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- PDB-5v7q: Cryo-EM structure of the large ribosomal subunit from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 5v7q
TitleCryo-EM structure of the large ribosomal subunit from Mycobacterium tuberculosis bound with a potent linezolid analog
Components
  • (50S ribosomal protein ...) x 28
  • 23S rRNA
  • 5S ribosomal RNA
  • LSU ribosomal protein L21p
KeywordsRIBOSOME / RNA dynamics
Function / homology
Function and homology information


peptidoglycan-based cell wall / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation ...peptidoglycan-based cell wall / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / 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 L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 ...Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal protein L6 / Ribosomal protein L22/L17 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L30; Chain: A, / Ribosomal Protein L22; Chain A / Outer Surface Protein A; domain 3 / Aldehyde Oxidoreductase; domain 3 / Rubrerythrin, domain 2 / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / RRM (RNA recognition motif) domain / Ribosomal protein L31 type A / Single Sheet / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Nucleic acid-binding proteins / : / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / 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 L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / 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 L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L28 / : / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L30, bacterial-type / : / L28p-like
Similarity search - Domain/homology
Chem-917 / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 ...Chem-917 / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single 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, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_author_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
6: 50S ribosomal protein L31
A: 23S rRNA
B: 5S ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: LSU ribosomal protein L21p
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,458,44932
Polymers1,458,13131
Non-polymers3171
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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50S ribosomal protein ... , 28 types, 28 molecules 012346CDEFGHJKLMNOPQSTUVWXYZ

#1: Protein 50S ribosomal protein L32


Mass: 6525.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IMI5, UniProt: P9WH99*PLUS
#2: Protein 50S ribosomal protein L33


Mass: 6512.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HU86, UniProt: P9WH95*PLUS
#3: Protein/peptide 50S ribosomal protein L34


Mass: 5643.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A1L6JUG3, UniProt: P9WH93*PLUS
#4: Protein 50S ribosomal protein L35


Mass: 7241.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045KKY9, UniProt: P9WH91*PLUS
#5: Protein/peptide 50S ribosomal protein L36


Mass: 4323.239 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A1L6JSF4, UniProt: P9WH89*PLUS
#6: Protein 50S ribosomal protein L31


Mass: 8770.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HLX7, UniProt: P9WHA1*PLUS
#9: Protein 50S ribosomal protein L2


Mass: 30644.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H5T7, UniProt: P9WHA5*PLUS
#10: Protein 50S ribosomal protein L3


Mass: 23127.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HU18, UniProt: P9WH87*PLUS
#11: Protein 50S ribosomal protein L4


Mass: 23779.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045J9H1, UniProt: P9WH85*PLUS
#12: Protein 50S ribosomal protein L5


Mass: 21052.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HUU0, UniProt: P9WH83*PLUS
#13: Protein 50S ribosomal protein L6


Mass: 19408.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JJU1, UniProt: P9WH81*PLUS
#14: Protein 50S ribosomal protein L9


Mass: 16196.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JW48, UniProt: P9WH79*PLUS
#15: Protein 50S ribosomal protein L13


Mass: 16333.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A0T9D5H2, UniProt: P9WHE1*PLUS
#16: Protein 50S ribosomal protein L14


Mass: 13419.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A0U0S3A8, UniProt: P9WHD9*PLUS
#17: Protein 50S ribosomal protein L15


Mass: 15534.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A0T7M0A0, UniProt: P9WHD7*PLUS
#18: Protein 50S ribosomal protein L16


Mass: 15724.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IWV9, UniProt: P9WHD5*PLUS
#19: Protein 50S ribosomal protein L17


Mass: 19512.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IVA2, UniProt: P9WHD3*PLUS
#20: Protein 50S ribosomal protein L18


Mass: 13211.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JK28, UniProt: P9WHD1*PLUS
#21: Protein 50S ribosomal protein L19


Mass: 13041.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IDD2, UniProt: P9WHC9*PLUS
#22: Protein 50S ribosomal protein L20


Mass: 14557.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045KJ85, UniProt: P9WHC5*PLUS
#24: Protein 50S ribosomal protein L22


Mass: 20424.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H760, UniProt: P9WHC1*PLUS
#25: Protein 50S ribosomal protein L23


Mass: 10976.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045J9M3, UniProt: P9WHB9*PLUS
#26: Protein 50S ribosomal protein L24


Mass: 11500.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IXU4, UniProt: P9WHB7*PLUS
#27: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 22466.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JAK4, UniProt: P9WHB5*PLUS
#28: Protein 50S ribosomal protein L27


Mass: 8987.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045K0G1, UniProt: P9WHB3*PLUS
#29: Protein 50S ribosomal protein L28


Mass: 6920.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IDB8
#30: Protein 50S ribosomal protein L29


Mass: 8872.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IQ64, UniProt: P9WHA7*PLUS
#31: Protein 50S ribosomal protein L30


Mass: 7361.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H4J2, UniProt: P9WHA3*PLUS

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RNA chain , 2 types, 2 molecules AB

#7: RNA chain 23S rRNA


Mass: 1017792.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: GenBank: 984989958
#8: RNA chain 5S ribosomal RNA


Mass: 37097.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: GenBank: 1092945381

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Protein / Non-polymers , 2 types, 2 molecules R

#23: Protein LSU ribosomal protein L21p / Ribosomal protein L21 (BL20)


Mass: 11173.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A1N6MHB1, UniProt: P9WHC3*PLUS
#32: Chemical ChemComp-917 / N-({(5S)-2-oxo-3-[4-(1,3-thiazol-5-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)acetamide / Llinezolid-114


Mass: 317.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15N3O3S

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RNA complex / Type: RIBOSOME / Entity ID: #1-#31 / Source: NATURAL
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 2.37 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99285 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007102983
ELECTRON MICROSCOPYf_angle_d0.905155232
ELECTRON MICROSCOPYf_dihedral_angle_d10.55154377
ELECTRON MICROSCOPYf_chiral_restr0.04619969
ELECTRON MICROSCOPYf_plane_restr0.0087675

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