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- EMDB-8937: Cryo-EM Structure of Mycobacterium smegmatis C(minus) 50S ribosom... -

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Basic information

Entry
Database: EMDB / ID: EMD-8937
TitleCryo-EM Structure of Mycobacterium smegmatis C(minus) 50S ribosomal subunit
Map data
SampleMycobacterium smegmatis C(minus) 70S ribosome with MPY:
(nucleic-acidNucleic acid) x 2 / (50S ribosomal protein ...) x 31 / Uncharacterized protein
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
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 L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily ...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 L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L11, bacterial-type / Ribosomal protein L16 signature 1. / Ribosomal protein L6 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L17 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L10 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10P / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, N-terminal / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / 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 L35, conserved site / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L35 signature. / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L34 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L18, bacterial-type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L6, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L36 / Ribosomal protein L14P, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L35 / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L20 / L28p-like / Ribosomal L32p protein family / Ribosomal protein L30, bacterial-type / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L16 / Ribosomal protein L20, C-terminal / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L20 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L32p / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L17
Similarity search - Domain/homology
50S ribosomal protein L21 / Uncharacterized protein / 50S ribosomal protein L19 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 50S ribosomal protein L27 / 50S ribosomal protein L32 / 50S ribosomal protein L25 / 50S ribosomal protein L17 / 50S ribosomal protein L33 2 ...50S ribosomal protein L21 / Uncharacterized protein / 50S ribosomal protein L19 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 50S ribosomal protein L27 / 50S ribosomal protein L32 / 50S ribosomal protein L25 / 50S ribosomal protein L17 / 50S ribosomal protein L33 2 / 50S ribosomal protein L28 / 50S ribosomal protein L31 / 50S ribosomal protein L9 / 50S ribosomal protein L34 / 50S ribosomal protein L13 / 50S ribosomal protein L30 / 50S ribosomal protein L36 / 50S ribosomal protein L15 / 50S ribosomal protein L6 / 50S ribosomal protein L5 / 50S ribosomal protein L24 / 50S ribosomal protein L14 / 50S ribosomal protein L29 / 50S ribosomal protein L16 / 50S ribosomal protein L22 / 50S ribosomal protein L2 / 50S ribosomal protein L23 / 50S ribosomal protein L4 / 50S ribosomal protein L3 / 50S ribosomal protein L10 / 50S ribosomal protein L11 / 50S ribosomal protein L18
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria) / Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsSharma MR / Li Y / Korripella R / Yang Y / Kaushal PS / Lin Q / Wade JT / Gray AG / Derbyshire KM / Agrawal RK / Ojha A
Funding support United States, 3 items
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)AI097191 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI107595 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, 2018-
Header (metadata) releaseOct 3, 2018-
Map releaseOct 3, 2018-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6dzp
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8937.map.gz / Format: CCP4 / Size: 357 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 454 pix.
= 485.78 Å
1.07 Å/pix.
x 454 pix.
= 485.78 Å
1.07 Å/pix.
x 454 pix.
= 485.78 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.033 / Movie #1: 0.033
Minimum - Maximum-0.19380207 - 0.29954392
Average (Standard dev.)0.00042198613 (±0.0072495956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions454454454
Spacing454454454
CellA=B=C: 485.78003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z454454454
origin x/y/z0.0000.0000.000
length x/y/z485.780485.780485.780
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS454454454
D min/max/mean-0.1940.3000.000

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Supplemental data

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Sample components

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Entire Mycobacterium smegmatis C(minus) 70S ribosome with MPY

EntireName: Mycobacterium smegmatis C(minus) 70S ribosome with MPY
Details: Cryo-EM structure of Mycobacterium smegmatis C (minus) 50S ribosomal subunit
Number of Components: 35

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Component #1: protein, Mycobacterium smegmatis C(minus) 70S ribosome with MPY

ProteinName: Mycobacterium smegmatis C(minus) 70S ribosome with MPY
Details: Cryo-EM structure of Mycobacterium smegmatis C (minus) 50S ribosomal subunit
Recombinant expression: No
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Component #2: nucleic-acid, 23S rRNA

nucleic acidName: 23S rRNA23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AAGUGUUUAA GGGCGCAUGG UGGAUGCCUU GGCACUGGGA GCCGAUGAAG GACGUAGGAG GCUGCGAUAA GCCUCGGGGA GCUGUCAACC GAGCGUUGAU CCGAGGAUGU CCGAAUGGGG AAACCCGGCA CGAGUGAUGU CGUGUCACCA GGCGCUGAAU AUAUAGGCGU ...Sequence:
AAGUGUUUAA GGGCGCAUGG UGGAUGCCUU GGCACUGGGA GCCGAUGAAG GACGUAGGAG GCUGCGAUAA GCCUCGGGGA GCUGUCAACC GAGCGUUGAU CCGAGGAUGU CCGAAUGGGG AAACCCGGCA CGAGUGAUGU CGUGUCACCA GGCGCUGAAU AUAUAGGCGU CUGGGGGGAA CGCGGGGAAG UGAAACAUCU CAGUACCCGU AGGAAGAGAA AACAAAAUGU GAUUCCGUGA GUAGUGGCGA GCGAAAGCGG AGGAUGGCUA AACCGUAUGC AUGUGAUACC GGGUAGGGGU UGUGUGUGCG GGGUUGUGGG ACCUAUCUUU CCGGCUCUAC CUGGCUGGAG GGCAGUGAGA AAAUGUUGUG GUUAGCGGAA AUGGCUUGGG AUGGCCUGCC GUAGACGGUG AGAGCCCGGU ACGUGAAAAC CCGACGUCUG UCUUGAUGGU GUUCCCGAGU AGCAGCGGGC CCGUGGAAUC UGCUGUGAAU CUGCCGGGAC CACCCGGUAA GCCUGAAUAC UUCCCAGUGA CCGAUAGCGG AUUAGUACCG UGAGGGAAUG GUGAAAAGUA CCCCGGGAGG GGAGUGAAAG AGUACCUGAA ACCGUGCGCU UACAAUCCGU CAGAGCCCUC GACGUGUCGU GGGGUGAUGG CGUGCCUUUU GAAGAAUGAG CCUGCGAGUC AGGGACAUGU CGCGAGGUUA ACCCGGGUGG GGUAGCCGCA GCGAAAGCGA GUCUGAAUAG GGCGUAUCCA CACAAGAGUG UGUGGUGUAG UGGUGUGUUC UGGACCCGAA GCGGAGUGAU CUACCCAUGG CCAGGGUGAA GCGCGGGUAA GACCGCGUGG AGGCCCGAAC CCACUUAGGU UGAAGACUGA GGGGAUGAGC UGUGGGUAGG GGUGAAAGGC CAAUCAAACU CCGUGAUAGC UGGUUCUCCC CGAAAUGCAU UUAGGUGCAG CGUCGCAUGU UUCUUGCCGG AGGUAGAGCU ACUGGAUGGC CGAUGGGCCC CACAGGGUUA CUGACGUCAG CCAAACUCCG AAUGCCGGUA AGUCCAAGAG UGCGGCAGUG AGACGGCGGG GGAUAAGCUC CGUGCGUCGA GAGGGAAACA GCCCAGAUCG CCGGCUAAGG CCCCUAAGCG UGUGCUAAGU GGAAAAGGAU GUGCAGUCGC GAAGACAACC AGGAGGUUGG CUUAGAAGCA GCCACCCUUG AAAGAGUGCG UAAUAGCUCA CUGGUCAAGU GAUUGUGCGC CGAUAAUGUA GCGGGGCUCA AGCACACCGC CGAAGCCGCG GCAGCCAACG UGUUGGCUGG GUAGGGGAGC GUCCUGCAUC CGGUGAAGCC GCCGAGUGAU CGAGUGGUGG AGGGUGUGGG AGUGAGAAUG CAGGCAUGAG UAGCGAUUAG GCAAGUGAGA ACCUUGCCCG CCGAAAGACC AAGGGUUCCU GGGCCAGGCC AGUCCGCCCA GGGUGAGUCG GGACCUAAGG CGAGGCCGAC AGGCGUAGUC GAUGGACAAC GGGUUGAUAU UCCCGUACCC GUGUAUGUGC GUCCAUGAUG AAUCAGCGGU ACUAACCAUC CAAAACCACC GUGACCGCAC CUUUCGGGGU GUGGCGUUGG UGGGGCUGCA UGGGACCUUC GUUGGUAGUA GUCAAGCGAU GGGGUGACGC AGGAAGGUAG CCGUACCGGU CAGUGGUAAU ACCGGGGUAA GCCUGUAGGG AGUCAGAUAG GUAAAUCCGU CUGGCAUAUA UCCUGAGAGG UGAUGCAUAG CCGAGUGAGG CGAAUUCGGU GAUCCUAUGC UGCCGAGAAA AGCCUCUAGC GAGGACAUAC ACGGCCCGUA CCCCAAACCA ACACAGGUGG UCAGGUAGAG AAUACUAAGG CGUACGAGUG AACUAUGGUU AAGGAACUCG GCAAAAUGCC CCCGUAACUU CGGGAGAAGG GGGACCCACA UGGCGUGUAA GCCUUUACGG CCCAAGCGUG AGUGGGUGGC ACAAACCAGU GAGAAGCGAC UGUUUACUAA AAACACAGGU CCGUGCGAAG UCGCAAGACG AUGUAUACGG ACUGACGCCU GCCCGGUGCU GGAAGGUUAA GAGGACCCGU UAACUCCCUU UGGGGGUGAA GCGGAGAAUU UAAGCCCCAG UAAACGGCGG UGGUAACUAU AACCAUCCUA AGGUAGCGAA AUUCCUUGUC GGGUAAGUUC CGACCUGCAC GAAUGGCGUA ACGACUUCUC AACUGUCUCA ACCAUAGACU CGGCGAAAUU GCACUACGAG UAAAGAUGCU CGUUACGCGC GGCAGGACGA AAAGACCCCG GGACCUUCAC UACAACUUGG UAUUGGUGCU CGAUACGGUU UGUGUAGGAU AGGUGGGAGA CUGUGAAGCU CACACGCCAG UGUGGGUGGA GUCGUUGUUG AAAUACCACU CUGAUCGUAU UGGGCCUCUA ACCUCGGACC GUAUAUCCGG UUCAGGGACA GUGCCUGGUG GGUAGUUUAA CUGGGGCGGU UGCCUCCUAA AAUGUAACGG AGGCGCCCAA AGGUUCCCUC AACCUGGACG GCAAUCAGGU GUUGAGUGUA AGUGCACAAG GGAGCUUGAC UGCGAGACGG ACAUGUCGAG CAGGGACGAA AGUCGGGACU AGUGAUCCGG CACCUCUGAG UGGAAGGGGU GUCGCUCAAC GGAUAAAAGG UACCCCGGGG AUAACAGGCU GAUCUUCCCC AAGAGUCCAU AUCGACGGGA UGGUUUGGCA CCUCGAUGUC GGCUCGUCGC AUCCUGGGGC UGGAGCAGGU CCCAAGGGUU GGGCUGUUCG CCCAUUAAAG CGGCACGCGA GCUGGGUUUA GAACGUCGUG AGACAGUUCG GUCUCUAUCC GCCGCGCGCG UCAGAAGCUU GAGGAAACCU GUCCCUAGUA CGAGAGGACC GGGACGGACG AACCUCUGGU AUACCAGUUG UCCCACCAGG GGCACGGCUG GAUAGCCACG UUCGGACAGG AUAACCGCUG AAAGCAUCUA AGCGGGAAAC CUCUUCCAAG ACCAGGCUUC UCACCCUCUA GGAGGGAUAA GGCCCCCCGC AGACCACGGG AUUGAUAGAC CAGACCUGGA AGCCUAGUAA UAGGUGCAGG GAACUGGCAC UAACCGGCCG AAAACUUAC
MassTheoretical: 1.01183475 MDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155

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Component #3: nucleic-acid, 5S rRNA

nucleic acidName: 5S rRNA5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUACGGCGG UCCAUAGCGG CAGGGAAACG CCCGGUCCCA UCCCGAACCC GGAAGCUAAG CCUGCCAGCG CCGAUGAUAC UACCCAUCCG GGUGGAAAAG UAGGACACCG CCGAACAC
MassTheoretical: 38.061816 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155

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Component #4: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.425945 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #5: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.011393 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #6: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.789754 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #7: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.021129 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #8: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.483361 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #9: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.949253 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #10: protein, 50S ribosomal protein L10

ProteinName: 50S ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.035736 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #11: protein, 50S ribosomal protein L11

ProteinName: 50S ribosomal protein L11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.023374 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #12: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.015493 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #13: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.400625 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #14: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.602244 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #15: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.77424 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #16: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.892246 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #17: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.580531 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #18: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.892806 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #19: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.494693 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #20: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.924698 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #21: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.222404 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #22: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.916641 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #23: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.228946 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #24: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.571078 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #25: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.249582 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #26: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.790895 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #27: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.022147 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #28: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.467719 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #29: protein, 50S ribosomal protein L33 2

ProteinName: 50S ribosomal protein L33 2Ribosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.61564 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #30: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.52258 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #31: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.298505 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #32: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.341277 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #33: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.141198 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #34: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.925234 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155

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Component #35: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.710179 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.5
Support filmunspecified
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
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 67 e/Å2 / Illumination Mode: OTHER
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C2 (2 fold cyclic) / Number of Projections: 66840
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.42 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Output model

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