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- EMDB-8934: Cryo-EM Structure of Mycobacterium smegmatis C(minus) 30S ribosom... -

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Basic information

Entry
Database: EMDB / ID: EMD-8934
TitleCryo-EM Structure of Mycobacterium smegmatis C(minus) 30S ribosomal subunit with MPY
Map dataCryo-EM structure of Mycobacterium smegmatis C(minus) 30S ribosomal subunit with MPY
Sample
  • Complex: Mycobacterium smegmatis (Cminus) 70S with MPY
    • RNA: x 1 types
    • Protein or peptide: x 22 types
KeywordsHibernation factor complex / RIBOSOME
Function / homology
Function and homology information


small ribosomal subunit rRNA binding / regulation of translation / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding ...small ribosomal subunit rRNA binding / regulation of translation / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA 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 S14, bacterial/plastid / 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 S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / : / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S14
Similarity search - Domain/homology
30S ribosomal protein S6 / Conserved domain protein / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 ...30S ribosomal protein S6 / Conserved domain protein / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Ribosome hibernation promoting factor / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein bS18A / Small ribosomal subunit protein uS14A / 50S ribosomal protein L31
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria) / Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) / Mycobacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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)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, 2018-
Header (metadata) releaseSep 19, 2018-
Map releaseSep 19, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6dzk
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8934.png

Downloads & links

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Map

FileDownload / File: emd_8934.map.gz / Format: CCP4 / Size: 357 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Mycobacterium smegmatis C(minus) 30S ribosomal subunit with MPY
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.03
Minimum - Maximum-0.09889924 - 0.21140203
Average (Standard dev.)0.00025929944 (±0.0044560917)
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-0.0990.2110.000

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Supplemental data

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Sample components

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Entire : Mycobacterium smegmatis (Cminus) 70S with MPY

EntireName: Mycobacterium smegmatis (Cminus) 70S with MPY
Components
  • Complex: Mycobacterium smegmatis (Cminus) 70S with MPY
    • RNA: 16S rRNA
    • Protein or peptide: Conserved domain protein
    • Protein or peptide: 30S ribosomal protein S3
    • Protein or peptide: 30S ribosomal protein S4
    • Protein or peptide: 30S ribosomal protein S5
    • Protein or peptide: 30S ribosomal protein S6
    • Protein or peptide: 30S ribosomal protein S7
    • Protein or peptide: 30S ribosomal protein S8
    • Protein or peptide: 30S ribosomal protein S9
    • Protein or peptide: 30S ribosomal protein S10
    • Protein or peptide: 30S ribosomal protein S11
    • Protein or peptide: 30S ribosomal protein S12
    • Protein or peptide: 30S ribosomal protein S13
    • Protein or peptide: 30S ribosomal protein S15
    • Protein or peptide: 30S ribosomal protein S16
    • Protein or peptide: 30S ribosomal protein S17
    • Protein or peptide: 30S ribosomal protein S19
    • Protein or peptide: 30S ribosomal protein S20
    • Protein or peptide: 30S ribosomal protein S2
    • Protein or peptide: 30S ribosomal protein S18 1
    • Protein or peptide: Ribosome hibernation promoting factor
    • Protein or peptide: 30S ribosomal protein S14
    • Protein or peptide: 50S ribosomal protein L31

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Supramolecule #1: Mycobacterium smegmatis (Cminus) 70S with MPY

SupramoleculeName: Mycobacterium smegmatis (Cminus) 70S with MPY / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Mycobacterium smegmatis 30S ribosomal subunit with MPY
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria)

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Macromolecule #1: 16S rRNA

MacromoleculeName: 16S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 490.111719 KDa
SequenceString: UUUGGAGAGU UUGAUCCUGG CUCAGGACGA ACGCUGGCGG CGUGCUUAAC ACAUGCAAGU CGAACGGAAA GGCCCUUUCG GGGGUACUC GAGUGGCGAA CGGGUGAGUA ACACGUGGGU GAUCUGCCCU GCACUUUGGG AUAAGCCUGG GAAACUGGGU C UAAUACCG ...String:
UUUGGAGAGU UUGAUCCUGG CUCAGGACGA ACGCUGGCGG CGUGCUUAAC ACAUGCAAGU CGAACGGAAA GGCCCUUUCG GGGGUACUC GAGUGGCGAA CGGGUGAGUA ACACGUGGGU GAUCUGCCCU GCACUUUGGG AUAAGCCUGG GAAACUGGGU C UAAUACCG AAUACACCCU GCUGGUCGCA UGGCCUGGUA GGGGAAAGCU UUUGCGGUGU GGGAUGGGCC CGCGGCCUAU CA GCUUGUU GGUGGGGUGA UGGCCUACCA AGGCGACGAC GGGUAGCCGG CCUGAGAGGG UGACCGGCCA CACUGGGACU GAG AUACGG CCCAGACUCC UACGGGAGGC AGCAGUGGGG AAUAUUGCAC AAUGGGCGCA AGCCUGAUGC AGCGACGCCG CGUG AGGGA UGACGGCCUU CGGGUUGUAA ACCUCUUUCA GCACAGACGA AGCGCAAGUG ACGGUAUGUG CAGAAGAAGG ACCGG CCAA CUACGUGCCA GCAGCCGCGG UAAUACGUAG GGUCCGAGCG UUGUCCGGAA UUACUGGGCG UAAAGAGCUC GUAGGU GGU UUGUCGCGUU GUUCGUGAAA ACUCACAGCU UAACUGUGGG CGUGCGGGCG AUACGGGCAG ACUAGAGUAC UGCAGGG GA GACUGGAAUU CCUGGUGUAG CGGUGGAAUG CGCAGAUAUC AGGAGGAACA CCGGUGGCGA AGGCGGGUCU CUGGGCAG U AACUGACGCU GAGGAGCGAA AGCGUGGGGA GCGAACAGGA UUAGAUACCC UGGUAGUCCA CGCCGUAAAC GGUGGGUAC UAGGUGUGGG UUUCCUUCCU UGGGAUCCGU GCCGUAGCUA ACGCAUUAAG UACCCCGCCU GGGGAGUACG GCCGCAAGGC UAAAACUCA AAGGAAUUGA CGGGGGCCCG CACAAGCGGC GGAGCAUGUG GAUUAAUUCG AUGCAACGCG AAGAACCUUA C CUGGGUUU GACAUGCACA GGACGCCGGC AGAGAUGUCG GUUCCCUUGU GGCCUGUGUG CAGGUGGUGC AUGGCUGUCG UC AGCUCGU GUCGUGAGAU GUUGGGUUAA GUCCCGCAAC GAGCGCAACC CUUGUCUCAU GUUGCCAGCA CGUUAUGGUG GGG ACUCGU GAGAGACUGC CGGGGUCAAC UCGGAGGAAG GUGGGGAUGA CGUCAAGUCA UCAUGCCCCU UAUGUCCAGG GCUU CACAC AUGCUACAAU GGCCGGUACA AAGGGCUGCG AUGCCGUGAG GUGGAGCGAA UCCUUUCAAA GCCGGUCUCA GUUCG GAUC GGGGUCUGCA ACUCGACCCC GUGAAGUCGG AGUCGCUAGU AAUCGCAGAU CAGCAACGCU GCGGUGAAUA CGUUCC CGG GCCUUGUACA CACCGCCCGU CACGUCAUGA AAGUCGGUAA CACCCGAAGC CGGUGGCCUA ACCCUUGUGG AGGGAGC CG UCGAAGGUGG GAUCGGCGAU UGGGACGAAG UCGUAACAAG GUAGCCGUAC CGGAAGGUGC GGCUGGAUC

GENBANK: GENBANK: CP000480.1

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Macromolecule #2: Conserved domain protein

MacromoleculeName: Conserved domain protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 4.033104 KDa
SequenceString:
GSVIKKRRKR MSKKKHRKLL RRTRVQRRKL GK

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Macromolecule #3: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 30.191227 KDa
SequenceString: MGQKINPHGF RLGITTEWKS RWYADKQYKD YVKEDVAIRK LLATGLERAG IADVEIERTR DRVRVDIHTA RPGIVIGRRG TEADRIRAD LEKLTGKQVQ LNILEVKNPE SQAQLVAQGV AEQLSNRVAF RRAMRKAIQS AMRQPNVKGI RVQCSGRLGG A EMSRSEFY ...String:
MGQKINPHGF RLGITTEWKS RWYADKQYKD YVKEDVAIRK LLATGLERAG IADVEIERTR DRVRVDIHTA RPGIVIGRRG TEADRIRAD LEKLTGKQVQ LNILEVKNPE SQAQLVAQGV AEQLSNRVAF RRAMRKAIQS AMRQPNVKGI RVQCSGRLGG A EMSRSEFY REGRVPLHTL RADIDYGLYE AKTTFGRIGV KVWIYKGDIV GGKRELAAAA PASDRPRRER PSGTRPRRSG SA GTTATST EAGRAATSDA PAAGTAAAAE APAESTES

UniProtKB: Small ribosomal subunit protein uS3

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Macromolecule #4: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 23.415787 KDa
SequenceString: MARYTGPATR KSRRLGVDLV GGDQSFEKRP YPPGQHGRAR IKESEYRQQL QEKQKARFSY GVMEKQFRRY YEEANRQPGK TGDNLLRIL ESRLDNVVYR AGLARTRRMA RQLVSHGHFL VNGVKVDIPS YRVSQYDIID VKEKSLNTLP FQIARETAGE R PIPSWLQV ...String:
MARYTGPATR KSRRLGVDLV GGDQSFEKRP YPPGQHGRAR IKESEYRQQL QEKQKARFSY GVMEKQFRRY YEEANRQPGK TGDNLLRIL ESRLDNVVYR AGLARTRRMA RQLVSHGHFL VNGVKVDIPS YRVSQYDIID VKEKSLNTLP FQIARETAGE R PIPSWLQV VGERQRILVH QLPERAQIDV PLTEQLIVEL YSK

UniProtKB: Small ribosomal subunit protein uS4

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Macromolecule #5: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 21.814893 KDa
SequenceString: AEQAGAGSAQ DNRGGRGRRD DRGGRGRDGG DKSNYIERVV SINRVSKVVK GGRRFSFTAL VIVGDGKGMV GVGYGKAKEV PAAIAKGVE EARKNFFRVP LIGSTITHPV QGEAAAGVVM LRPASPGTGV IAGGAARAVL ECAGVHDILA KSLGSDNAIN V VHATVAAL ...String:
AEQAGAGSAQ DNRGGRGRRD DRGGRGRDGG DKSNYIERVV SINRVSKVVK GGRRFSFTAL VIVGDGKGMV GVGYGKAKEV PAAIAKGVE EARKNFFRVP LIGSTITHPV QGEAAAGVVM LRPASPGTGV IAGGAARAVL ECAGVHDILA KSLGSDNAIN V VHATVAAL KLLQRPEEVA ARRGLPIEDV APAGMLKARR ESEALAAAAA REGSA

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #6: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 10.991637 KDa
SequenceString:
MRPYEIMVIL DPTLDERTVA PSLETFLNVI RKDGGTVDKV DIWGRRRLAY EIAKHAEGIY AVIDVKAEPA TVSELDRQLN LNESVLRTK VLRTDKH

UniProtKB: 30S ribosomal protein S6

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Macromolecule #7: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 17.660375 KDa
SequenceString:
MPRKGPAPKR PLVNDPVYGS QLVTQLVNKV LLEGKKSLAE RIVYGALEQA REKTGTDPVV TLKRALDNVK PALEVRSRRV GGATYQVPV EVRPDRSTTL ALRWLVNFSR QRREKTMVER LANEILDASN GLGASVKRRE DTHKMAEANR AFAHYRW

UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #8: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 14.361442 KDa
SequenceString:
TMTDPIADFL TRLRNANSAY HDEVTLPHSK LKANIAEILK REGYISDYRT EDARVGKSLV VQLKYGPSRE RSIAGLRRVS KPGLRVYAK STNLPRVLGG LGVAIISTSS GLLTDRQAAR QGVGGEVLAY VW

UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #9: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 16.794365 KDa
SequenceString:
MTDVTETEVV TESAEPREPV IIDRPIQTVG RRKEAVVRVR LVPGTGQFNL DGRTLENYFP NKVHQQLIKA PLVTVDRVDQ FDIYAHLDG GGPSGQAGAL RLAIARALIL VQPEDRPALK KAGFLTRDPR AIERKKYGLK KARKAPQYSK R

UniProtKB: Small ribosomal subunit protein uS9

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Macromolecule #10: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 11.454313 KDa
SequenceString:
MAGQKIRIRL KAYDHEAIDA SARKIVETVT RTGASVVGPV PLPTEKNVYC VIRSPHKYKD SREHFEMRTH KRLIDILDPT PKTVDALMR IDLPASVDVN IQ

UniProtKB: Small ribosomal subunit protein uS10

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Macromolecule #11: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 14.671762 KDa
SequenceString:
MAQAKKGGTA AKKGQKTRRR EKKNVPHGAA HIKSTFNNTI VSITDPQGNV IAWASSGHVG FKGSRKSTPF AAQLAAENAA RKAQEHGVK KVDVFVKGPG SGRETAIRSL QAAGLEVGTI SDVTPQPHNG CRPPKRRRV

UniProtKB: Small ribosomal subunit protein uS11

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Macromolecule #12: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 13.896366 KDa
SequenceString:
MPTIQQLVRK GRRDKIAKVK TAALKGSPQR RGVCTRVYTT TPKKPNSALR KVARVKLTSQ VEVTAYIPGE GHNLQEHSMV LVRGGRVKD LPGVRYKIIR GSLDTQGVKN RKQARSRYGA KKEKS

UniProtKB: Small ribosomal subunit protein uS12

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Macromolecule #13: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 14.249619 KDa
SequenceString:
MARLVGVDLP RDKRMEIALT YIYGIGRTRS NEILAATGID KNMRTKDLTD DQVTVLRDYI EGNLKVEGDL RREVQADIRR KIEIGCYQG LRHRRGLPVR GQRTKTNART RKGPKRTIAG KKKAR

UniProtKB: Small ribosomal subunit protein uS13

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Macromolecule #14: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 10.2369 KDa
SequenceString:
ALTAEQKKEI LGQYGLHDTD TGSPEAQVAL LTKRIQDLTE HLKVHKHDHH SRRGLLLLVG RRRRLLKYVA QVDVARYRSL IERLGLRR

UniProtKB: Small ribosomal subunit protein uS15

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Macromolecule #15: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 16.795207 KDa
SequenceString:
MAVKIKLTRL GKIRNPQYRI IVADARTRRD GRAIEVIGRY HPKEEPSLIQ IDSERAQYWL GVGAQPTEPV LALLKITGDW QKFKGLPGA EGTLKVKEPK PSKLDLFNAA LAEAESGTTA AATTPKKKKA PKKDEAAEAP AEAAEAPAEA ADAASES

UniProtKB: Small ribosomal subunit protein bS16

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Macromolecule #16: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 11.127002 KDa
SequenceString:
MADQKGPKYT PAAEKPRGRR KTAIGYVVSD KMQKTIVVEL EDRKSHPLYG KIIRTTKKVK AHDENGEAGI GDRVSLMETR PLSATKRWR LVEILEKAK

UniProtKB: Small ribosomal subunit protein uS17

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Macromolecule #17: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 10.800602 KDa
SequenceString:
MPRSLKKGPF VDDHLLKKVD VQNEKNTKQV IKTWSRRSTI IPDFIGHTFA VHDGRKHVPV FVTEAMVGHK LGEFAPTRTF KGHIKDDRK SKRR

UniProtKB: Small ribosomal subunit protein uS19

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Macromolecule #18: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 9.556104 KDa
SequenceString:
MANIKSQIKR IRTNERRRLR NQSVKSSLRT AIRGFREAVD AGDKDKASEL LHATSRKLDK AASKGVIHPN QAANKKSALA LALNKL

UniProtKB: Small ribosomal subunit protein bS20

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Macromolecule #19: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 30.14523 KDa
SequenceString: MAVVTMKQLL DSGAHFGHQT RRWNPKMKRF IFTDRNGIYI IDLQQTLTYI DKAYEFVKET VAHGGTVLFV GTKKQAQESI AEEATRVGM PYVNQRWLGG MLTNFSTVHK RLQRLKELEA MEQTGGFEGR TKKEILMLTR EKNKLERSLG GIRDMQKVPS A VWVVDTNK ...String:
MAVVTMKQLL DSGAHFGHQT RRWNPKMKRF IFTDRNGIYI IDLQQTLTYI DKAYEFVKET VAHGGTVLFV GTKKQAQESI AEEATRVGM PYVNQRWLGG MLTNFSTVHK RLQRLKELEA MEQTGGFEGR TKKEILMLTR EKNKLERSLG GIRDMQKVPS A VWVVDTNK EHIAVGEARK LGIPVIAILD TNCDPDVVDY PIPGNDDAIR SAALLTKVIA SAVAEGLQAR AGQGSGEKPA EG AEPLAEW EQELLAGATA GAADASAEGA AAPESSTDAS

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #20: 30S ribosomal protein S18 1

MacromoleculeName: 30S ribosomal protein S18 1 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 9.606369 KDa
SequenceString:
MMAVKKSRKR TAATELKKPR RNQLEALGVT TIDYKDVAVL RTFLSERGKI RSRHVTGLTP QQQRQVATAI KNAREMALLP MAGPR

UniProtKB: Small ribosomal subunit protein bS18A

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Macromolecule #21: Ribosome hibernation promoting factor

MacromoleculeName: Ribosome hibernation promoting factor / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 26.447615 KDa
SequenceString: MSSHSMDSSR TMVVEDDRES TAGTTPERPH AEVVVKGRNV EVPDHFRTYV SEKLSRLERF DKTIYLFDVE LDHERNRRQR KNCQHVEIT ARGRGPVVRG EACADSFYTA FESAVQKLEG RLRRAKDRRK IHYGDKTPVS LAEATAKDPL AGLDVSREDG E ARYNDGVA ...String:
MSSHSMDSSR TMVVEDDRES TAGTTPERPH AEVVVKGRNV EVPDHFRTYV SEKLSRLERF DKTIYLFDVE LDHERNRRQR KNCQHVEIT ARGRGPVVRG EACADSFYTA FESAVQKLEG RLRRAKDRRK IHYGDKTPVS LAEATAKDPL AGLDVSREDG E ARYNDGVA EHEPGRIVRI KDHPATPMTV DDALYEMELV GHDFFLFHDK ETDRPSVVYR RHAFDYGLIR LA

UniProtKB: Ribosome hibernation promoting factor

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Macromolecule #22: 30S ribosomal protein S14

MacromoleculeName: 30S ribosomal protein S14 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 11.66153 KDa
SequenceString:
AKKSKIVKNE QRRELVQRYA ERRAELKRTI RDPASSPERR AAAVSALQRL PRDSSPVRLR NRDVVDGRPR GHLRKFGLSR VRVREMAHR GELPGVRKAS W

UniProtKB: Small ribosomal subunit protein uS14A

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Macromolecule #23: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 9.141198 KDa
SequenceString:
MKPGIHPDYH PVVFQDAATG AQFLTRSTAT STRTIEWPTP SGPKTYPLIV VDVTSDSHPF WTGSARHIDS AGQVEKFRRR YG

UniProtKB: 50S ribosomal protein L31

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridSupport film - Material: CARBON / Support film - topology: CONTINUOUS / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 67.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 205510
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5o61

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 66840
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.01)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 10 / Avg.num./class: 66840 / Software - Name: RELION (ver. 2.01)
Software - details: Relion used for image processing and Refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6dzk:
Cryo-EM Structure of Mycobacterium smegmatis C(minus) 30S ribosomal subunit with MPY

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