kcal/mol
Surface area853550 Å2

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Components

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RNA chain , 3 types, 3 molecules hAB

#1: RNA chain 16S rRNA /


Mass: 490111.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 16 S RNA
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: GenBank: 118168627
#23: RNA chain 23 S rRNA (3119-MER)


Mass: 1011834.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: GenBank: 118168627
#24: RNA chain 5S RNA (118-MER)


Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: GenBank: 118168627

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Protein/peptide , 2 types, 2 molecules j3

#2: Protein/peptide CONSERVED PROTEIN DOMAIN / Conservation


Mass: 4033.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155
#56: Protein/peptide Uncharacterized protein


Mass: 2710.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QTP4

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30S ribosomal protein ... , 19 types, 19 molecules klmnpq4stuvxz5678r9

#3: Protein 30S ribosomal protein S3 /


Mass: 23617.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD7
#4: Protein 30S ribosomal protein S4 /


Mass: 23284.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL7
#5: Protein 30S ribosomal protein S5 /


Mass: 18481.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG6
#6: Protein 30S ribosomal protein S6 /


Mass: 10991.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis (bacteria) / References: UniProt: A0A0D6J3X3
#7: Protein 30S ribosomal protein S7 /


Mass: 17529.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS97
#8: Protein 30S ribosomal protein S8 /


Mass: 14361.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG3
#9: Protein 30S ribosomal protein S9 /


Mass: 14093.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSP9
#10: Protein 30S ribosomal protein S10 /


Mass: 11252.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD0
#11: Protein 30S ribosomal protein S11 /


Mass: 12151.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL6
#12: Protein 30S ribosomal protein S12 /


Mass: 13678.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS96
#13: Protein 30S ribosomal protein S13 /


Mass: 13374.481 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL5
#14: Protein 30S ribosomal protein S15 /


Mass: 10236.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QVQ3
#15: Protein 30S ribosomal protein S16 /


Mass: 12635.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QV37
#16: Protein 30S ribosomal protein S17 /


Mass: 10680.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSE0
#17: Protein 30S ribosomal protein S19 /


Mass: 9379.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD5
#18: Protein 30S ribosomal protein S20 /


Mass: 9424.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R102
#19: Protein 30S ribosomal protein S2 /


Mass: 25576.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QVB8
#20: Protein 30S ribosomal protein S18 1 / Ribosome


Mass: 9449.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R549
#22: Protein 30S ribosomal protein S14 /


Mass: 11661.530 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R550

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Protein , 1 types, 1 molecules Y

#21: Protein Ribosome hibernation promoting factor / HPF


Mass: 12238.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QTK6

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50S ribosomal protein ... , 31 types, 31 molecules CDEFGHIJKLMNOPQRSTUVWXZabcdefgy

#25: Protein 50S ribosomal protein L2 /


Mass: 30008.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD4
#26: Protein 50S ribosomal protein L3 /


Mass: 22621.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD1
#27: Protein 50S ribosomal protein L4 /


Mass: 22346.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD2
#28: Protein 50S ribosomal protein L5 /


Mass: 20588.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG1
#29: Protein 50S ribosomal protein L6 /


Mass: 19165.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG4
#30: Protein 50S ribosomal protein L9 /


Mass: 15949.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R7F6
#31: Protein 50S ribosomal protein L10 /


Mass: 13095.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS62
#32: Protein 50S ribosomal protein L11 /


Mass: 14109.185 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS45
#33: Protein 50S ribosomal protein L13 /


Mass: 16015.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSP8
#34: Protein 50S ribosomal protein L14 /


Mass: 13400.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSF9
#35: Protein 50S ribosomal protein L15 /


Mass: 15383.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: I7G436
#36: Protein 50S ribosomal protein L16 /


Mass: 15498.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD8
#37: Protein 50S ribosomal protein L17 /


Mass: 13210.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL9
#38: Protein 50S ribosomal protein L18 /


Mass: 13580.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: I7FGD9
#39: Protein 50S ribosomal protein L19 /


Mass: 12892.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QV42
#40: Protein 50S ribosomal protein L20 /


Mass: 14035.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QYU6
#41: Protein 50S ribosomal protein L21 /


Mass: 10724.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R151
#42: Protein 50S ribosomal protein L22 /


Mass: 12408.192 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD6
#43: Protein 50S ribosomal protein L23 /


Mass: 10748.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD3
#44: Protein 50S ribosomal protein L24 /


Mass: 11228.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG0
#45: Protein 50S ribosomal protein L25 / / General stress protein CTC


Mass: 20331.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R3D2
#46: Protein 50S ribosomal protein L27 /


Mass: 8322.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R150
#47: Protein 50S ribosomal protein L29 /


Mass: 7590.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD9
#48: Protein 50S ribosomal protein L30 /


Mass: 6761.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG7
#49: Protein 50S ribosomal protein L32 /


Mass: 6050.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R3I9
#50: Protein 50S ribosomal protein L33 2 / Ribosome


Mass: 6484.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R551
#51: Protein/peptide 50S ribosomal protein L34 /


Mass: 5391.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R7K0
#52: Protein 50S ribosomal protein L35 /


Mass: 7167.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QYU7
#53: Protein/peptide 50S ribosomal protein L36 /


Mass: 4341.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL4
#54: Protein 50S ribosomal protein L31 /


Mass: 9141.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R554
#55: Protein 50S ribosomal protein L28 /


Mass: 8794.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155

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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-MPY complex / Type: RIBOSOME
Details: Mycobacterium smegmatis ribosome (Cminus) 70S-MPY complex
Entity ID: #1-#53, #55-#56 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %

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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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 67.1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
4RELION2.01CTF correction
12RELION2.01classificationRelion used for image processing and Refinement
13RELION23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 205510
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66840 / Algorithm: FOURIER SPACE / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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