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

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Basic information

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 / ribosome / translation
Function / homologyL28p-like / Ribosomal protein S8 superfamily / Ribosomal protein S14p/S29e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily ...L28p-like / Ribosomal protein S8 superfamily / Ribosomal protein S14p/S29e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / 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 S3, C-terminal domain superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S2 / Ribosomal protein S6 signature. / 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, superfamily / Ribosomal protein S14, type Z / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S15 / Ribosomal protein S5, N-terminal domain / Ribosomal protein S7, conserved site / Ribosomal protein S8 signature. / Ribosomal protein S13 signature. / Ribosomal protein S4 signature. / Ribosomal protein S5 signature. / Ribosomal protein S3 signature. / Ribosomal protein S14 signature. / Ribosomal protein S15 signature. / Ribosomal protein S10 signature. / Ribosomal protein S9 signature. / Ribosomal protein S19 signature. / Ribosomal protein S18 signature. / Ribosomal protein S17 signature. / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e / Mitochondrial domain of unknown function (DUF1713) / KH domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S20 / S4 domain / Ribosomal protein S6 / Ribosomal protein L31 / Ribosomal protein S18 / Ribosomal protein S16 / Ribosomal protein S13/S18 / Ribosomal protein S11 / Ribosomal protein S8 / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S16, conserved site / Ribosomal protein S2 signature 1. / Ribosomal protein S3, C-terminal / Ribosomal protein S15, bacterial-type / K Homology domain / K Homology domain, type 2 / RNA-binding S4 domain / Ribosomal protein S20 / Ribosomal protein S19/S15 / Ribosomal protein L31 / Ribosomal protein S11 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S13 / Ribosomal protein S2 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S14 / Ribosomal protein S9, conserved site / Ribosomal protein S5 / Ribosomal protein S9 / Ribosomal protein S8 / Ribosomal protein S15 / Ribosomal protein S6 / Ribosomal protein S16 / Ribosomal protein S17/S11 / Ribosomal protein S5/S7 / Ribosomal protein L31 signature. / Ribosomal protein S13 family profile. / Type-2 KH domain profile. / S5 double stranded RNA-binding domain profile. / S4 RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S12, bacterial-type / Ribosomal protein S3, bacterial / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S5 domain 2-type fold
Function and homology information
Specimen sourceMycobacterium smegmatis str. MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.45 Å resolution
AuthorsHentschel, J. / Burnside, C. / Mignot, I. / Leibundgut, M. / Boehringer, D. / Ban, N.
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
DateDeposition: Jun 2, 2017 / Release: Jul 12, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 12, 2017Structure modelrepositoryInitial release
1.1Jul 19, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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
Polyers810,83924
Non-polymers5,405219
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)114790
ΔGint (kcal/M)-2579
Surface area (Å2)287600
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: (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: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
#23: RNA chain mRNA fragment


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

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Protein/peptide , 2 types, 2 molecules Bg

#2: Protein/peptide Conserved domain protein / Protein domain / bS22 / 30S ribosomal protein bS22


Mass: 4164.300 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QR10
#24: Protein/peptide 50S ribosomal protein L31 / / bL31


Mass: 8312.485 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R215

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

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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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

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Non-polymers , 2 types, 219 molecules

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


Mass: 24.305 Da / Num. of mol.: 217 / Formula: Mg / Magnesium
#26: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn / Zinc

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 30S small ribosomal subunit / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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
MicroscopyMicroscope model: 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
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Details: FEI EPU data collection / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
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
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 224584 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER
Refine
Refine IDR factor R freeR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection R freeNumber reflection obsPercent reflection R freePercent reflection obsOverall SU MLSigma FOverall phase errorSolvent shrinkage radiiSolvent vdw probe radiiStereochemistry target valuesSolvent model details
10.24180.23050.23083.45149.3593447713781112.5099.960.450.9825.380.901.11MLHLFLAT BULK SOLVENT MODEL
ELECTRON MICROSCOPY
Refine LS restraints
Refine 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
Refine LS shell

Refine ID: ELECTRON MICROSCOPY

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
3.45100.50500.48733.4902117145113100.00
3.49020.40650.37023.5313114644889100.00
3.53130.36320.34543.5743114844700100.00
3.57430.34080.33333.6196111644974100.00
3.61960.34760.32293.6672114044320100.00
3.66720.31750.31223.7174112044893100.00
3.71740.31180.30583.7705117245358100.00
3.77050.29980.29193.8268103644190100.00
3.82680.30260.28493.8865120045022100.00
3.88650.28050.27753.9502114444920100.00
3.95020.28180.26894.0183117644520100.00
4.01830.27500.26334.0913117144742100.00
4.09130.27980.25264.1700117945310100.00
4.17000.25960.24184.2551119244555100.00
4.25510.25120.23484.3475113144542100.00
4.34750.24720.22624.4486111844342100.00
4.44860.22910.22384.5598116145230100.00
4.55980.24020.21624.6830111944757100.00
4.68300.22500.20644.8207111544876100.00
4.82070.21490.20314.9761118344991100.00
4.97610.21030.19375.1538118944868100.00
5.15380.20330.19125.3599108444778100.00
5.35990.19380.18225.6035113444519100.00
5.60350.20050.17735.8985109045135100.00
5.89850.17900.17306.2674115044635100.00
6.26740.18560.17556.7502116344802100.00
6.75020.17790.16257.4274112044794100.00
7.42740.15320.15268.4975122545050100.00
8.49750.14920.143810.6880116544432100.00
10.68800.15060.149749.364212194437799.00

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