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- EMDB-8641: Cryo-EM structure of the large ribosomal subunit from Mycobacteri... -

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Basic information

Entry
Database: EMDB / ID: EMD-8641
TitleCryo-EM structure of the large ribosomal subunit from Mycobacterium tuberculosis
Map dataProtein RNA complexes
Sample
  • Complex: RNA complex
    • Protein or peptide: x 29 types
    • RNA: x 2 types
  • Ligand: x 1 types
KeywordsRNA dynamics / Ribosome
Function / homology
Function and homology information


cell wall / peptidoglycan-based cell wall / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding ...cell wall / peptidoglycan-based cell wall / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein 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 L17 signature. / 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 L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / 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 L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / 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 / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L30 signature.
Similarity search - Domain/homology
Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 ...Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / 50S ribosomal protein L15 / Large ribosomal subunit protein uL13 / 50S ribosomal protein L14 / : / : / : / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL33B / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / 50S ribosomal protein L14 / 50S ribosomal protein L13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYang K / Chang J-Y / Cui Z / Zhang J
CitationJournal: Nucleic Acids Res / Year: 2017
Title: Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis.
Authors: Kailu Yang / Jeng-Yih Chang / Zhicheng Cui / Xiaojun Li / Ran Meng / Lijun Duan / Jirapat Thongchol / Joanita Jakana / Christoph M Huwe / James C Sacchettini / Junjie Zhang /
Abstract: Ribosomes from Mycobacterium tuberculosis (Mtb) possess species-specific ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we present the near-atomic structures of the ...Ribosomes from Mycobacterium tuberculosis (Mtb) possess species-specific ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we present the near-atomic structures of the Mtb 50S ribosomal subunit and the complete Mtb 70S ribosome, solved by cryo-electron microscopy. Upon joining of the large and small ribosomal subunits, a 100-nt long expansion segment of the Mtb 23S rRNA, named H54a or the 'handle', switches interactions from with rRNA helix H68 and rProtein uL2 to with rProtein bS6, forming a new intersubunit bridge 'B9'. In Mtb 70S, bridge B9 is mostly maintained, leading to correlated motions among the handle, the L1 stalk and the small subunit in the rotated and non-rotated states. Two new protein densities were discovered near the decoding center and the peptidyl transferase center, respectively. These results provide a structural basis for studying translation in Mtb as well as developing new tuberculosis drugs.
History
DepositionMar 20, 2017-
Header (metadata) releaseAug 9, 2017-
Map releaseSep 20, 2017-
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: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5v7q
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8641.png

Downloads & links

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Map

FileDownload / File: emd_8641.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationProtein RNA complexes
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.44 Å/pix.
x 208 pix.
= 298.48 Å		1.44 Å/pix.
x 208 pix.
= 298.48 Å		1.44 Å/pix.
x 208 pix.
= 298.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.435 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.14505774 - 0.3066677
Average (Standard dev.)0.0016178174 (±0.012174379)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 298.47998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4351.4351.435
M x/y/z208208208
origin x/y/z0.0000.0000.000
length x/y/z298.480298.480298.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS208208208
D min/max/mean-0.1450.3070.002

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Supplemental data

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Sample components

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Entire : RNA complex

EntireName: RNA complex
Components
  • Complex: RNA complex
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33
    • 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 L31
    • RNA: 23S rRNA23S ribosomal RNA
    • RNA: 5S ribosomal RNA
    • 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 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: LSU ribosomal protein L21p
    • 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 L25
    • 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 L30
  • Ligand: N-({(5S)-2-oxo-3-[4-(1,3-thiazol-5-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)acetamide

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Supramolecule #1: RNA complex

SupramoleculeName: RNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#31
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 6.525757 KDa
SequenceString:
MAVPKRRKSR SNTRSRRSQW KAAKTELVGV TVAGHAHKVP RRLLKAARLG LIDFDKR

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #2: 50S ribosomal protein L33

MacromoleculeName: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 6.512581 KDa
SequenceString:
MASSTDVRPK ITLACEVCKH RNYITKKNRR NDPDRLELKK FCPNCGKHQA HRETR

UniProtKB: Large ribosomal subunit protein bL33

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Macromolecule #3: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 5.643697 KDa
SequenceString:
MTKGKRTFQP NNRRRARVHG FRLRMRTRAG RSIVSSRRRK GRRTLSA

UniProtKB: UNIPROTKB: A0A1L6JUG3

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Macromolecule #4: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 7.24143 KDa
SequenceString:
MPKAKTHSGA SKRFRRTGTG KIVRQKANRR HLLEHKPSTR TRRLDGRTVV AANDTKRVTS LLNG

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #5: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 4.323239 KDa
SequenceString:
VKVNPSVKPI CDKCRLIRRH GRVMVICSDP RHKQRQG

UniProtKB: UNIPROTKB: A0A1L6JSF4

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Macromolecule #6: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 8.770074 KDa
SequenceString:
MKSDIHPAYE ETTVVCGCGN TFQTRSTKPG GRIVVEVCSQ CHPFYTGKQK ILDSGGRVAR FEKRYGKRKV GADKAVSTGK

UniProtKB: Large ribosomal subunit protein bL31

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Macromolecule #9: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 30.644002 KDa
SequenceString: MAIRKYKPTT PGRRGASVSD FAEITRSTPE KSLVRPLHGR GGRNAHGRIT TRHKGGGHKR AYRMIDFRRN DKDGVNAKVA HIEYDPNRT ARIALLHYLD GEKRYIIAPN GLSQGDVVES GANADIKPGN NLPLRNIPAG TLIHAVELRP GGGAKLARSA G SSIQLLGK ...String:
MAIRKYKPTT PGRRGASVSD FAEITRSTPE KSLVRPLHGR GGRNAHGRIT TRHKGGGHKR AYRMIDFRRN DKDGVNAKVA HIEYDPNRT ARIALLHYLD GEKRYIIAPN GLSQGDVVES GANADIKPGN NLPLRNIPAG TLIHAVELRP GGGAKLARSA G SSIQLLGK EASYASLRMP SGEIRRVDVR CRATVGEVGN AEQANINWGK AGRMRWKGKR PSVRGVVMNP VDHPHGGGEG KT SGGRHPV SPWGKPEGRT RNANKSSNKF IVRRRRTGKK HSR

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #10: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 23.127533 KDa
SequenceString: MARKGILGTK LGMTQVFDES NRVVPVTVVK AGPNVVTRIR TPERDGYSAV QLAYGEISPR KVNKPLTGQY TAAGVNPRRY LAELRLDDS DAATEYQVGQ ELTAEIFADG SYVDVTGTSK GKGFAGTMKR HGFRGQGASH GAQAVHRRPG SIGGCATPAR V FKGTRMAG ...String:
MARKGILGTK LGMTQVFDES NRVVPVTVVK AGPNVVTRIR TPERDGYSAV QLAYGEISPR KVNKPLTGQY TAAGVNPRRY LAELRLDDS DAATEYQVGQ ELTAEIFADG SYVDVTGTSK GKGFAGTMKR HGFRGQGASH GAQAVHRRPG SIGGCATPAR V FKGTRMAG RMGNDRVTVL NLLVHKVDAE NGVLLIKGAV PGRTGGLVMV RSAIKRGEK

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #11: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 23.779936 KDa
SequenceString: MAAQEQKTLK IDVKTPAGKV DGAIELPAEL FDVPANIALM HQVVTAQRAA ARQGTHSTKT RGEVSGGGRK PYRQKGTGRA RQGSTRAPQ FTGGGVVHGP KPRDYSQRTP KKMIAAALRG ALSDRARNGR IHAITELVEG QNPSTKSARA FLASLTERKQ V LVVIGRSD ...String:
MAAQEQKTLK IDVKTPAGKV DGAIELPAEL FDVPANIALM HQVVTAQRAA ARQGTHSTKT RGEVSGGGRK PYRQKGTGRA RQGSTRAPQ FTGGGVVHGP KPRDYSQRTP KKMIAAALRG ALSDRARNGR IHAITELVEG QNPSTKSARA FLASLTERKQ V LVVIGRSD EAGAKSVRNL PGVHILAPDQ LNTYDVLRAD DVVFSVEALN AYIAANTTTS EEVSA

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #12: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 21.052303 KDa
SequenceString:
MTTAQKVQPR LKERYRSEIR DALRKQFGYG NVMQIPTVTK VVVNMGVGEA ARDAKLINGA VNDLALITGQ KPEVRRARKS IAQFKLREG MPVGVRVTLR GDRMWEFLDR LTSIALPRIR DFRGLSPKQF DGVGNYTFGL AEQAVFHEVD VDKIDRVRGM D INVVTSAA TDDEGRALLR ALGFPFKEN

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #13: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 19.408363 KDa
SequenceString:
MSRIGKQPIP VPAGVDVTIE GQSISVKGPK GTLGLTVAEP IKVARNDDGA IVVTRPDDER RNRSLHGLSR TLVSNLVTGV TQGYTTKME IFGVGYRVQL KGSNLEFALG YSHPVVIEAP EGITFAVQAP TKFTVSGIDK QKVGQIAANI RRLRRPDPYK G KGVRYEGE QIRRKVGKTG K

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #14: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 16.196654 KDa
SequenceString:
MKLILTADVD HLGSIGDTVE VKDGYGRNFL LPRGLAIVAS RGAQKQADEI RRARETKSVR DLEHANEIKA AIEALGPIAL PVKTSADSG KLFGSVTAAD VVAAIKKAGG PNLDKRIVRL PKTHIKAVGT HFVSVHLHPE IDVEVSLDVV AQS

UniProtKB: Large ribosomal subunit protein bL9

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Macromolecule #15: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 16.333896 KDa
SequenceString:
VPTYAPKAGD TTRSWYVIDA TDVVLGRLAV AAANLLRGKH KPTFAPNVDG GDFVIVINAD KVAISGDKLQ HKMVYRHSGY PGGLHKRTI GELMQRHPDR VVEKAILGML PKNRLSRQIQ RKLRVYAGPE HPHSAQQPVP YELKQVAQ

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #16: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 13.419649 KDa
SequenceString:
VIQQESRLKV ADNTGAKEIL CIRVLGGSSR RYAGIGDVIV ATVKDAIPGG NVKRGDVVKA VVVRTVKERR RPDGSYIKFD ENAAVIIKP DNDPRGTRIF GPVGRELREK RFMKIISLAP EVL

UniProtKB: 50S ribosomal protein L14

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Macromolecule #17: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 15.534062 KDa
SequenceString:
VTLKLHDLRP ARGSKIARTR VGRGDGSKGK TAGRGTKGTR ARKQVPVTFE GGQMPIHMRL PKLKGFRNRF RTEYEIVNVG DINRLFPQG GAVGVDDLVA KGAVRKNALV KVLGDGKLTA KVDVSAHKFS GSARAKITAA GGSATEL

UniProtKB: 50S ribosomal protein L15

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Macromolecule #18: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 15.724277 KDa
SequenceString:
MLIPRKVKHR KQHHPRQRGI ASGGTTVNFG DYGIQALEHA YVTNRQIESA RIAINRHIKR GGKVWINIFP DRPLTKKPAE TRMGSGKGS PEWWVANVKP GRVLFELSYP NEGVARAALT RAIHKLPIKA RIITREEQF

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #19: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 19.512273 KDa
SequenceString:
MPKPTKGPRL GGSSSHQKAI LANLATSLFE HGRITTTEPK ARALRPYAEK LITHAKKGAL HNRREVLKKL RDKDVVHTLF AEIGPFFAD RDGGYTRIIK IEARKGDNAP MAVIELVREK TVTSEANRAR RVAAAQAKAK KAAAMPTEES EAKPAEEGDV V GASEPDAK APEEPPAEAP EN

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #20: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 13.211122 KDa
SequenceString:
MAQSVSATRR ISRLRRHTRL RKKLSGTAER PRLVVHRSAR HIHVQLVNDL NGTTVAAASS IEADVRGVPG DKKARSVRVG QLIAERAKA AGIDTVVFDR GGYTYGGRIA ALADAARENG LSF

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #21: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 13.041126 KDa
SequenceString:
MNRLDFVDKP SLRDDIPAFN PGDTINVHVK VIEGAKERLQ VFKGVVIRRQ GGGIRETFTV RKESYGVGVE RTFPVHSPNI DHIEVVTRG DVRRAKLYYL RELRGKKAKI KEKR

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #22: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 14.557777 KDa
SequenceString:
MARVKRAVNA HKKRRSILKA SRGYRGQRSR LYRKAKEQQL HSLNYAYRDR RARKGEFRKL WIARINAAAR LNDITYNRLI QGLKAAGVE VDRKNLADIA ISDPAAFTAL VDVARAALPE DVNAPSGEAA

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #23: LSU ribosomal protein L21p

MacromoleculeName: LSU ribosomal protein L21p / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 11.173147 KDa
SequenceString:
MMATYAIVKT GGKQYKVAVG DVVKVEKLES EQGEKVSLPV ALVVDGATVT TDAKALAKVA VTGEVLGHTK GPKIRIHKFK NKTGYHKRQ GHRQQLTVLK VTGIA

UniProtKB: UNIPROTKB: A0A1N6MHB1

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Macromolecule #24: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 20.424594 KDa
SequenceString: MTAATKATEY PSAVAKARFV RVSPRKARRV IDLVRGRSVS DALDILRWAP QAASGPVAKV IASAAANAQN NGGLDPATLV VATVYADQG PTAKRIRPRA QGRAFRIRRR TSHITVVVES RPAKDQRSAK SSRARRTEAS KAASKVGATA PAKKAAAKAP A KKAPASSG ...String:
MTAATKATEY PSAVAKARFV RVSPRKARRV IDLVRGRSVS DALDILRWAP QAASGPVAKV IASAAANAQN NGGLDPATLV VATVYADQG PTAKRIRPRA QGRAFRIRRR TSHITVVVES RPAKDQRSAK SSRARRTEAS KAASKVGATA PAKKAAAKAP A KKAPASSG VKKTPAKKAP AKKAPAKASE TSAAKGGSD

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #25: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 10.976785 KDa
SequenceString:
MATLADPRDI ILAPVISEKS YGLLDDNVYT FLVRPDSNKT QIKIAVEKIF AVKVASVNTA NRQGKRKRTR TGYGKRKSTK RAIVTLAPG SRPIDLFGAP A

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #26: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 11.500274 KDa
SequenceString:
MKVHKGDTVL VISGKDKGAK GKVLQAYPDR NRVLVEGVNR IKKHTAISTT QRGARSGGIV TQEAPIHVSN VMVVDSDGKP TRIGYRVDE ETGKRVRISK RNGKDI

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #27: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 22.466166 KDa
SequenceString: MAKSASNQLR VTVRTETGKG ASRRARRAGK IPAVLYGHGA EPQHLELPGH DYAAVLRHSG TNAVLTLDIA GKEQLALTKA LHIHPIRRT IQHADLLVVR RGEKVVVEVS VVVEGQAGPD TLVTQETNSI EIEAEALSIP EQLTVSIEGA EPGTQLTAGQ I ALPAGVSL ...String:
MAKSASNQLR VTVRTETGKG ASRRARRAGK IPAVLYGHGA EPQHLELPGH DYAAVLRHSG TNAVLTLDIA GKEQLALTKA LHIHPIRRT IQHADLLVVR RGEKVVVEVS VVVEGQAGPD TLVTQETNSI EIEAEALSIP EQLTVSIEGA EPGTQLTAGQ I ALPAGVSL ISDPDLLVVN VVKAPTAEEL EGEVAGAEEA EEAAVEAGEA EAAGESE

UniProtKB: Large ribosomal subunit protein bL25

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Macromolecule #28: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 8.987272 KDa
SequenceString:
MAHKKGASSS RNGRDSAAQR LGVKRYGGQV VKAGEILVRQ RGTKFHPGVN VGRGGDDTLF AKTAGAVEFG IKRGRKTVSI VGSTTA

UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #29: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 6.920075 KDa
SequenceString:
MAAVCDICGK GPGFGKSVSH SHRRTSRRWD PNIQTVHAVT RPGGNKKRLN VCTSCIKAGK ITRG

UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #30: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 8.872015 KDa
SequenceString:
MAVGVSPGEL RELTDEELAE RLRESKEELF NLRFQMATGQ LNNNRRLRTV RQEIARIYTV LRERELGLAT GPDGKES

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #31: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 7.361569 KDa
SequenceString:
MSQLKITQVR STIGARWKQR ESLRTLGLRR IRHSVIREDN AATRGLIAVV RHLVEVEPAQ TGGKT

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #7: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 1.017792562 MDa
SequenceString: UUGUAAGUGU CUAAGGGCGC AUGGUGGAUG CCUUGGCAUC GAGAGCCGAU GAAGGACGUG GGAGGCUGCG AUAUGCCUCG GGGAGCUGU CAACCGAGCG UGGAUCCGAG GAUUUCCGAA UGGGGAAACC CAGCACGAGU GAUGUCGUGC UACCCGCAUC U GAAUAUAU ...String:
UUGUAAGUGU CUAAGGGCGC AUGGUGGAUG CCUUGGCAUC GAGAGCCGAU GAAGGACGUG GGAGGCUGCG AUAUGCCUCG GGGAGCUGU CAACCGAGCG UGGAUCCGAG GAUUUCCGAA UGGGGAAACC CAGCACGAGU GAUGUCGUGC UACCCGCAUC U GAAUAUAU AGGGUGCGGG AGGGAACGCG GGGAAGUGAA ACAUCUCAGU ACCCGUAGGA GGAGAAAACA AUUGUGAUUC CG CAAGUAG UGGCGAGCGA ACGCGGAACA GGCUAAACCG CACGCAUGGG UAACCGGGUA GGGGUUGUGU GUGCGGGGUU GUG GGAGGA UAUGUCUCAG CGCUACCCGG CUGAGAGGCA GUCAGAAAGU GUCGUGGUUA GCGGAAGUGG CCUGGGAUGG UCUG CCGUA GACGGUGAGA GCCCGGUACG CGAAAACCCG GCACCUGCCU AGUAUCAAUU CCCGAGUAGC AGCGGGCCCG UGGAA UCCG CUGUGAAUCC GCCGGGACCA CCCGGUAAGC CUAAAUACUC CUCGAUGACC GAUAGCGGAU UAGUACCGUG AGGGAA UGG UGAAAAGUAC CCCGGGAGGG GAGUGAAAGA GUACCUGAAA CCGUGUGCCU ACAAUCCGUC AGAGCCUCCU UUUCCUC UC CGGAGGAGGG UGGUGAUGGC GUGCCUUUUG AAGAAUGAGC CUGCGAGUCA GGGACAUGUC GCAAGGUUAA CCCGUGUG G GGUAGCCGCA GCGAAAGCGA GUCUGAAUAG GGCGACCCAC ACGCGCAUAC GCGCGUGUGA AUAGUGGCGU GUUCUGGAC CCGAAGCGGA GUGAUCUACC CAUGGCCAGG GUGAAGCGCG GGUAAGACCG CGUGGAGGCC CGAACCCACU UAGGUUGAAG ACUGAGGGG AUGAGCUGUG GGUAGGGGUG AAAGGCCAAU CAAACUCCGU GAUAGCUGGU UCUCCCCGAA AUGCAUUUAG G UGCAGCGU UGCGUGGUUC ACCGCGGAGG UAGAGCUACU GGAUGGCCGA UGGGCCCUAC UAGGUUACUG ACGUCAGCCA AA CUCCGAA UGCCGUGGUG UAAAGCGUGG CAGUGAGACG GCGGGGGAUA AGCUCCGUAC GUCGAAAGGG AAACAGCCCA GAU CGCCGG CUAAGGCCCC CAAGCGUGUG CUAAGUGGGA AAGGAUGUGC AGUCGCAAAG ACAACCAGGA GGUUGGCUUA GAAG CAGCC ACCCUUGAAA GAGUGCGUAA UAGCUCACUG GUCAAGUGAU UGUGCGCCGA UAAUGUAGCG GGGCUCAAGC ACACC GCCG AAGCCGCGGC ACAUCCACCU UGUGGUGGGU GUGGGUAGGG GAGCGUCCCU CAUUCAGCGA AGCCACCGGG UGACCG GUG GUGGAGGGUG GGGGAGUGAG AAUGCAGGCA UGAGUAGCGA CAAGGCAAGU GAGAACCUUG CCCGCCGAAA GACCAAG GG UUCCUGGGCC AGGCCAGUCC GCCCAGGGUG AGUCGGGACC UAAGGCGAGG CCGACAGGCG UAGUCGAUGG ACAACGGG U UGAUAUUCCC GUACCCGUGU GUGGGCGCCC GUGACGAAUC AGCGGUACUA ACCACCCAAA ACCGGAUCGA UCACUCCCC UUCGGGGGUG UGGAGUUCUG GGGCUGCGUG GGAACUUCGC UGGUAGUAGU CAAGCGAAGG GGUGACGCAG GAAGGUAGCC GUACCAGUC AGUGGUAACA CUGGGGCAAG CCGGUAGGGA GAGCGAUAGG CAAAUCCGUC GCUCACUAAU CCUGAGAGGU G ACGCAUAG CCGGUUGAGG CGAAUUCGGU GAUCCUCUGC UGCCAAGAAA AGCCUCUAGC GAGCACACAC ACGGCCCGUA CC CCAAACC GACACAGGUG GUCAGGUAGA GCAUACCAAG GCGUACGAGA UAACUAUGGU UAAGGAACUC GGCAAAAUGC CCC CGUAAC UUCGGGAGAA GGGGGACCGG AAUAUCGUGA ACACCCUUGC GGUGGGAGCG GGAUCCGGUC GCAGAAACCA GUGA GGAGC GACUGUUUAC UAAAAACACA GGUCCGUGCG AAGUCGCAAG ACGAUGUAUA CGGACUGACG CCUGCCCGGU GCUGG AAGG UUAAGAGGAC CCGUUAACCC GCAAGGGUGA AGCGGAGAAU UUAAGCCCCA GUAAACGGCG GUGGUAACUA UAACCA UCC UAAGGUAGCG AAAUUCCUUG UCGGGUAAGU UCCGACCUGC ACGAAUGGCG UAACGACUUC UCAACUGUCU CAACCAU AG ACUCGGCGAA AUUGCACUAC GAGUAAAGAU GCUCGUUACG CGCGGCAGGA CGAAAAGACC CCGGGACCUU CACUACAA C UUGGUAUUGA UGUUCGGUAC GGUUUGUGUA GGAUAGGUGG GAGACUGUGA AACCUCGACG CCAGUUGGGG CGGAGUCGU UGUUGAAAUA CCACUCUGAU CGUAUUGGGC AUCUAACCUC GAACCCUGAA UCGGGUUUAG GGACAGUGCC UGGCGGGUAG UUUAACUGG GGCGGUUGCC UCCUAAAAUG UAACGGAGGC GCCCAAAGGU UCCCUCAACC UGGACGGCAA UCAGGUGGCG A GUGUAAAU GCACAAGGGA GCUUGACUGC GAGACUUACA AGUCAAGCAG GGACGAAAGU CGGGAUUAGU GAUCCGGCAC CC CCGAGUG GAAGGGGUGU CGCUCAACGG AUAAAAGGUA CCCCGGGGAU AACAGGCUGA UCUUCCCCAA GAGUCCAUAU CGA CGGGAU GGUUUGGCAC CUCGAUGUCG GCUCGUCGCA UCCUGGGGCU GGAGCAGGUC CCAAGGGUUG GGCUGUUCGC CCAU UAAAG CGGCACGCGA GCUGGGUUUA GAACGUCGUG AGACAGUUCG GUCUCUAUCC GCCGCGCGCG UCAGAAACUU GAGGA AACC UGUCCCUAGU ACGAGAGGAC CGGGACGGAC GAACCUCUGG UGCACCAGUU GUCCCGCCAG GGGCACCGCU GGAUAG CCA CGUUCGGUCA GGAUAACCGC UGAAAGCAUC UAAGCGGGAA ACCUUCUCCA AGAUCAGGUU UCUCACCCAC UUGGUGG GA UAAGGCCCCC CGCAGAACAC GGGUUCAAUA GGUCAGACCU GGAAGCUCAG UAAUGGGUGU AGGGAACUGG UGCUAACC G GCCGAAAACU UACAACA

GENBANK: GENBANK: CP010339.1

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Macromolecule #8: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 8 / Number of copies: 1
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 37.097238 KDa
SequenceString:
UUACGGCGGC CACAGCGGCA GGGAAACGCC CGGUCCCAUU CCGAACCCGG AAGCUAAGCC UGCCAGCGCC GAUGAUACUG CCCCUCCGG GUGGAAAAGU AGGACACCGC CGAACA

GENBANK: GENBANK: CP013475.1

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Macromolecule #32: N-({(5S)-2-oxo-3-[4-(1,3-thiazol-5-yl)phenyl]-1,3-oxazolidin-5-yl...

MacromoleculeName: N-({(5S)-2-oxo-3-[4-(1,3-thiazol-5-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)acetamide
type: ligand / ID: 32 / Number of copies: 1 / Formula: 917
Molecular weightTheoretical: 317.363 Da
Chemical component information

ChemComp-917:
N-({(5S)-2-oxo-3-[4-(1,3-thiazol-5-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)acetamide

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.37 e/Å2

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Image processing

Startup modelType of model: EMDB MAP
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99285
FSC plot (resolution estimation)

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