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- EMDB-31398: Cryo-EM structure of Mycobacterium tuberculosis 50S ribosome subu... -

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Basic information

Entry
Database: EMDB / ID: EMD-31398
TitleCryo-EM structure of Mycobacterium tuberculosis 50S ribosome subunit bound with clarithromycin
Map dataThe 50S ribosome subunit from Mycobacterium tuberculosis (Mtb)
Sample
  • Complex: Mycobacterium tuberculosis ribosome 50S subunit
    • Complex: 50S ribosomal subunitProkaryotic large ribosomal subunit
      • Protein or peptide: x 29 types
    • RNA: x 2 types
  • Ligand: x 3 types
Function / homology
Function and homology information


large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / metal ion binding ...large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / metal ion binding / plasma membrane / 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 uL14 / 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 uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein uL14 / 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 / Large ribosomal subunit protein uL13 / 50S ribosomal protein L36 / 50S ribosomal protein L34 / 50S ribosomal protein L15 / Large ribosomal subunit protein bL21
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Ra (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang W / Sun Y / Gao N / Li Z
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)11179012 China
National Natural Science Foundation of China (NSFC)31725007 China
National Basic Research Program of China (973 Program)2011CB710800 China
CitationJournal: Emerg Microbes Infect / Year: 2022
Title: Cryo-EM structure of 50S ribosomal subunit bound with clarithromycin reveals dynamic and specific interactions with macrolides.
Authors: Wen Zhang / ZhiFei Li / Yufan Sun / Peng Cui / Jianhua Liang / Qinghe Xing / Jing Wu / Yanhui Xu / Wenhong Zhang / Ying Zhang / Lin He / Ning Gao /
Abstract: Tuberculosis (TB) is the leading infectious disease caused by (). Clarithromycin (CTY), an analog of erythromycin (ERY), is more potent against multidrug-resistance (MDR) TB. ERY and CTY were ...Tuberculosis (TB) is the leading infectious disease caused by (). Clarithromycin (CTY), an analog of erythromycin (ERY), is more potent against multidrug-resistance (MDR) TB. ERY and CTY were previously reported to bind to the nascent polypeptide exit tunnel (NPET) near peptidyl transferase center (PTC), but the only available CTY structure in complex with () ribosome could be misinterpreted due to resolution limitation. To date, the mechanism of specificity and efficacy of CTY for remains elusive since the ribosome-CTY complex structure is still unknown. Here, we employed new sample preparation methods and solved the ribosome-CTY complex structure at 3.3Å with cryo-EM technique, where the crucial gate site A2062 ( numbering) is located at the CTY binding site within NPET. Two alternative conformations of A2062, a novel -conformation as well as a swayed conformation bound with water molecule at interface, may play a role in coordinating the binding of specific drug molecules. The previously overlooked C-H hydrogen bond (H-bond) and π interaction may collectively contribute to the enhanced binding affinity. Together, our structure data provide a structural basis for the dynamic binding as well as the specificity of CTY and explain of how a single methyl group in CTY improves its potency, which provides new evidence to reveal previously unclear mechanism of translational modulation for future drug design and anti-TB therapy. Furthermore, our sample preparation method may facilitate drug discovery based on the complexes with low water solubility drugs by cryo-EM technique.
History
DepositionJun 3, 2021-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateJun 29, 2022-
Current statusJun 29, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31398.png

Downloads & links

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Map

FileDownload / File: emd_31398.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe 50S ribosome subunit from Mycobacterium tuberculosis (Mtb)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.060943186 - 0.099367745
Average (Standard dev.)7.4472982e-06 (±0.004966106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 374.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Mycobacterium tuberculosis ribosome 50S subunit

EntireName: Mycobacterium tuberculosis ribosome 50S subunit
Components
  • Complex: Mycobacterium tuberculosis ribosome 50S subunit
    • Complex: 50S ribosomal subunitProkaryotic large ribosomal subunit
      • 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
      • 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: 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 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
    • RNA: 23S rRNA23S ribosomal RNA
    • RNA: 5S ribosomal RNA
  • Ligand: CLARITHROMYCIN
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Mycobacterium tuberculosis ribosome 50S subunit

SupramoleculeName: Mycobacterium tuberculosis ribosome 50S subunit / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#31

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Supramolecule #2: 50S ribosomal subunit

SupramoleculeName: 50S ribosomal subunit / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1-#6, #9-#31
Source (natural)Organism: Mycobacterium tuberculosis H37Ra (bacteria)
Recombinant expressionOrganism: 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 H37Ra (bacteria)
Molecular weightTheoretical: 6.525757 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MAVPKRRKSR SNTRSRRSQW KAAKTELVGV TVAGHAHKVP RRLLKAARLG LIDFDKR

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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 H37Ra (bacteria)
Molecular weightTheoretical: 6.512581 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MASSTDVRPK ITLACEVCKH RNYITKKNRR NDPDRLELKK FCPNCGKHQA HRETR

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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 H37Ra (bacteria)
Molecular weightTheoretical: 5.643697 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MTKGKRTFQP NNRRRARVHG FRLRMRTRAG RSIVSSRRRK GRRTLSA

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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 H37Ra (bacteria)
Molecular weightTheoretical: 7.24143 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MPKAKTHSGA SKRFRRTGTG KIVRQKANRR HLLEHKPSTR TRRLDGRTVV AANDTKRVTS LLNG

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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 H37Ra (bacteria)
Molecular weightTheoretical: 4.323239 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
VKVNPSVKPI CDKCRLIRRH GRVMVICSDP RHKQRQG

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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 H37Ra (bacteria)
Molecular weightTheoretical: 8.770074 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MKSDIHPAYE ETTVVCGCGN TFQTRSTKPG GRIVVEVCSQ CHPFYTGKQK ILDSGGRVAR FEKRYGKRKV GADKAVSTGK

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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 H37Ra (bacteria)
Molecular weightTheoretical: 30.644002 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
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

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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 H37Ra (bacteria)
Molecular weightTheoretical: 23.127533 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
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

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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 H37Ra (bacteria)
Molecular weightTheoretical: 23.779936 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
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

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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 H37Ra (bacteria)
Molecular weightTheoretical: 21.052303 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MTTAQKVQPR LKERYRSEIR DALRKQFGYG NVMQIPTVTK VVVNMGVGEA ARDAKLINGA VNDLALITGQ KPEVRRARKS IAQFKLREG MPVGVRVTLR GDRMWEFLDR LTSIALPRIR DFRGLSPKQF DGVGNYTFGL AEQAVFHEVD VDKIDRVRGM D INVVTSAA TDDEGRALLR ALGFPFKEN

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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 H37Ra (bacteria)
Molecular weightTheoretical: 19.408363 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MSRIGKQPIP VPAGVDVTIE GQSISVKGPK GTLGLTVAEP IKVARNDDGA IVVTRPDDER RNRSLHGLSR TLVSNLVTGV TQGYTTKME IFGVGYRVQL KGSNLEFALG YSHPVVIEAP EGITFAVQAP TKFTVSGIDK QKVGQIAANI RRLRRPDPYK G KGVRYEGE QIRRKVGKTG K

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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 H37Ra (bacteria)
Molecular weightTheoretical: 16.196654 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MKLILTADVD HLGSIGDTVE VKDGYGRNFL LPRGLAIVAS RGAQKQADEI RRARETKSVR DLEHANEIKA AIEALGPIAL PVKTSADSG KLFGSVTAAD VVAAIKKAGG PNLDKRIVRL PKTHIKAVGT HFVSVHLHPE IDVEVSLDVV AQS

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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 H37Ra (bacteria)
Molecular weightTheoretical: 16.333896 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
VPTYAPKAGD TTRSWYVIDA TDVVLGRLAV AAANLLRGKH KPTFAPNVDG GDFVIVINAD KVAISGDKLQ HKMVYRHSGY PGGLHKRTI GELMQRHPDR VVEKAILGML PKNRLSRQIQ RKLRVYAGPE HPHSAQQPVP YELKQVAQ

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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 H37Ra (bacteria)
Molecular weightTheoretical: 13.419649 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
VIQQESRLKV ADNTGAKEIL CIRVLGGSSR RYAGIGDVIV ATVKDAIPGG NVKRGDVVKA VVVRTVKERR RPDGSYIKFD ENAAVIIKP DNDPRGTRIF GPVGRELREK RFMKIISLAP EVL

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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 H37Ra (bacteria)
Molecular weightTheoretical: 15.534062 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
VTLKLHDLRP ARGSKIARTR VGRGDGSKGK TAGRGTKGTR ARKQVPVTFE GGQMPIHMRL PKLKGFRNRF RTEYEIVNVG DINRLFPQG GAVGVDDLVA KGAVRKNALV KVLGDGKLTA KVDVSAHKFS GSARAKITAA GGSATEL

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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 H37Ra (bacteria)
Molecular weightTheoretical: 15.724277 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MLIPRKVKHR KQHHPRQRGI ASGGTTVNFG DYGIQALEHA YVTNRQIESA RIAINRHIKR GGKVWINIFP DRPLTKKPAE TRMGSGKGS PEWWVANVKP GRVLFELSYP NEGVARAALT RAIHKLPIKA RIITREEQF

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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 H37Ra (bacteria)
Molecular weightTheoretical: 19.512273 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MPKPTKGPRL GGSSSHQKAI LANLATSLFE HGRITTTEPK ARALRPYAEK LITHAKKGAL HNRREVLKKL RDKDVVHTLF AEIGPFFAD RDGGYTRIIK IEARKGDNAP MAVIELVREK TVTSEANRAR RVAAAQAKAK KAAAMPTEES EAKPAEEGDV V GASEPDAK APEEPPAEAP EN

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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 H37Ra (bacteria)
Molecular weightTheoretical: 13.211122 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MAQSVSATRR ISRLRRHTRL RKKLSGTAER PRLVVHRSAR HIHVQLVNDL NGTTVAAASS IEADVRGVPG DKKARSVRVG QLIAERAKA AGIDTVVFDR GGYTYGGRIA ALADAARENG LSF

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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 H37Ra (bacteria)
Molecular weightTheoretical: 13.041126 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MNRLDFVDKP SLRDDIPAFN PGDTINVHVK VIEGAKERLQ VFKGVVIRRQ GGGIRETFTV RKESYGVGVE RTFPVHSPNI DHIEVVTRG DVRRAKLYYL RELRGKKAKI KEKR

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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 H37Ra (bacteria)
Molecular weightTheoretical: 14.557777 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MARVKRAVNA HKKRRSILKA SRGYRGQRSR LYRKAKEQQL HSLNYAYRDR RARKGEFRKL WIARINAAAR LNDITYNRLI QGLKAAGVE VDRKNLADIA ISDPAAFTAL VDVARAALPE DVNAPSGEAA

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Macromolecule #23: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Ra (bacteria)
Molecular weightTheoretical: 11.173147 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MMATYAIVKT GGKQYKVAVG DVVKVEKLES EQGEKVSLPV ALVVDGATVT TDAKALAKVA VTGEVLGHTK GPKIRIHKFK NKTGYHKRQ GHRQQLTVLK VTGIA

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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 H37Ra (bacteria)
Molecular weightTheoretical: 20.424594 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
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

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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 H37Ra (bacteria)
Molecular weightTheoretical: 10.976785 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MATLADPRDI ILAPVISEKS YGLLDDNVYT FLVRPDSNKT QIKIAVEKIF AVKVASVNTA NRQGKRKRTR TGYGKRKSTK RAIVTLAPG SRPIDLFGAP A

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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 H37Ra (bacteria)
Molecular weightTheoretical: 11.500274 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MKVHKGDTVL VISGKDKGAK GKVLQAYPDR NRVLVEGVNR IKKHTAISTT QRGARSGGIV TQEAPIHVSN VMVVDSDGKP TRIGYRVDE ETGKRVRISK RNGKDI

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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 H37Ra (bacteria)
Molecular weightTheoretical: 22.466166 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
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

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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 H37Ra (bacteria)
Molecular weightTheoretical: 8.987272 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MAHKKGASSS RNGRDSAAQR LGVKRYGGQV VKAGEILVRQ RGTKFHPGVN VGRGGDDTLF AKTAGAVEFG IKRGRKTVSI VGSTTA

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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 H37Ra (bacteria)
Molecular weightTheoretical: 6.920075 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MAAVCDICGK GPGFGKSVSH SHRRTSRRWD PNIQTVHAVT RPGGNKKRLN VCTSCIKAGK ITRG

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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 H37Ra (bacteria)
Molecular weightTheoretical: 8.872015 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MAVGVSPGEL RELTDEELAE RLRESKEELF NLRFQMATGQ LNNNRRLRTV RQEIARIYTV LRERELGLAT GPDGKES

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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 H37Ra (bacteria)
Molecular weightTheoretical: 7.361569 KDa
Recombinant expressionOrganism: Mycobacterium tuberculosis (bacteria)
SequenceString:
MSQLKITQVR STIGARWKQR ESLRTLGLRR IRHSVIREDN AATRGLIAVV RHLVEVEPAQ TGGKT

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Macromolecule #7: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Mycobacterium tuberculosis H37Ra (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

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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 H37Ra (bacteria)
Molecular weightTheoretical: 37.097238 KDa
SequenceString:
UUACGGCGGC CACAGCGGCA GGGAAACGCC CGGUCCCAUU CCGAACCCGG AAGCUAAGCC UGCCAGCGCC GAUGAUACUG CCCCUCCGG GUGGAAAAGU AGGACACCGC CGAACA

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Macromolecule #32: CLARITHROMYCIN

MacromoleculeName: CLARITHROMYCIN / type: ligand / ID: 32 / Number of copies: 1 / Formula: CTY
Molecular weightTheoretical: 747.953 Da
Chemical component information

ChemComp-CTY:
CLARITHROMYCIN / antibiotic*YM / Clarithromycin

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Macromolecule #33: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 33 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #34: water

MacromoleculeName: water / type: ligand / ID: 34 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 IS (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34912

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Atomic model buiding 1

Initial modelPDB ID:

5v7q

Output model

PDB-7f0d:
Cryo-EM structure of Mycobacterium tuberculosis 50S ribosome subunit bound with clarithromycin

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