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Open data
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Basic information
Entry | Database: PDB / ID: 7asp | ||||||
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Title | Staphylococcus aureus 70S after 50 minutes incubation at 37C | ||||||
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![]() | RIBOSOME / H68 / translation / protein synthesis | ||||||
Function / homology | ![]() large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit ...large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / 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: 2.86 Å | ||||||
![]() | Cimicata, G. / Bashan, A. / Yonath, A. | ||||||
Funding support | 1items
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![]() | ![]() Title: Staphylococcus aureus 50S after 30 minutes incubation a 37C Authors: Cimicata, G. / Bashan, A. / Yonath, A. | ||||||
History |
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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 | ![]() | 2.8 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 159 KB | Display | |
Data in CIF | ![]() | 287.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11903MC ![]() 7asmC ![]() 7asnC ![]() 7asoC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Components
-RNA chain , 3 types, 3 molecules YX3
#1: RNA chain | Mass: 946687.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: ...Details: GAUUAAGUUAUUAAGGGCGCACGGUGGAUGCCUUGGCACUAGAAGCCGAUGAAGGACGUUACUAACGACGAUAUGCUUUGGGGAGCUGUAAGCUUUGAUCCAGAGAUUUCCGAAUGGGGAAACCCAGCAUGAGUUAUGUCAUGUUAUCGAUAUGUGAAUACAUAGCAUAUCAGAAGGCACACCCGGAGAACUGAAACAUCUUAGUACCCGGAGGAAGAGAAAGAAAAUUCGAUUCCCUUAGUAGCGGCGAGCGAAACGGGAAGAGCCCAAACCAACAAGCUUGCUUGUUGGGGUUGUAGGACACUCUGUACGGAGUUACAAAGGACGACAUUAGACGAAUCAUCUGGAAAGAUGAAUCAAAGAAGGUAAUAAUCCUGUAGUCGAAAAUGUUGUCUCUCUUGAGUGGAUCCUGAGUACGACGGAGCACGUGAAAUUCCGUCGGAAUCUGGGAGGACCAUCUCCUAAGGCUAAAUACUCUCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGGGAGUGAAAUAGAACCUGAAACCGUGUGCUUACAAGUAGUCAGAGCCCGUUAAUGGGUGAUGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUUUGAUGCAAGGUUAAGCAGUAAAUGUGGAGCCGUAGCGAAAGCGAGUCUGAAUAGGGCGUUUAGUAUUUGGUCGUAGACCCGAAACCAGGUGAUCUACCCUUGGUCAGGUUGAAGUUCAGGUAACACUGAAUGGAGGACCGAACCGACUUACGUUGAAAAGUGAGCGGAUGAACUGAGGGUAGCGGAGAAAUUCCAAUCGAACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGUGAUGAUUAUUGGAGGUAGAGCACUGUUUGGACGAGGGGCCCCUCUCGGGUUACCGAAUUCAGACAAACUCCGAAUGCCAAUUAAUUUAACUUGGGAGUCAGAACAUGGGUGAUAAGGUCCGUGUUCGAAAGGGAAACAGCCCAGACCACCAGCUAAGGUCCCAAAAUAUAUGUUAAGUGGAAAAGGAUGUGGCGUUGCCCAGACAACUAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAAUAGCUCACUAGUCGAGUGACACUGCGCCGAAAAUGUACCGGGGCUAAACAUAUUACCGAAGCUGUGGAUUGUCCUUUGGACAAUGGUAGGAGAGCGUUCUAAGGGCGUUGAAGCAUGAUCGUAAGGACAUGUGGAGCGCUUAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGGGUGAGAAUCCCGUCCACCGAUUGACUAAGGUUUCCAGAGGAAGGCUCGUCCGCUCUGGGUUAGUCGGGUCCUAAGCUGAGGCCGACAGGCGUAGGCGAUGGAUAACAGGUUGAUAUUCCUGUACCACCUAUAAUCGUUUUAAUCGAUGGGGGGACGCAGUAGGAUAGGCGAAGCGUGCGAUUGGAUUGCACGUCUAAGCAGUAAGGCUGAGUAUUAGGCAAAUCCGGUACUCGUUAAGGCUGAGCUGUGAUGGGGAGAAGACAUUGAGUCUUCGAGUCGUUGAUUUCACACUGCCGAGAAAAGCCUCUAGAUAGAAAAUAGGUGCCCGUACCGCAAACCGACACAGGUAGUCAAGAUGAGAAUUCUAAGGUGAGCGAGCGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGGUAACUUCGGGAGAAGGGGUGCUCUUUAGGGUUAACGCCCAGAAGAGCCGCAGUGAAUAGGCCCAAGCGACUGUUUAUCAAAAACACAGGUCUCUGCUAAACCGUAAGGUGAUGUAUAGGGGCUGACGCCUGCCCGGUGCUGGAAGGUUAAGAGGAGUGGUUAGCUUCUGCGAAGCUACGAAUCGAAGCCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCCGCACGAAAGGCGUAACGAUUUGGGCACUGUCUCAACGAGAGACUCGGUGAAAUCAUAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGGACGGAAAGACCCCGUGGAGCUUUACUGUAGCCUGAUAUUGAAAUUCGGCACAGCUUGUACAGGAUAGGUAGGAGCCUUUGAAACGUGAGCGCUAGCUUACGUGGAGGCGCUGGUGGGAUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACUUAUCGUGGUGGGAGACAGUGUCAAGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCUCAAAGGUUCCCUCAGAAUGGUUGGAAAUCAUUCAUAGAGUGUAAAGGCAUAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAGGGUCGAAAGACGGACUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAUAAAAGCUACCCCGGGGAUAACAGGCUUAUCUCCCCCAAGAGUUCACAUCGACGGGGAGGUUUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCUAUCCGUCGUGGGCGUAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGAUGGACAUACCUCUGGUGUACCAGUUGUCGUGCCAACGGCAUAGCUGGGUAGCUAUGUGUGGACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAACUUCGGUUAUAAGAUCCCUCAAAGAUGAUGAGGUUAAUAGGUUCGAGGUGGAAGCAUGGUGACAUGUGGAGCUGACGAAUACUAAUCGAUCGAAGACUUAAUCAA Source: (natural) ![]() ![]() |
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#2: RNA chain | Mass: 502019.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: ...Details: UUUAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAGCGAACGGACGAGAAGCUUGCUUCUCUGAUGUUAGCGGCGGACGGGUGAGUAACACGUGGAUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUUGAACCGCAUGGUUCAAAAGUGAAAGACGGUCUUGCUGUCACUUAUAGAUGGAUCCGCGCUGCAUUAGCUAGUUGGUAAGGUAACGGCUUACCAAGGCAACGAUACGUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGGCGAAAGCCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGUCUUCGGAUCGUAAAACUCUGUUAUUAGGGAAGAACAUAUGUGUAAGUAACUGUGCACAUCUUGACGGUACCUAAUCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGCGCGUAGGCGGUUUUUUAAGUCUGAUGUGAAAGCCCACGGCUCAACCGUGGAGGGUCAUUGGAAACUGGAAAACUUGAGUGCAGAAGAGGAAAGUGGAAUUCCAUGUGUAGCGGUGAAAUGCGCAGAGAUAUGGAGGAACACCAGUGGCGAAGGCGACUUUCUGGUCUGUAACUGACGCUGAUGUGCGAAAGCGUGGGGAUCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGUGUUAGGGGGUUUCCGCCCCUUAGUGCUGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGACCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAAAUCUUGACAUCCUUUGACAACUCUAGAGAUAGAGCCUUCCCCUUCGGGGGACAAAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAAGCUUAGUUGCCAUCAUUAAGUUGGGCACUCUAAGUUGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGAUUUGGGCUACACACGUGCUACAAUGGACAAUACAAAGGGCAGCGAAACCGCGAGGUCAAGCAAAUCCCAUAAAGUUGUUCUCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGCUGGAAUCGCUAGUAAUCGUAGAUCAGCAUGCUACGGUGAAUACGUUCCCGGGUAUUGUACACACCGCCCGUCACACCACGAGAGUUUGUAACACCCGAAGCCGGUGGAGUAACCUUUUAGGAGCUAGCCGUCGAAGGUGGGACAAAUGAUUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUU Source: (natural) ![]() ![]() |
#3: RNA chain | Mass: 36692.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+50S ribosomal protein ... , 25 types, 26 molecules A1B24CDEGHIJKLMNOPQRSTUVWF
-30S ribosomal protein ... , 17 types, 17 molecules abcdefghijklmnopq
#8: Protein | Mass: 9243.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#9: Protein | Mass: 12047.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 15189.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 12843.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 7186.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 10503.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 9291.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#20: Protein | Mass: 9366.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#22: Protein | Mass: 6574.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#23: Protein | Mass: 8480.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#25: Protein | Mass: 22684.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#28: Protein | Mass: 22849.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#29: Protein | Mass: 16522.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#31: Protein | Mass: 11239.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#33: Protein | Mass: 14622.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#35: Protein | Mass: 17695.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#37: Protein | Mass: 14312.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules Z
#45: Protein/peptide | Mass: 5406.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-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: 70S / Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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: 47 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18_3845: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 383752 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192105 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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