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Open data
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Basic information
Entry | Database: PDB / ID: 5xyu | ||||||
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Title | Small subunit of Mycobacterium smegmatis ribosome | ||||||
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![]() | RIBOSOME / Mycobacterium smegmatis ribosome / rRNA / rprotein | ||||||
Function / homology | ![]() ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å | ||||||
![]() | Li, Z. / Zhang, Y. / Zheng, L. / Ge, X. / Sanyal, S. / Gao, N. | ||||||
![]() | ![]() 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 / ![]() ![]() | ||||||
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 895 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 970.1 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 83.8 KB | Display | |
Data in CIF | ![]() | 136.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6790MC ![]() 6789C ![]() 5xymC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-30S ribosomal protein ... , 18 types, 18 molecules CDEFGHIJKLMNOPQRST
#2: Protein | Mass: 30191.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD7 |
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#3: Protein | Mass: 23415.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL7 |
#4: Protein | Mass: 21946.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG6 |
#5: Protein | Mass: 10200.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R7F9 |
#6: Protein | Mass: 17660.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS97 |
#7: Protein | Mass: 14492.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG3 |
#8: Protein | Mass: 16794.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSP9 |
#9: Protein | Mass: 11454.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD0 |
#10: Protein | Mass: 14671.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL6 |
#11: Protein | Mass: 13896.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS96 |
#12: Protein | Mass: 14249.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL5 |
#13: Protein | Mass: 6976.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG2 |
#14: Protein | Mass: 10368.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QVQ3 |
#15: Protein | Mass: 16795.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QV37 |
#16: Protein | Mass: 11127.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSE0 |
#17: Protein | Mass: 9524.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R7F7 |
#18: Protein | Mass: 10800.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD5 |
#19: Protein | Mass: 9556.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R102 |
-RNA chain / Protein/peptide / Non-polymers , 3 types, 50 molecules AU![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#1: RNA chain | Mass: 495373.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: GenBank: 118168627 |
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#20: Protein/peptide | Mass: 4164.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QR10 |
#21: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Small subunit of Mycobacterium smegmatis ribosome / Type: RIBOSOME / Entity ID: #1-#20 / Source: NATURAL |
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Source (natural) | Organism: ![]() Strain: ATCC 700084 / mc(2)155 |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47338 / Symmetry type: POINT |