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- PDB-7xam: Mycobacterium smegmatis 50S ribosomal subunit from Stationary pha... -

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Basic information

Entry
Database: PDB / ID: 7xam
TitleMycobacterium smegmatis 50S ribosomal subunit from Stationary phase of growth
Components
  • (50S ribosomal protein ...) x 32
  • 23S rRNA
  • 5S rRNA
KeywordsRIBOSOME / 50S Subunit / Domain IV of 23S rRNA / Alternate conformation / Helix 68
Function / homology
Function and homology information


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 ...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 / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L9, C-terminal domain / Ribosomal Protein L9; domain 2 / Ribosomal protein L9, N-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal Protein L9; domain 1 / Ribosomal protein L11/L12, C-terminal domain / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal Protein L15; Chain: K; domain 2 - #10 ...Ribosomal protein L9, C-terminal domain / Ribosomal Protein L9; domain 2 / Ribosomal protein L9, N-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal Protein L9; domain 1 / Ribosomal protein L11/L12, C-terminal domain / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / 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 L22; Chain A / Outer Surface Protein A; domain 3 / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / : / : / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / 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 L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein 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 L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / 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 L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Uncharacterized protein / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL34
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSengupta, J. / Baid, P.
Funding support India, 4items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)MLP-139 India
Department of Science & Technology (DST, India)SB/SO/BB-0025/2014 India
Department of Science & Technology (DST, India)CRG/2019/001788 India
Department of Biotechnology (DBT, India)BT/PR15017/BRB/10/1445 India
CitationJournal: Int J Biol Macromol / Year: 2023
Title: Cryo-EM captures a unique conformational rearrangement in 23S rRNA helices of the Mycobacterium 50S subunit.
Authors: Priya Baid / Jayati Sengupta /
Abstract: Structural investigations of the ribosomes isolated from pathogenic and non-pathogenic Mycobacterium species have identified several mycobacteria-specific structural features of ribosomal RNA and ...Structural investigations of the ribosomes isolated from pathogenic and non-pathogenic Mycobacterium species have identified several mycobacteria-specific structural features of ribosomal RNA and proteins. Here, we report structural evidence of a hitherto unknown conformational switch of mycobacterium 23S rRNA helices (H54a and H67-H71). Cryo-electron microscopy (cryo-EM) structures (~3-4 Å) of the M. smegmatis (Msm) log-phase 50S ribosomal subunit revealed conformational variability in H67-H71 region of the 23S rRNA, and manifested that, while H68 possesses the usual stretched conformation in one class of the maps, another one exhibits a bulge-out, fused density of H68-H69 at the inter-subunit surface, indicating an intrinsic dynamics of these rRNA helices. Remarkably, altered conformation of H68 forming a more prominent bulge-out structure at the inter-subunit surface of the 50S subunit due to the conformational rearrangements of 23S rRNA H67-H71 region was clearly visualized in a 3 Å cryo-EM map of the 50S subunit obtained from the stationary phase ribosome dataset. The Msm50S subunit having such bulge-out conformation at the intersubunit surface would be incompatible for associating with the 30S subunit due to its inability to form major inter-subunit bridges. Evidently, availability of active 70S ribosome pool can be modulated by stabilizing either one of the H68 conformation.
History
DepositionMar 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / em_3d_fitting_list / refine
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_3d_fitting_list.initial_refinement_model_id / _refine.ls_d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
3: 50S ribosomal protein bL37
A: 23S rRNA
B: 5S rRNA
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
I: 50S ribosomal protein L10
J: 50S ribosomal protein L11
K: 50S ribosomal protein L13
L: 50S ribosomal protein L14
M: 50S ribosomal protein L15
N: 50S ribosomal protein L16
O: 50S ribosomal protein L17
P: 50S ribosomal protein L18
Q: 50S ribosomal protein L19
R: 50S ribosomal protein L20
S: 50S ribosomal protein L21
T: 50S ribosomal protein L22
U: 50S ribosomal protein L23
V: 50S ribosomal protein L24
W: 50S ribosomal protein L25
X: 50S ribosomal protein L27
Y: 50S ribosomal protein L28
Z: 50S ribosomal protein L29
a: 50S ribosomal protein L30
b: 50S ribosomal protein L32
c: 50S ribosomal protein L33 1
d: 50S ribosomal protein L34
e: 50S ribosomal protein L35
f: 50S ribosomal protein L36
g: 50S ribosomal protein L31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,495,738445
Polymers1,485,58434
Non-polymers10,154411
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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50S ribosomal protein ... , 32 types, 32 molecules 3CDEFGHIJKLMNOPQRSTUVWXYZabcdefg

#1: Protein/peptide 50S ribosomal protein bL37


Mass: 2841.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTP4
#4: Protein 50S ribosomal protein L2


Mass: 30425.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD4
#5: Protein 50S ribosomal protein L3


Mass: 23011.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD1
#6: Protein 50S ribosomal protein L4


Mass: 22920.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD2
#7: Protein 50S ribosomal protein L5


Mass: 21152.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG1
#8: Protein 50S ribosomal protein L6


Mass: 19483.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG4
#9: Protein 50S ribosomal protein L9


Mass: 15949.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R7F6
#10: Protein 50S ribosomal protein L10


Mass: 18035.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS62
#11: Protein 50S ribosomal protein L11


Mass: 15023.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS45
#12: Protein 50S ribosomal protein L13


Mass: 16146.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSP8
#13: Protein 50S ribosomal protein L14


Mass: 13400.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSF9
#14: Protein 50S ribosomal protein L15


Mass: 15602.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG8
#15: Protein 50S ribosomal protein L16


Mass: 15774.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD8
#16: Protein 50S ribosomal protein L17


Mass: 21892.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSL9
#17: Protein 50S ribosomal protein L18


Mass: 13711.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG5
#18: Protein 50S ribosomal protein L19


Mass: 12892.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QV42
#19: Protein 50S ribosomal protein L20


Mass: 14494.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QYU6
#20: Protein 50S ribosomal protein L21


Mass: 11055.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R151
#21: Protein 50S ribosomal protein L22


Mass: 16353.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD6
#22: Protein 50S ribosomal protein L23


Mass: 11047.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD3
#23: Protein 50S ribosomal protein L24


Mass: 11228.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG0
#24: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 22571.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R3D2
#25: Protein 50S ribosomal protein L27


Mass: 9249.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R150
#26: Protein 50S ribosomal protein L28


Mass: 6891.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QV03
#27: Protein 50S ribosomal protein L29


Mass: 8790.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD9
#28: Protein 50S ribosomal protein L30


Mass: 7022.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG7
#29: Protein 50S ribosomal protein L32


Mass: 6467.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R3I9
#30: Protein 50S ribosomal protein L33 1


Mass: 6468.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS39
#31: Protein/peptide 50S ribosomal protein L34


Mass: 5522.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R7K0
#32: Protein 50S ribosomal protein L35


Mass: 7298.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QYU7
#33: Protein/peptide 50S ribosomal protein L36


Mass: 4341.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSL4
#34: Protein 50S ribosomal protein L31


Mass: 8312.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R215

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RNA chain , 2 types, 2 molecules AB

#2: RNA chain 23S rRNA


Mass: 1012140.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: GenBank: 118168627
#3: RNA chain 5S rRNA


Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: GenBank: 118168627

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Non-polymers , 2 types, 411 molecules

#35: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 407 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#36: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: Mycobacterium smegmatis 50S ribosomal subunit from Stationary Phase of growth
Type: RIBOSOME / Entity ID: #1-#34 / Source: NATURAL
Molecular weightValue: 1.8 MDa / Experimental value: YES
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3300 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 54 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 172541 / Num. of class averages: 9 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 5O60

5o60


Accession code: 5O60 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.5 Å

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