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- PDB-5zep: M. smegmatis hibernating state 70S ribosome structure -

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Basic information

Entry
Database: PDB / ID: 5zep
TitleM. smegmatis hibernating state 70S ribosome structure
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 31
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • Conserved domain protein
  • E-tRNAfMet
  • Ribosome hibernation promoting factor
  • Uncharacterized protein
  • bS1
KeywordsRIBOSOME / hibernating-state / complex
Function / homology
Function and homology information


small ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding ...small ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA 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 / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal ...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 / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / 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 L11, bacterial-type / 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 L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L16 signature 1. / Ribosomal protein L10P / Ribosomal protein L10 / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / : / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L20 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S4, bacterial-type
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S6 / Conserved domain protein / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S6 / Conserved domain protein / Large ribosomal subunit protein bL33A / 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 uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / 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 / Large ribosomal subunit protein bL28 / 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 bL31 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein bS18B / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMishra, S. / Ahmed, T. / Tyagi, A. / Shi, J. / Bhushan, S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore) Singapore
CitationJournal: Sci Rep / Year: 2018
Title: Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA.
Authors: Satabdi Mishra / Tofayel Ahmed / Anu Tyagi / Jian Shi / Shashi Bhushan /
Abstract: Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these ...Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these different functional states of ribosomes to understand their mechanism of action. Here, we present single particle cryo-EM reconstructions of the Mycobacterium smegmatis 70S ribosomes in the hibernating state (with HPF), trans-translating state (with tmRNA), and the P/P state (with P-tRNA) resolved to 4.1, 12.5, and 3.4 Å, respectively. A comparison of the P/P state with the hibernating state provides possible functional insights about the Mycobacteria-specific helix H54a rRNA segment. Interestingly, densities for all the four OB domains of bS1 protein is visible in the hibernating 70S ribosome displaying the molecular details of bS1-70S interactions. Our structural data shows a Mycobacteria-specific H54a-bS1 interaction which seems to prevent subunit dissociation and degradation during hibernation without the formation of 100S dimer. This indicates a new role of bS1 protein in 70S protection during hibernation in Mycobacteria in addition to its conserved function during translation initiation.
History
DepositionFeb 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release

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Assembly

Deposited unit
a: 16S rRNA
c: 30S ribosomal protein S3
e: 30S ribosomal protein S5
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
o: 30S ribosomal protein S15
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18 2
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
n: 30S ribosomal protein S14 type Z
b: 30S ribosomal protein S2
d: 30S ribosomal protein S4
f: 30S ribosomal protein S6
m: 30S ribosomal protein S13
p: 30S ribosomal protein S16
u: Conserved domain protein
w: E-tRNAfMet
x: Ribosome hibernation promoting factor
0: bS1
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
Y: 50S ribosomal protein L28
Z: 50S ribosomal protein L29
v: 50S ribosomal protein L30
y: 50S ribosomal protein L31
z: 50S ribosomal protein L32
1: 50S ribosomal protein L33 1
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
5: Uncharacterized protein
B: 5S rRNA
A: 23S rRNA


Theoretical massNumber of molelcules
Total (without water)2,372,17358
Polymers2,372,17358
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 4 types, 4 molecules awBA

#1: RNA chain 16S rRNA


Mass: 495373.656 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
#22: RNA chain E-tRNAfMet


Mass: 24786.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1036415628
#57: RNA chain 5S rRNA


Mass: 38038.777 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
#58: RNA chain 23S rRNA


Mass: 1012140.938 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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30S ribosomal protein ... , 19 types, 19 molecules ceghijkloqrstnbdfmp

#2: Protein 30S ribosomal protein S3 / uS3


Mass: 30191.227 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: UniProt: A0QSD7
#3: Protein 30S ribosomal protein S5 / uS5


Mass: 21946.090 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: UniProt: A0QSG6
#4: Protein 30S ribosomal protein S7 / uS7


Mass: 17660.375 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: UniProt: A0QS97
#5: Protein 30S ribosomal protein S8 / uS8


Mass: 14492.638 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: UniProt: A0QSG3
#6: Protein 30S ribosomal protein S9 / uS9


Mass: 16794.365 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: UniProt: A0QSP9
#7: Protein 30S ribosomal protein S10 / uS10


Mass: 11454.313 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: UniProt: A0QSD0
#8: Protein 30S ribosomal protein S11 / us11


Mass: 14671.762 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: UniProt: A0QSL6
#9: Protein 30S ribosomal protein S12 / uS12


Mass: 13896.366 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: UniProt: A0QS96
#10: Protein 30S ribosomal protein S15 / uS15


Mass: 10368.097 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: UniProt: A0QVQ3
#11: Protein 30S ribosomal protein S17 / uS17


Mass: 11127.002 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: UniProt: A0QSE0
#12: Protein 30S ribosomal protein S18 2 / bS18


Mass: 9524.188 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: UniProt: A0R7F7
#13: Protein 30S ribosomal protein S19 / uS19


Mass: 10800.602 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: UniProt: A0QSD5
#14: Protein 30S ribosomal protein S20 / bS20


Mass: 9556.104 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 / References: UniProt: A0R102
#15: Protein 30S ribosomal protein S14 type Z / uS14


Mass: 6976.409 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: UniProt: A0QSG2
#16: Protein 30S ribosomal protein S2 / uS2


Mass: 30145.230 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: UniProt: A0QVB8
#17: Protein 30S ribosomal protein S4 / uS4


Mass: 23415.787 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: UniProt: A0QSL7
#18: Protein 30S ribosomal protein S6 / bS6


Mass: 10991.637 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: UniProt: A0A0D6J3X3
#19: Protein 30S ribosomal protein S13 / uS13


Mass: 14249.619 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: UniProt: A0QSL5
#20: Protein 30S ribosomal protein S16 / bS16


Mass: 16795.207 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: UniProt: A0QV37

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Protein/peptide , 2 types, 2 molecules u5

#21: Protein/peptide Conserved domain protein / bS22


Mass: 4164.300 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: UniProt: A0QR10
#56: Protein/peptide Uncharacterized protein


Mass: 2841.375 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: UniProt: A0QTP4

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Protein , 2 types, 2 molecules x0

#23: Protein Ribosome hibernation promoting factor / HFT


Mass: 26447.615 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: UniProt: A0QTK6
#24: Protein bS1 / bS1


Mass: 40783.270 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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50S ribosomal protein ... , 31 types, 31 molecules CDEFGHIJKLMNOPQRSTUVWXYZvyz1234

#25: Protein 50S ribosomal protein L2 / uL2


Mass: 30425.945 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: UniProt: A0QSD4
#26: Protein 50S ribosomal protein L3 / uL3


Mass: 23011.393 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: UniProt: A0QSD1
#27: Protein 50S ribosomal protein L4 / uL4


Mass: 22920.949 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: UniProt: A0QSD2
#28: Protein 50S ribosomal protein L5 / uL5


Mass: 21152.328 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: UniProt: A0QSG1
#29: Protein 50S ribosomal protein L6 / uL6


Mass: 19483.361 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: UniProt: A0QSG4
#30: Protein 50S ribosomal protein L9 / bL9


Mass: 15949.253 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: UniProt: A0R7F6
#31: Protein 50S ribosomal protein L10 / uL10


Mass: 18035.736 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: UniProt: A0QS62
#32: Protein 50S ribosomal protein L11 / uL11


Mass: 15023.374 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: UniProt: A0QS45
#33: Protein 50S ribosomal protein L13 / uL13


Mass: 16146.689 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: UniProt: A0QSP8
#34: Protein 50S ribosomal protein L14 / uL14


Mass: 13400.625 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: UniProt: A0QSF9
#35: Protein 50S ribosomal protein L15 / uL15


Mass: 15602.244 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: UniProt: A0QSG8
#36: Protein 50S ribosomal protein L16 / uL16


Mass: 15774.240 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: UniProt: A0QSD8
#37: Protein 50S ribosomal protein L17 / bL17


Mass: 21892.246 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: UniProt: A0QSL9
#38: Protein 50S ribosomal protein L18 / uL18


Mass: 13711.728 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: UniProt: I7FGD9, UniProt: A0QSG5*PLUS
#39: Protein 50S ribosomal protein L19 / bL19


Mass: 12892.806 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: UniProt: A0QV42
#40: Protein 50S ribosomal protein L20 / bL20


Mass: 14494.693 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: UniProt: A0QYU6
#41: Protein 50S ribosomal protein L21 / bL21


Mass: 11055.894 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: UniProt: A0R151
#42: Protein 50S ribosomal protein L22 / uL22


Mass: 16353.600 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: UniProt: A0QSD6
#43: Protein 50S ribosomal protein L23 / uL23


Mass: 11047.836 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: UniProt: A0QSD3
#44: Protein 50S ribosomal protein L24 / uL24


Mass: 11228.946 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: UniProt: A0QSG0
#45: Protein 50S ribosomal protein L25 / bL25 / General stress protein CTC


Mass: 22571.078 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: UniProt: I7GFB2, UniProt: A0R3D2*PLUS
#46: Protein 50S ribosomal protein L27 / bL27


Mass: 9249.582 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: UniProt: A0R150
#47: Protein 50S ribosomal protein L28 / bL28


Mass: 6891.016 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: UniProt: I7FJ52, UniProt: A0QV03*PLUS
#48: Protein 50S ribosomal protein L29 / uL29


Mass: 8790.895 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: UniProt: A0QSD9
#49: Protein 50S ribosomal protein L30 / uL30


Mass: 7022.147 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: UniProt: A0QSG7
#50: Protein 50S ribosomal protein L31 / bL31


Mass: 8312.485 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: UniProt: A0R215
#51: Protein 50S ribosomal protein L32 / bL32


Mass: 6467.719 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: UniProt: A0R3I9
#52: Protein 50S ribosomal protein L33 1 / bL33


Mass: 6468.501 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: UniProt: A0QS39
#53: Protein/peptide 50S ribosomal protein L34 / bL34


Mass: 5522.580 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: UniProt: A0R7K0
#54: Protein 50S ribosomal protein L35 / bL35


Mass: 7298.505 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: UniProt: A0QYU7
#55: Protein/peptide 50S ribosomal protein L36 / bL36


Mass: 4341.277 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: UniProt: A0QSL4

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Details

Sequence detailsThe real sequence of entity 24, protein bS1, should be ...The real sequence of entity 24, protein bS1, should be MPSPSVTSPQVAVNDIGSAEDFLAAIDKTIKYFNDGDIVEGTIVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVSVGDEVEALVLTKEDKEGRLILSKKRAQYERAWGTIEELKEKDEAVKGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLQPYIGKEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGAIRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVQVGDEVTVEVLDVDMDRERVSLSLKATQEDPWRHFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELSERHVEVPDQVVQVGDDAMVKVIDIDLERRRISLSLKQANEDYTEEFDPSKYGMADSYDEQGNYIFPEGFDPETNEWLEGFDKQREEWEARYAEAERRHKMHTAQMEKFAAAEAEAANAPVSNGSSRSEESSGGTLASDAQLAALREKLAGNA. The residues cannot be assigned accurately due to disorder.

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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

Component
IDNameTypeEntity IDParent-IDSource
1Translating-state 70S ribosome structure from M.smegmatisRIBOSOMEall0NATURAL
270S ribosome structure from M.smegmatisRIBOSOME#1-#21, #23-#581NATURAL
3E-tRNAfMetCOMPLEX#221NATURAL
Molecular weightValue: 2.6 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDCellular location
12Mycobacterium smegmatis str. MC2 155 (bacteria)246196cytoplasm
23Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 391837 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å

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