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- PDB-5o5j: Structure of the 30S small ribosomal subunit from Mycobacterium s... -

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Entry
Database: PDB / ID: 5o5j
TitleStructure of the 30S small ribosomal subunit from Mycobacterium smegmatis
Components
  • (30S ribosomal protein ...) x 19
  • 16S rRNA
  • 50S ribosomal protein L31
  • Conserved domain proteinProtein domain
  • mRNA fragment
  • tRNA-Phe anticodon stem
KeywordsRIBOSOME / translation
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / zinc ion binding / metal ion binding
Ribosomal protein S6 superfamily / Ribosomal protein S17, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type ...Ribosomal protein S6 superfamily / Ribosomal protein S17, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S6, conserved site / Ribosomal protein S4/S9 / Ribosomal protein S5, N-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S14/S29 / Ribosomal protein L31 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S9, bacterial/plastid / L28p-like / Ribosomal protein L31 type A / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19/S15, superfamily / Ribosomal protein S14, type Z / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S3, conserved site / Domain of unknown function DUF1713 / Ribosomal protein S5 / Ribosomal protein S11 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S2 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S3, C-terminal / Ribosomal protein S14 / Ribosomal protein S9 / Ribosomal protein S19/S15 / Ribosomal protein S8 / Ribosomal protein S15 / Ribosomal protein S6 / Nucleic acid-binding, OB-fold / Ribosomal protein S16 / Ribosomal protein S17/S11 / Ribosomal protein S5/S7 / Ribosomal protein L31 / Ribosomal protein S13 / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein S13-like, H2TH / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / Ribosomal protein S12/S23 / RNA-binding S4 domain / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S12, bacterial-type / Ribosomal protein S5, C-terminal / Ribosomal protein S15, bacterial-type / K Homology domain / K Homology domain, type 2 / Ribosomal protein S3, bacterial-type / Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal protein S20 / Ribosomal protein S13/S18, C-terminal domain / 30s ribosomal protein s13; domain 2 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Helix hairpin bin / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal protein S3 C-terminal domain / Ribosomal protein S11/S14
30S ribosomal protein S6 / gb:118168627: / Conserved domain protein / 30S ribosomal protein S11 / 50S ribosomal protein L31 / 30S ribosomal protein S20 / 30S ribosomal protein S15 / 30S ribosomal protein S2 / 30S ribosomal protein S16 / 30S ribosomal protein S9 ...30S ribosomal protein S6 / gb:118168627: / Conserved domain protein / 30S ribosomal protein S11 / 50S ribosomal protein L31 / 30S ribosomal protein S20 / 30S ribosomal protein S15 / 30S ribosomal protein S2 / 30S ribosomal protein S16 / 30S ribosomal protein S9 / 30S ribosomal protein S4 / 30S ribosomal protein S13 / 30S ribosomal protein S12 / 30S ribosomal protein S5 / 30S ribosomal protein S8 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S17 / 30S ribosomal protein S3 / 30S ribosomal protein S19 / 30S ribosomal protein S10 / 30S ribosomal protein S18 2 / 30S ribosomal protein S7
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsHentschel, J. / Burnside, C. / Mignot, I. / Leibundgut, M. / Boehringer, D. / Ban, N.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_163478 Switzerland
NCCR RNA and disease program, SNSF51NF40_141735 Switzerland
CitationJournal: Cell Rep / Year: 2017
Title: The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.
Authors: Jendrik Hentschel / Chloe Burnside / Ingrid Mignot / Marc Leibundgut / Daniel Boehringer / Nenad Ban /
Abstract: The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death ...The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 17, 2018Group: Data collection / Refinement description / Category: refine
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
A: 16S rRNA
B: Conserved domain protein
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14 type Z
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18 2
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
V: 30S ribosomal protein S2
W: tRNA-Phe anticodon stem
X: mRNA fragment
g: 50S ribosomal protein L31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)816,244243
Polymers810,83924
Non-polymers5,405219
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area114790 Å2
ΔGint-2579 kcal/mol
Surface area287600 Å2
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules AWX

#1: RNA chain 16S rRNA


Mass: 495373.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: GenBank: 118168627
#22: RNA chain tRNA-Phe anticodon stem


Mass: 6140.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
#23: RNA chain mRNA fragment


Mass: 1791.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)

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30S ribosomal protein ... , 19 types, 19 molecules CDEFGHIJKLMNOPQRSTV

#3: Protein 30S ribosomal protein S3 / / uS3


Mass: 30191.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD7
#4: Protein 30S ribosomal protein S4 / / uS4


Mass: 23415.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSL7
#5: Protein 30S ribosomal protein S5 / / uS5


Mass: 21946.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG6
#6: Protein 30S ribosomal protein S6 / / bS6


Mass: 10991.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0A0D6J3X3
#7: Protein 30S ribosomal protein S7 / / uS7


Mass: 17660.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QS97
#8: Protein 30S ribosomal protein S8 / / uS8


Mass: 14492.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG3
#9: Protein 30S ribosomal protein S9 / / uS9


Mass: 16794.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSP9
#10: Protein 30S ribosomal protein S10 / / uS10


Mass: 11454.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD0
#11: Protein 30S ribosomal protein S11 / / uS11


Mass: 14671.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSL6
#12: Protein 30S ribosomal protein S12 / / uS12


Mass: 13896.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QS96
#13: Protein 30S ribosomal protein S13 / / uS13


Mass: 14249.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSL5
#14: Protein 30S ribosomal protein S14 type Z / Ribosome / uS14


Mass: 6976.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG2
#15: Protein 30S ribosomal protein S15 / / uS15


Mass: 10368.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QVQ3
#16: Protein 30S ribosomal protein S16 / / bS16


Mass: 16795.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QV37
#17: Protein 30S ribosomal protein S17 / / uS17


Mass: 11127.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSE0
#18: Protein 30S ribosomal protein S18 2 / Ribosome / bS18


Mass: 9524.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R7F7
#19: Protein 30S ribosomal protein S19 / / uS19


Mass: 10800.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD5
#20: Protein 30S ribosomal protein S20 / / bS20


Mass: 9556.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R102
#21: Protein 30S ribosomal protein S2 / / uS2


Mass: 30145.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QVB8

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Protein/peptide / Protein , 2 types, 2 molecules Bg

#24: Protein 50S ribosomal protein L31 / / bL31


Mass: 8312.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R215
#2: Protein/peptide Conserved domain protein / Protein domain / bS22 / 30S ribosomal protein bS22


Mass: 4164.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QR10

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Non-polymers , 2 types, 219 molecules

#25: Chemical...
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 217 / Source method: obtained synthetically / Formula: Mg
#26: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 30S small ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#24 / Source: NATURAL
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE-PROPANE / Humidity: 96 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 100719 X
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Details: FEI EPU data collection
Image scansMovie frames/image: 7

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
EM software
IDNameVersionCategory
1EMAN Boxer1.9particle selection
4CTFFIND3CTF correction
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
12RELION1.43D reconstruction
19PHENIXmodel refinement
CTF correctionDetails: CTF correction in Relion / Type: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224584 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
RefinementResolution: 3.451→49.359 Å / SU ML: 0.45 / σ(F): 0.98 / Phase error: 25.38 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2418 34477 2.5 %
Rwork0.2305 --
Obs0.2308 1378111 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00856171
ELECTRON MICROSCOPYf_angle_d1.13283477
ELECTRON MICROSCOPYf_dihedral_angle_d17.46625957
ELECTRON MICROSCOPYf_chiral_restr0.04810576
ELECTRON MICROSCOPYf_plane_restr0.0064881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
3.451-3.49020.50511710.487345113ELECTRON MICROSCOPY100
3.4902-3.53130.406511460.370244889ELECTRON MICROSCOPY100
3.5313-3.57430.363211480.345444700ELECTRON MICROSCOPY100
3.5743-3.61960.340811160.333344974ELECTRON MICROSCOPY100
3.6196-3.66720.347611400.322944320ELECTRON MICROSCOPY100
3.6672-3.71740.317511200.312244893ELECTRON MICROSCOPY100
3.7174-3.77050.311811720.305845358ELECTRON MICROSCOPY100
3.7705-3.82680.299810360.291944190ELECTRON MICROSCOPY100
3.8268-3.88650.302612000.284945022ELECTRON MICROSCOPY100
3.8865-3.95020.280511440.277544920ELECTRON MICROSCOPY100
3.9502-4.01830.281811760.268944520ELECTRON MICROSCOPY100
4.0183-4.09130.27511710.263344742ELECTRON MICROSCOPY100
4.0913-4.170.279811790.252645310ELECTRON MICROSCOPY100
4.17-4.25510.259611920.241844555ELECTRON MICROSCOPY100
4.2551-4.34750.251211310.234844542ELECTRON MICROSCOPY100
4.3475-4.44860.247211180.226244342ELECTRON MICROSCOPY100
4.4486-4.55980.229111610.223845230ELECTRON MICROSCOPY100
4.5598-4.6830.240211190.216244757ELECTRON MICROSCOPY100
4.683-4.82070.22511150.206444876ELECTRON MICROSCOPY100
4.8207-4.97610.214911830.203144991ELECTRON MICROSCOPY100
4.9761-5.15380.210311890.193744868ELECTRON MICROSCOPY100
5.1538-5.35990.203310840.191244778ELECTRON MICROSCOPY100
5.3599-5.60350.193811340.182244519ELECTRON MICROSCOPY100
5.6035-5.89850.200510900.177345135ELECTRON MICROSCOPY100
5.8985-6.26740.17911500.17344635ELECTRON MICROSCOPY100
6.2674-6.75020.185611630.175544802ELECTRON MICROSCOPY100
6.7502-7.42740.177911200.162544794ELECTRON MICROSCOPY100
7.4274-8.49750.153212250.152645050ELECTRON MICROSCOPY100
8.4975-10.6880.149211650.143844432ELECTRON MICROSCOPY100
10.688-49.36420.150612190.149744377ELECTRON MICROSCOPY99

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