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- PDB-5xyu: Small subunit of Mycobacterium smegmatis ribosome -

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Basic information

Entry
Database: PDB / ID: 5xyu
TitleSmall subunit of Mycobacterium smegmatis ribosome
Components
  • (30S ribosomal protein ...) x 18
  • 16S RNA
  • Conserved domain proteinProtein domain
KeywordsRIBOSOME / Mycobacterium smegmatis ribosome / rRNA / rprotein
Function / homologyRibosomal protein S10 domain / Ribosomal protein S3, C-terminal domain superfamily / 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 / Ribosomal protein S3, C-terminal domain superfamily / 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 S8 superfamily / Ribosomal protein S15 / Ribosomal protein S6 superfamily / Ribosomal protein S16 signature. / 30s ribosomal protein S13, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / 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 S6, plastid/chloroplast / Ribosomal protein S14p/S29e / Ribosomal protein S5, N-terminal domain / Ribosomal protein S16, conserved site / Ribosomal protein S7 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 S8 signature. / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein S10p/S20e / KH domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S20 / S4 domain / Ribosomal protein S6 / 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 S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S14 / K Homology domain / K Homology domain, type 2 / RNA-binding S4 domain / Ribosomal protein S20 / Ribosomal protein S19/S15 / Ribosomal protein S11 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S13 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S3, C-terminal / Ribosomal protein S5 / Ribosomal protein S5, C-terminal / 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 S6 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 S15, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S3, bacterial / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site
Function and homology information
Specimen sourceMycobacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.45 Å resolution
AuthorsLi, Z. / Zhang, Y. / Zheng, L. / Ge, X. / Sanyal, S. / Gao, N.
CitationJournal: Protein Cell / Year: 2018
Title: Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers.
Authors: Zhifei Li / Xueliang Ge / Yixiao Zhang / Lvqin Zheng / Suparna Sanyal / Ning Gao
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 10, 2017 / Release: Sep 27, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 27, 2017Structure modelrepositoryInitial release
1.1Apr 11, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year

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Structure visualization

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Assembly

Deposited unit
A: 16S RNA
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
U: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)764,82568
Polyers763,65920
Non-polymers1,16748
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)84890
ΔGint (kcal/M)-1114
Surface area (Å2)262500

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Components

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30S ribosomal protein ... , 18 types, 18 molecules CDEFGHIJKLMNOPQRST

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


Mass: 30191.227 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD7
#3: Protein/peptide 30S ribosomal protein S4 / / uS4


Mass: 23415.787 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL7
#4: Protein/peptide 30S ribosomal protein S5 / / uS5


Mass: 21946.090 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG6
#5: Protein/peptide 30S ribosomal protein S6 / / bS6


Mass: 10200.688 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R7F9
#6: Protein/peptide 30S ribosomal protein S7 / / uS7


Mass: 17660.375 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS97
#7: Protein/peptide 30S ribosomal protein S8 / / uS8


Mass: 14492.638 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG3
#8: Protein/peptide 30S ribosomal protein S9 / / uS9


Mass: 16794.365 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSP9
#9: Protein/peptide 30S ribosomal protein S10 / / uS10


Mass: 11454.313 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD0
#10: Protein/peptide 30S ribosomal protein S11 / / uS11


Mass: 14671.762 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL6
#11: Protein/peptide 30S ribosomal protein S12 / / uS12


Mass: 13896.366 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS96
#12: Protein/peptide 30S ribosomal protein S13 / / uS13


Mass: 14249.619 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL5
#13: Protein/peptide 30S ribosomal protein S14 type Z / Ribosome / uS14


Mass: 6976.409 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG2
#14: Protein/peptide 30S ribosomal protein S15 / / uS15


Mass: 10368.097 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QVQ3
#15: Protein/peptide 30S ribosomal protein S16 / / bS16


Mass: 16795.207 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QV37
#16: Protein/peptide 30S ribosomal protein S17 / / uS17


Mass: 11127.002 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSE0
#17: Protein/peptide 30S ribosomal protein S18 2 / Ribosome / bS18


Mass: 9524.188 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R7F7
#18: Protein/peptide 30S ribosomal protein S19 / / uS19


Mass: 10800.602 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD5
#19: Protein/peptide 30S ribosomal protein S20 / / bS20


Mass: 9556.104 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R102

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RNA chain / Protein/peptide / Non-polymers , 3 types, 50 molecules AU

#1: RNA chain 16S RNA


Mass: 495373.656 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: GenBank: 118168627
#20: Protein/peptide Conserved domain protein / Protein domain / uL41


Mass: 4164.300 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QR10
#21: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 48 / Formula: Mg / Magnesium

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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: Small subunit of Mycobacterium smegmatis ribosome / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20
Source: NATURAL
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 47338 / Symmetry type: POINT

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