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- PDB-5o61: The complete structure of the Mycobacterium smegmatis 70S ribosome -

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Basic information

Entry
Database: PDB / ID: 5o61
TitleThe complete structure of the Mycobacterium smegmatis 70S ribosome
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 31
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • Conserved domain proteinProtein domain
  • LSU ribosomal protein L28P
  • P/P-site Phe-tRNA(Phe)
  • mRNA fragment
KeywordsRIBOSOME / translation
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / ribosome biogenesis / small ribosomal subunit / transferase activity / tRNA binding / ribosome / rRNA binding ...large ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / ribosome biogenesis / small ribosomal subunit / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / zinc ion binding / metal ion binding
Ribosomal protein L31 / Ribosomal protein L28/L24 / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L5 domain superfamily / Ribosomal protein L10 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S14, type Z / Ribosomal protein L4 domain superfamily ...Ribosomal protein L31 / Ribosomal protein L28/L24 / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L5 domain superfamily / Ribosomal protein L10 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S14, type Z / Ribosomal protein L4 domain superfamily / Ribosomal protein S19/S15, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / 30s ribosomal protein S13, C-terminal / Ribosomal protein L35 / Ribosomal protein S10 domain / Ribosomal protein L31 type A / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein L36 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L18e/L15P / L21-like superfamily / Ribosomal protein L25, beta domain / Ribosomal protein S18, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein S11, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L34, conserved site / Ribosomal protein L9, N-terminal / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein L11, C-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L5, bacterial-type / Ribosomal protein S19 conserved site / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein S13, conserved site / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S6 / Ribosomal protein S8 / Ribosomal protein S9/S16 / Ribosomal protein S10p/S20e / Ribosomal protein S11 / Ribosomal protein S12/S23 / Ribosomal protein S13/S18 / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S16 / Ribosomal protein S17 / Ribosomal protein S20 / Ribosomal protein L4/L1 family / Ribosomal protein S5, N-terminal domain / Ribosomal protein L5 / ribosomal L5P family C-terminus / Ribosomal protein L9, N-terminal domain / Ribosomal protein L10 / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal prokaryotic L21 protein / KOW motif / Ribosomal L27 protein / Ribosomal L32p protein family / Ribosomal protein L33 / Ribosomal protein S5, C-terminal domain / S4 domain / Ribosomal protein L17 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L9, C-terminal domain superfamily
30S ribosomal protein S3 / 50S ribosomal protein L2 / 30S ribosomal protein S19 / 50S ribosomal protein L22 / 30S ribosomal protein S14 type Z / 50S ribosomal protein L16 / 50S ribosomal protein L29 / 30S ribosomal protein S17 / 50S ribosomal protein L4 / 50S ribosomal protein L23 ...30S ribosomal protein S3 / 50S ribosomal protein L2 / 30S ribosomal protein S19 / 50S ribosomal protein L22 / 30S ribosomal protein S14 type Z / 50S ribosomal protein L16 / 50S ribosomal protein L29 / 30S ribosomal protein S17 / 50S ribosomal protein L4 / 50S ribosomal protein L23 / 50S ribosomal protein L33 1 / 50S ribosomal protein L3 / 30S ribosomal protein S10 / 30S ribosomal protein S7 / 30S ribosomal protein S12 / 50S ribosomal protein L10 / 50S ribosomal protein L11 / 50S ribosomal protein L24 / Conserved domain protein / 30S ribosomal protein S6 / 50S ribosomal protein L14 / gb:118168627: / 30S ribosomal protein S8 / 30S ribosomal protein S16 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 30S ribosomal protein S5 / 50S ribosomal protein L5 / 50S ribosomal protein L15 / 50S ribosomal protein L36 / 30S ribosomal protein S13 / 30S ribosomal protein S11 / 30S ribosomal protein S4 / 50S ribosomal protein L17 / 50S ribosomal protein L13 / 30S ribosomal protein S9 / Uncharacterized protein / 50S ribosomal protein L28 / 50S ribosomal protein L19 / 50S ribosomal protein L15 / 30S ribosomal protein S2 / 30S ribosomal protein S15 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 30S ribosomal protein S20 / 50S ribosomal protein L27 / 50S ribosomal protein L21 / 50S ribosomal protein L31 / 50S ribosomal protein L25 / 50S ribosomal protein L32 / 50S ribosomal protein L9 / 30S ribosomal protein S18 2 / 50S ribosomal protein L34 / 50S ribosomal protein L28 / 50S ribosomal protein L30
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsHentschel, J. / Burnside, C. / Mignot, I. / Leibundgut, M. / Boehringer, D. / Ban, N.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_163478 Switzerland
NCCR RNA and disease program, SNSF51NF40_141735 Switzerland
CitationJournal: Cell Rep / Year: 2017
Title: The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.
Authors: Jendrik Hentschel / Chloe Burnside / Ingrid Mignot / Marc Leibundgut / Daniel Boehringer / Nenad Ban /
Abstract: The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death ...The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
3: 50S ribosomal protein bL37
A: 23S rRNA
B: 5S rRNA
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: LSU ribosomal protein L28P
Z: 50S ribosomal protein L29
a: 50S ribosomal protein L30
b: 50S ribosomal protein L32
c: 50S ribosomal protein L33 1
d: 50S ribosomal protein L34
e: 50S ribosomal protein L35
f: 50S ribosomal protein L36
g: 50S ribosomal protein L31
BA: 16S rRNA
BB: Conserved domain protein
BC: 30S ribosomal protein S3
BD: 30S ribosomal protein S4
BE: 30S ribosomal protein S5
BF: 30S ribosomal protein S6
BG: 30S ribosomal protein S7
BH: 30S ribosomal protein S8
BI: 30S ribosomal protein S9
BJ: 30S ribosomal protein S10
BK: 30S ribosomal protein S11
BL: 30S ribosomal protein S12
BM: 30S ribosomal protein S13
BN: 30S ribosomal protein S14 type Z
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BQ: 30S ribosomal protein S17
BR: 30S ribosomal protein S18 2
BS: 30S ribosomal protein S19
BT: 30S ribosomal protein S20
BV: 30S ribosomal protein S2
BW: P/P-site Phe-tRNA(Phe)
BX: mRNA fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,322,204689
Polymers2,306,45557
Non-polymers15,748632
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area268650 Å2
ΔGint-2235 kcal/mol
Surface area826670 Å2
MethodPISA

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Components

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50S ribosomal protein ... , 31 types, 31 molecules 3CDEFGHIJKLMNOPQRSTUVWXZabcdefg

#1: Protein/peptide 50S ribosomal protein bL37 / / bl37


Mass: 2841.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QTP4
#4: 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)
References: UniProt: A0QSD4
#5: 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)
References: UniProt: A0QSD1
#6: 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)
References: UniProt: A0QSD2
#7: 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)
References: UniProt: A0QSG1
#8: 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)
References: UniProt: A0QSG4
#9: Protein 50S ribosomal protein L9 / / bL9


Mass: 15949.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 44-73 modeled as poly-alanine
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R7F6
#10: 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)
References: UniProt: A0QS62
#11: 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)
References: UniProt: A0QS45
#12: 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)
References: UniProt: A0QSP8
#13: 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)
References: UniProt: A0QSF9
#14: 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)
References: UniProt: I7G436, UniProt: A0QSG8*PLUS
#15: 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)
References: UniProt: A0QSD8
#16: 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)
References: UniProt: A0QSL9
#17: 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)
References: UniProt: A0QSG5
#18: 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)
References: UniProt: A0QV42
#19: 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)
References: UniProt: A0QYU6
#20: 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)
References: UniProt: A0R151
#21: 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)
References: UniProt: A0QSD6
#22: 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)
References: UniProt: A0QSD3
#23: Protein 50S ribosomal protein L24 / / uL24


Mass: 11228.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 48-55 not modeled
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG0
#24: Protein 50S ribosomal protein L25 / / bL25


Mass: 22571.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R3D2
#25: 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)
References: UniProt: A0R150
#27: 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)
References: UniProt: A0QSD9
#28: 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)
References: UniProt: A0QSG7
#29: 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)
References: UniProt: A0R3I9
#30: Protein 50S ribosomal protein L33 1 / Ribosome / bL33


Mass: 6468.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QS39
#31: 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)
References: UniProt: A0R7K0
#32: 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)
References: UniProt: A0QYU7
#33: 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)
References: UniProt: A0QSL4
#34: Protein 50S ribosomal protein L31 / / bL31


Mass: 8312.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: residues 49-55 not modeled, intersubunit bridge forming protein
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R215

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RNA chain , 5 types, 5 molecules ABBABWBX

#2: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 1012140.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: GenBank: 118168627
#3: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: GenBank: 118168627
#35: 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)
References: GenBank: 118168627
#56: RNA chain P/P-site Phe-tRNA(Phe)


Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Model and sequence adopted from Escherichia coli tRNA(Phe)
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
#57: RNA chain mRNA fragment


Mass: 1791.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)

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

#37: 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)
References: UniProt: A0QSD7
#38: 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)
References: UniProt: A0QSL7
#39: 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)
References: UniProt: A0QSG6
#40: 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)
References: UniProt: A0A0D6J3X3
#41: 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)
References: UniProt: A0QS97
#42: 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)
References: UniProt: A0QSG3
#43: 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)
References: UniProt: A0QSP9
#44: 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)
References: UniProt: A0QSD0
#45: 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)
References: UniProt: A0QSL6
#46: 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)
References: UniProt: A0QS96
#47: 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)
References: UniProt: A0QSL5
#48: Protein 30S ribosomal protein S14 type Z / Ribosome / uS14


Mass: 6976.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG2
#49: 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)
References: UniProt: A0QVQ3
#50: 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)
References: UniProt: A0QV37
#51: 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)
References: UniProt: A0QSE0
#52: Protein 30S ribosomal protein S18 2 / Ribosome / bS18


Mass: 9524.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R7F7
#53: 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)
References: UniProt: A0QSD5
#54: 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)
References: UniProt: A0R102
#55: 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)
References: UniProt: A0QVB8

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Protein / Protein/peptide , 2 types, 2 molecules YBB

#26: Protein LSU ribosomal protein L28P / bL28


Mass: 6891.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: I7FJ52, UniProt: A0QV03*PLUS
#36: Protein/peptide Conserved domain protein / Protein domain / bS22


Mass: 4164.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QR10

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Non-polymers , 3 types, 632 molecules

#58: Chemical...
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 625 / Source method: obtained synthetically / Formula: Mg
#59: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#60: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H11NO2
Details: Model and sequence adopted from Escherichia coli tRNA(Phe)
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)

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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: #1-#57 / Source: NATURAL
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 R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE-PROPANE / Humidity: 96 %

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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 / Calibrated magnification: 100719 X
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Details: FEI EPU data collection
Image scansMovie frames/image: 7

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Processing

EM software
IDNameVersionCategory
1EMAN Boxer1.9particle selection
4CTFFIND3CTF correction
9PHENIXmodel refinement
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
13RELION1.43D reconstruction
CTF correctionDetails: CTF correction in Relion / Type: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224584 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER

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