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- EMDB-13285: free 50S in untreated Mycoplasma pneumoniae cells -

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Basic information

Entry
Database: EMDB / ID: EMD-13285
Titlefree 50S in untreated Mycoplasma pneumoniae cells
Map data
Sample
  • Cell: Cryo-electron tomograms of untreated Mycoplasma pneumoniae cells
    • Protein or peptide: x 29 types
    • RNA: x 2 types
KeywordsIn-cell cryo-electron tomography / sub-tomogram analysis / ribosome / translation intermediate state
Function / homology
Function and homology information


large ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation ...large ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / cytoplasm
Similarity search - Function
Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / : / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily ...Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / : / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein 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 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/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / 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 L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L16 / : / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L21 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family
Similarity search - Domain/homology
Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL9 ...Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesMycoplasma pneumoniae M129 (bacteria) / Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 9.2 Å
AuthorsXue L / Lenz S
Funding support Germany, United Kingdom, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)760067 Germany
German Research Foundation (DFG)426290502 Germany
Wellcome Trust103139 United Kingdom
Wellcome Trust203149 United Kingdom
Citation
Journal: Nature / Year: 2022
Title: Visualizing translation dynamics at atomic detail inside a bacterial cell.
Authors: Liang Xue / Swantje Lenz / Maria Zimmermann-Kogadeeva / Dimitry Tegunov / Patrick Cramer / Peer Bork / Juri Rappsilber / Julia Mahamid /
Abstract: Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to ...Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to visualize the structural dynamics of translation inside the bacterium Mycoplasma pneumoniae. To interpret the functional states in detail, we first obtain a high-resolution in-cell average map of all translating ribosomes and build an atomic model for the M. pneumoniae ribosome that reveals distinct extensions of ribosomal proteins. Classification then resolves 13 ribosome states that differ in their conformation and composition. These recapitulate major states that were previously resolved in vitro, and reflect intermediates during active translation. On the basis of these states, we animate translation elongation inside native cells and show how antibiotics reshape the cellular translation landscapes. During translation elongation, ribosomes often assemble in defined three-dimensional arrangements to form polysomes. By mapping the intracellular organization of translating ribosomes, we show that their association into polysomes involves a local coordination mechanism that is mediated by the ribosomal protein L9. We propose that an extended conformation of L9 within polysomes mitigates collisions to facilitate translation fidelity. Our work thus demonstrates the feasibility of visualizing molecular processes at atomic detail inside cells.
#1: Journal: Biorxiv / Year: 2021
Title: Visualizing translation dynamics at atomic detail inside a bacterial cell
Authors: Xue L / Lenz S / Zimmermann-Kogadeeva M / Tegunov D / Cramer P / Bork P / Rappsilber J / Mahamid J
History
DepositionJul 30, 2021-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13285.png

Downloads & links

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Map

FileDownload / File: emd_13285.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
2.4 Å/pix.
x 200 pix.
= 480. Å		2.4 Å/pix.
x 200 pix.
= 480. Å		2.4 Å/pix.
x 200 pix.
= 480. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.41
Minimum - Maximum-0.42319766 - 1.4191148
Average (Standard dev.)0.015718902 (±0.099521585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 480.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_13285_msk_1.map
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Half map: #2

Fileemd_13285_half_map_1.map
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Half map: #1

Fileemd_13285_half_map_2.map
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Sample components

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Entire : Cryo-electron tomograms of untreated Mycoplasma pneumoniae cells

EntireName: Cryo-electron tomograms of untreated Mycoplasma pneumoniae cells
Components
  • Cell: Cryo-electron tomograms of untreated Mycoplasma pneumoniae cells
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L36
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L9
    • Protein or peptide: 50S ribosomal protein L10
    • Protein or peptide: 50S ribosomal protein L11
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L16
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L31
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33 1
    • RNA: 23S ribosomal RNA
    • RNA: 5S ribosomal RNA

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Supramolecule #1: Cryo-electron tomograms of untreated Mycoplasma pneumoniae cells

SupramoleculeName: Cryo-electron tomograms of untreated Mycoplasma pneumoniae cells
type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Ribosome sub-tomograms extracted in silico from tomograms of intact cell, refinement with a 70S mask
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria)

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Macromolecule #1: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 5.616773 KDa
SequenceString:
MKRTYQPSKL KRAKTHGFLA RMATASGRKV LKLRRKKQRA QLTVSSER

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #2: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 6.793135 KDa
SequenceString:
MKVKSAAKKR FKLTKSGQIK RKHAYTSHLA PHKTTKQKRH LRKQGTVSAS DFKRIGNLI

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #3: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 4.400488 KDa
SequenceString:
MKVRASVKPI CKDCKIIKRH QIVRVICKTQ KHKQRQG

UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #4: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 31.966871 KDa
SequenceString: MPIKKIISRS NSGIHHSTVI DYKKLLTTNK NKPEKSLLVT LKKHGGRNNQ GKITVRHQGG RNKRKYRIID FKRTHYDNIE ATVKSIEYD PNRSCFVSLI TYANGAKSYI ISPDGIKVGD KILASEHPID IKPGFSMPLA FIPEGTQVHN IELHPKGGGQ I ARSAGSYA ...String:
MPIKKIISRS NSGIHHSTVI DYKKLLTTNK NKPEKSLLVT LKKHGGRNNQ GKITVRHQGG RNKRKYRIID FKRTHYDNIE ATVKSIEYD PNRSCFVSLI TYANGAKSYI ISPDGIKVGD KILASEHPID IKPGFSMPLA FIPEGTQVHN IELHPKGGGQ I ARSAGSYA RILGQDETGK YVILQLLSGE TRKFLKECRA TVGVVSNLDH NLVVIGKAGR NRHRGIRPTV RGSAMNPNDH PH GGGEGRS PVGRDAPRTP WGKRHMGVKT RNMKKASTNL IIRNRKGEQY

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #5: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 31.298172 KDa
SequenceString: MEIRGIFGVK VGMSQVFTTN NERLPITVIY CEPNQVAGVK TEAKDKYSAT LLSFDTVENK KLNKPQQGFF EKNNLKPTKH LQEIRNMTG FEMGQQITPQ NLFQVGEYVD VSAISKGRGF TGAIKRWNFK IGPLGHGAGY PHRFQGSVQA GRGGASAQRV F KGKKMSGH ...String:
MEIRGIFGVK VGMSQVFTTN NERLPITVIY CEPNQVAGVK TEAKDKYSAT LLSFDTVENK KLNKPQQGFF EKNNLKPTKH LQEIRNMTG FEMGQQITPQ NLFQVGEYVD VSAISKGRGF TGAIKRWNFK IGPLGHGAGY PHRFQGSVQA GRGGASAQRV F KGKKMSGH YGHEKVTVQN LRIVGFDEAN MLVLVSGAIA GPEGGVVLIR TAKKKPGVVK PIELAVQTEK APEAKPAKLS KK KQAKELA KAQAANQQTV EAKVDTPVVE PKPTEVKKAA PVVEKKGEDK

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #6: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 23.632572 KDa
SequenceString: MAKLKLIKID GSFETEPVKL SPGLIAKELK QQPVFDAVLV EQASWRQGTH SILTKGEVRG GGKKPYKQKH TGKARQGSTR NPHFVGGGI VFGPKPNRNY SLKLNKKAHT AALHTVWSEK LASDNTHLVD QNLFNKTEGK TKVMMQFLKS AKLLDKNVLF V VNTLNTNL ...String:
MAKLKLIKID GSFETEPVKL SPGLIAKELK QQPVFDAVLV EQASWRQGTH SILTKGEVRG GGKKPYKQKH TGKARQGSTR NPHFVGGGI VFGPKPNRNY SLKLNKKAHT AALHTVWSEK LASDNTHLVD QNLFNKTEGK TKVMMQFLKS AKLLDKNVLF V VNTLNTNL EQSTSNIKNV QVKHLDKVSV RDLMLANALL VEKEVLKALE GKFK

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #7: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 20.270834 KDa
SequenceString:
MNNLKAHYQK TIAKELQKSF AFSSIMQVPR LEKIVINMGV GDAIRDSKFL ESALNELHLI SGQKPVATKA KNAISTYKLR AGQLIGCKV TLRGERMWAF LEKLIYVALP RVRDFRGLSL KSFDGRGNYT IGIKEQIIFP EIVYDDIKRI RGFDVTLVTS T NKDSEALA LLRALNLPLV KG

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #8: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 20.624062 KDa
SequenceString:
MSKIGNRTIT LDPAKVNLNF QKDHIAVKGP LGQIELKLPP NLPLKFELKD NNLQITRNNE LKQSKIFHGT YNALITNAII GVTQGFEKK LRLVGVGYRA NVEGETLNLQ LGYSHPIKEK IPKGLTVKVE KNTEITISGI SKELVGQFAT EVRKWRKPEP Y KGKGVLYF DEVIVRKAGK TAEGKK

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #9: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129
Molecular weightTheoretical: 17.185037 KDa
SequenceString:
MKVILKQDVS NLGKRFDVVD VKDGYAIHFL FPKKLAAPLT KKSLQDRDLF LKKQQEHYEI NKALSHKLKE VIEQTELHFS LKEHNGRPY GSIITKQIIN QAHTKGMALQ KFMFKDNVRL GFGDHEITLH IFEDTTAVLK VKVTPDNGVK

UniProtKB: Large ribosomal subunit protein bL9

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Macromolecule #10: 50S ribosomal protein L10

MacromoleculeName: 50S ribosomal protein L10 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 17.645719 KDa
SequenceString:
MEAKKDKAQQ VADVSHLLST SAGFVIFDYT SMSAIEATSI RKKLFKNGSK IKVIKNNILR RALKAGKFEG IDETAIKGKL AVAVGVNEI VETLKAVDGV VKAKEAMNFV CGYFDNRAFN SADLEKIAKL PGRNELYGMF LSVLQAPLRK FLYALEAVKA A K

UniProtKB: Large ribosomal subunit protein uL10

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Macromolecule #11: 50S ribosomal protein L11

MacromoleculeName: 50S ribosomal protein L11 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 14.80361 KDa
SequenceString:
MAKKTITRIA KINLLGGQAK PGPALASVGI NMGEFTKQFN EKTKDKQGEM IPCVITAYND KSFDFILKTT PVSILLKQAA KLEKGAKNA KTIVGKITMA KAKEIAQYKL VDLNANTVEA ALKMVLGTAK QMGIEVIE

UniProtKB: Large ribosomal subunit protein uL11

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Macromolecule #12: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 16.821477 KDa
SequenceString:
MQKTSMLTKE QANKRRQWYI VDAAGLVLGK LAVKAADLIR GKNKVDFTPN QDCGDYLIII NSDQVVLTGN KKENEFWYHH SQYIGGIKK VSGRDMLKKQ SDKLVYNAVK GMLPDNRLSR RWITKVHVFK GDKHNMEAQK PTTLNWS

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #13: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 13.478906 KDa
SequenceString:
MVSFMTRLNV ADNTGAKQVG IIKVLGSTRK RYAFLGDVVV VSVKDAIPSG MVKKGQVLRA VIVRTKKGQQ RKDGTHLKFD DNACVLIKE DKSPRGTRIF GPVARELRER GYNKILSLAV EVV

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #14: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 16.768812 KDa
SequenceString:
MELNQLKSVP KARNHKTKTL GRGHGSGLGK TSGRGQKGQK ARKSGLTRPG FEGGQTPLYR RLPKFGNARK GFLKQEWVVL NLNKIAKLK LDKINRASLI EKQVISAKSQ LPIKLIGHTK LEKPLHFEVH KVSKQALKAV ENANGSVKLL EK

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #15: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 15.646479 KDa
SequenceString:
MLQPKRTKYR KPHNVSYEGK AKGNSYVAFG EYGLVATKGN WIDARAIESA RIAISKCLGK TGKMWIRIFP HMSKTKKPLE VRMGSGKGN PEFWVAVVKQ GTVMFEVANI PESQMIKALT RAGHKLPVTW KILKREEVSA

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #16: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 14.270727 KDa
SequenceString:
MSYINKPGKT SAWRVMTVRQ QVSAVLAYGK IETTLKKAKN TQKRLDKLIT LAKVDNFNNR RQVKKWLLNT NLFDVDQLMD HLFSKVAPK YEKTPGGYSR VLKLGPRRGD ATEMAILQLT DAKYK

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #17: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 13.073256 KDa
SequenceString:
MKTRTEQRRL RHKRIVKKIR ATNHDNRVVL MVIKSLNHIS VQAWDFSQNI VLASSSSLAL KLKNGNKDNA KLVGQDIADK LVKLKLTNV VFDTGGSKYH GRIAALAEAA RERGLNF

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #18: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129
Molecular weightTheoretical: 13.870327 KDa
SequenceString:
MKKINKQALI DLVEQKQLKA YVPEFSAGDE VNVAIKLKEK EKVRIQNFTG TVLRRRGKGI SETFIVRKTT DGIPIEKNFQ IHNPNISIE LKRRGKVRRA YISYMRERSG KAAKIKERKQ

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #19: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 14.742431 KDa
SequenceString:
MRIKGGKQTR VRRKKWLKQA SGSFGTRHAS YKVAKQTVIQ AAKYAYRDRR NKKRDFRSLW ILRLNAALRE QGMTYSVFIN LLKKHNIEI NRKVLSELAI KEPSKFNLIV QKVKSEQPKA AKPAALGN

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #20: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 11.664824 KDa
SequenceString:
MHAIVVCGSK QYLVHENDTF FVEKLEAPVG KEIQLDKVLM LDEKIGAPYL EKARVVCVVE KHGLQRKVNV IKHISQKHHL KKYGHRQPY TKLKVVRFVH D

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #21: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 17.355402 KDa
SequenceString:
MIAFAKQFRV RISPQKARLV CQLIVGKKTA DAQNILSNTP KKAATLIAKL LNSAIANATN NHGMNGDALY VFECVANQGP SMKRTIPRA KGSSNMITKR SSNLVVKLSD NPNERQELIK QQKALVKKRV EGQQKAKMAR QKAVTSVVKA PSKTQGGVQK

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #22: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 25.89274 KDa
SequenceString: MDVTNVLLKP VLTEKVYFNQ MGETKKYVFV VNPKASKTRV KLAFELVYGI KPLKVNTLIR KPTTIRGGSR FPGLSKLEKL AVITLPKGI AISVTGEAPE KTDKPADKTT LKESTVKEIK DTKNSPEAVV KTAVEALQIK PTAAPVTTAP LQTVAVKVAK E VKEVKVEK ...String:
MDVTNVLLKP VLTEKVYFNQ MGETKKYVFV VNPKASKTRV KLAFELVYGI KPLKVNTLIR KPTTIRGGSR FPGLSKLEKL AVITLPKGI AISVTGEAPE KTDKPADKTT LKESTVKEIK DTKNSPEAVV KTAVEALQIK PTAAPVTTAP LQTVAVKVAK E VKEVKVEK PVKVEKPTKP AKVAKEAKTT KVAKETKAEK SVQTTKVAKE TKTEKSAKTT KTTATKTTKT KTTKKEVKK

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #23: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 12.461865 KDa
SequenceString:
MQRIKKGDKV VVITGKNKGG SGIVLKIMPA RQQAIVEGLN KVTRHKKKDQ TTKRAAKQST GKVQQEAPIF LSKLALFDQK AKQQTIGKI KYVMDPKTNK KTRVFKKSNN TL

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #24: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 11.527338 KDa
SequenceString:
MNNKYFLTKI DLQFFASKKG VGSTKNGRDS HAKRLGAKKA DGQMIRTGQI IYRQRGTRVY PGVNVGLGSD DTLFALSDGL VKYQKFGPK QGKTRVSVVK HKLDA

UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #25: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 7.549902 KDa
SequenceString:
MAKKDQLTLR GPLYGNNRSH SKTITRRKWN VNLQPCKVKT ADGKTTRILV STRTLRTLKK HNRLS

UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #26: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 13.003328 KDa
SequenceString:
MTVAKELRQK SSEELVKLVI KLKGELLEYR FKLAHGELDK PHLINQTRRL LATILTILTE RKLNWQEEQA KYKLLTKKTN EAAVNAWKQ HLEANKAKLL KSRAKREDAS KK

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #27: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 10.980657 KDa
SequenceString:
MKKDFHFPSQ SVSFKCASCS NSFTIESTLK QKEITIDICG KCHPFYIGEL TKQTVHGRAE KLSGKFNAGK AFLENKTPKK AKGKTEEYT KHRSLNEL

UniProtKB: Large ribosomal subunit protein bL31

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Macromolecule #28: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 6.641897 KDa
SequenceString:
MAVQQRRSSK HRRDKRRSHD ALTAQALSVC QKCGKKKLFH RVCSCGMYGD LRVKKAY

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #29: 50S ribosomal protein L33 1

MacromoleculeName: 50S ribosomal protein L33 1 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129
Molecular weightTheoretical: 6.298612 KDa
SequenceString:
MAVKRSTRLG CNDCREINYL TFKNVKKNPE KLALNKFCSR CRKVVVHKEV KRK

UniProtKB: Large ribosomal subunit protein bL33A

+
Macromolecule #30: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 30 / Number of copies: 1
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria)
Molecular weightTheoretical: 940.9115 KDa
SequenceString: UACAAUAAGU UACUAAGGGC UUAUGGUGGA UGCCUUGGCA CUAAUAGGCG AUGAAGGACG UGUUAACCUG CGAUAAGCUU CGGGUAGGU GGUAAGAACC UCAGAUCCGG AGAUUUCCGA AUGGAGCAAU CCGGUAGUUG GAAACAGCUA UCAUUAAUUG A UGAAUAAA ...String:
UACAAUAAGU UACUAAGGGC UUAUGGUGGA UGCCUUGGCA CUAAUAGGCG AUGAAGGACG UGUUAACCUG CGAUAAGCUU CGGGUAGGU GGUAAGAACC UCAGAUCCGG AGAUUUCCGA AUGGAGCAAU CCGGUAGUUG GAAACAGCUA UCAUUAAUUG A UGAAUAAA UAGUCAAUUA AAGCAAUACG UGGUGAAGUG AAACAUCUCA GUAGCCACAG GAAAAGAAAA CGAAUGUGAU UC CGUGUGU AGUGGCGAGC GAAAGCGGAA CAGGCCAAAC UUAUCAUUAG AUAGGGGUUG UAGGGCUUGC AAUGUGGACU UGA AAACGA UAGAAGAAGC UGUUGGAAAG CAGCGCGCAA AAGGGUGAUA GCCCCGUAUU UGAAAUUGUU UUCAUACCUA GCGA GAUCC CUGAGUAGCU CGGAAAACGU UAUUUUGAGU GAAUCUGCCC AGACCAUUGG GUAAGCCUAA AUACUAAUUA GUGAC CGAU AGCGAAACAG UACCGUGAGG GAAAGGUGAA AAGAACCCAG AGAUGGGAGU GAAAUAGAUU CUGAAACCAU AUGCCU ACA ACGUGUCAGA GCACAUUAAU GUGUGAUGGC GUGCGUUUUG AAGUAUGAGC CGGCGAGUUA UGAUAGCAAG CGUUAGU UA ACCAGGAGAU GGGGAGCUGU AGCGAAAGCG AGUUUUAAAA GAGCGUUUGU UUGUUAUUAU AGACCCGAAA CGGGUUGA G CUAGUCAUGA GCAGGUUGAA GGUUGAGUAA CAUCAACUGG AGGACCGAAC CGACUCUCGU UGAAACGAUA GCGGAUGAC UUGUGAUUAG GGGUGAAAUU CCAAUCGAAA UCCGUGAUAG CUGGUUCUCG UCGAAAUAGC UUUAAGGCUA GCGUGAGAUC ACAAAUAAG UGGAGGUAAA GCUACUGAAU GUAUGAUGGC GCCACCUAGG CGUACUGAAU ACAAUUAAAC UCUGAAUGCC A UUUAUUUU AUUCUCGCAG UCAGACAGUG GGGGAUAAGC UUCAUUGUCA AGAGGGGAAG AGCCCAGAUC AUUAAAUAAG GU CCCCAAA AUAUACUAAG UGGAAAAGGA UGUGAAAGUG CUAAAACAGC AAGGAUGUUG GCUUAGAAGC AGCCAUCGUU UAA AGAGUG CGUAACAGCU CACUUGUCGA GUGUUUUUGC GCCGAAGAUG UAACGGGGCU AAGUAUAUUA CCGAAUUUAU GGAU AAGAU UUAUAUCUUG UGGUAGACGA GCGUUGUAUU GGAGUUGAAG UCAAAGCGUG AGCAUUGGUG GAUCCAAUAC AAGUG AGAA UGCCGGCAUG AGUAACGCUU GGGAGUGAGA AUCUCCCAAA CCGAUUGACU AAGGUUUCCU GGACCAGGGU CGUCCU UCC AGGGUUAGUC UGGACCUAAG CUGAGGCUGA AAAGCGUAGG CGAUGGACAA CAGGUUAAUA UUCCUGUACU UACAGUU AG ACUGAUGGAG UGACAAAGAA GGUUUUCCAC CCCCAUAAUU GGAUUUGGGG AUAAAUCAUA AGGUGGUACA AUAGGCAA A UCCGUUGUGC AUAACAUUGA GUGAUGAUGU CGAGUGAAUG AGUGAUCAAG UAGCGAAGGU GGUAUUAAUC AUGCUUUCA AGAAAAGCUU CUAGGGUUAA UCUAGCUGUA ACCAGUACCG AGAACGAACA CACGUAGUCA AGGAGAGGAU CCUAAGGUUA GCGAGUGAA CUAUAGCCAA GGAACUCUGC AAAUUAACCC CGUAAGUUAG CGAGAAGGGG UGCUUAUGUA AAAGUAAGCC G CAGUGAAG AACGAGGGGG GACUGUUUAA CUAAAACACA ACUCUAUGCC AAACCGUAAG GUGAUGUAUA UGGGGUGACA CC UGCCCAG UGCUGGAAGG UUAAAGAAGG AGGUUAGCGC AAGCGAAGCU UUUAACUGAA GCCCCAGUGA ACGGCGGCCG UAA CUAUAA CGGUCCUAAG GUAGCGAAAU UCCUAGUCGG GUAAAUUCCG UCCCGCUUGA AUGGUGUAAC CAUCUCUUGA CUGU CUCGG CUAUAGACUC GGUGAAAUCC AGGUACGGGU GAAGACACCC GUUAGGCGCA ACGGGACGGA AAGACCCCGU GAAGC UUUA CUGUAGCUUA AUAUUGAUCA GGACAUUAUC AUGUAGAGAA UAGGUAGGAG CAAUCGAUGC AAGUUCGCUA GGACUU GUU GAUGCGAAAG GUGGAAUACU ACCCUUGGUU GUGUGCUGUU CUAAUUGGUA ACUGUUAUCC AGUUUCAAGA CAGUGUU AG GUGGGCAGUU UGACUGGGGC GGUCGCCUCC UAAAAGGUAA CGGAGGCGUA CAAAGGUACC UUCAGUACGG UUGGAAAU C GUAUGUAGAG UGUAAUGGUG UAAGGGUGCU UGACUGUGAG ACAUACAGGU CGAACAGGUG AGAAAUCAGG UCAUAGUGA UCCGGUGGUC CAGUAUGGAA UGGCCAUCGC UCAACGGAUA AAAGCUACUC CGGGGAUAAC AGGCUGAUAC UGCCCAAGAG UUCAUAUCG ACGGCAGUGU UUGGCACCUC GAUGUCGACU CAUCUCAUCC UCGAGCUGAA GCAGGUUCGA AGGGUUCGGC U GUUCGCCG AUUAAAGAGA UACGUGAGUU GGGUUCAAAC CGUCGUGAGA CAGGUUGGUC CCUAUCUAUU GUGCCCGUAG GA AGAUUGA AGAGUGUUGC UUCUAGUACG AGAGGACCGA AGCGAGGACA CCUCUUAUGC UCCAGUUGUA GCGCCAGCUG CAC CGCUGG GUAGUAACGU GUCUAUUAGA UAAACGCUGA AAGCAUCUAA GUGUGAAACU AUCUCAAAGA UUAAUCUUCC CAUU UCGCA AGAAAGUAAG AGCCGUCAAA GACGAUGACG UUGAUAGGUU ACAGGUGUAA GCAUAGUGAU AUGUUGAGCU GAGUA AUAC UAAUUGCUCG AGGACUUAUU GGA

+
Macromolecule #31: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 31 / Number of copies: 1
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria)
Molecular weightTheoretical: 34.796676 KDa
SequenceString:
UUUGGUGCCC AUGUCGCUGU GGAAACACCU GGUUCCAUUU CGAACCCAGC AGUUAAGCAC AGUGGAGCCG AAUGUAGCUG UUUCAGUGA GAAUAGGAAA GCACCAAGC

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
Details: back-side blotting for 2-3 seconds before plunging using a manual plunger without an environmental chamber.
DetailsMycoplasma pneumoniae M129 cells grown on gold Quantifoil grids at 37 Celsius before plunge freezing.

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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: 3.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.75 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number subtomograms used: 15954
ExtractionNumber tomograms: 356 / Number images used: 77539 / Software - Name: Warp (ver. 3.0.7 beta or 3.0.9)
Final 3D classificationSoftware - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7ood


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7pat:
free 50S in untreated Mycoplasma pneumoniae cells

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