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Yorodumi- PDB-8uvs: Crystal structure of the wild-type Thermus thermophilus 70S ribos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8uvs | ||||||||||||
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Title | Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with spectinomycin derivative 2694, mRNA, deacylated A- and E-site tRNAphe, and deacylated P-site tRNAmet at 2.75A resolution | ||||||||||||
Components |
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Keywords | RIBOSOME/INHIBITOR / Spectinomycin / aminomethyl spectinomycin / antibiotic / 70S ribosome / X-ray structure / inhibition of translation / infectious diseases / antimicrobial drug discovery / semisynthetic chemistry / drug development / RIBOSOME / RIBOSOME-INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information large ribosomal subunit / ribosomal large subunit assembly / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding ...large ribosomal subunit / ribosomal large subunit assembly / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) Thermus thermophilus HB8 (bacteria) Escherichia phage T4 (virus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||||||||
Authors | Killam, B.Y. / Phelps, G.A. / Lee, R.E. / Polikanov, Y.S. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: Development of 2nd generation aminomethyl spectinomycins that overcome native efflux in Mycobacterium abscessus. Authors: Phelps, G.A. / Cheramie, M.N. / Fernando, D.M. / Selchow, P. / Meyer, C.J. / Waidyarachchi, S.L. / Dharuman, S. / Liu, J. / Meuli, M. / Molin, M.D. / Killam, B.Y. / Murphy, P.A. / Reeve, S.M. ...Authors: Phelps, G.A. / Cheramie, M.N. / Fernando, D.M. / Selchow, P. / Meyer, C.J. / Waidyarachchi, S.L. / Dharuman, S. / Liu, J. / Meuli, M. / Molin, M.D. / Killam, B.Y. / Murphy, P.A. / Reeve, S.M. / Wilt, L.A. / Anderson, S.M. / Yang, L. / Lee, R.B. / Temrikar, Z.H. / Lukka, P.B. / Meibohm, B. / Polikanov, Y.S. / Hobbie, S.N. / Bottger, E.C. / Sander, P. / Lee, R.E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8uvs.cif.gz | 7.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8uvs.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8uvs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8uvs_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8uvs_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 8uvs_validation.xml.gz | 656.6 KB | Display | |
Data in CIF | 8uvs_validation.cif.gz | 1 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/8uvs ftp://data.pdbj.org/pub/pdb/validation_reports/uv/8uvs | HTTPS FTP |
-Related structure data
Related structure data | 8uvrC 6xhwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-RNA chain , 6 types, 14 molecules 1A2A1B2B1a2a1v2v1w1y2w2y1x2x
#1: RNA chain | Mass: 948007.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382 #2: RNA chain | Mass: 39188.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: AP008226.1 #32: RNA chain | Mass: 493863.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382 #53: RNA chain | Mass: 7804.735 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic 24-nt M-F-Stop mRNA / Source: (synth.) Escherichia phage T4 (virus) #54: RNA chain | Mass: 24644.873 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Deacylated phenylalanine-specific tRNAphe / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE-600 / Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600 / References: GenBank: 1850831943 #55: RNA chain | Mass: 24846.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Deacylated initiator formyl-methionyl-tRNAmet / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE-600 / Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600 / References: GenBank: 732678099 |
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+50S ribosomal protein ... , 29 types, 58 molecules 1D2D1E2E1F2F1G2G1H2H1I2I1N2N1O2O1P2P1Q2Q1R2R1S2S1T2T1U2U1V2V...
-30S ribosomal protein ... , 20 types, 40 molecules 1b2b1c2c1d2d1e2e1f2f1g2g1h2h1i2i1j2j1k2k1l2l1m2m1n2n1o2o1p2p...
#33: Protein | Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80371 #34: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80372 #35: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80373 #36: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ5 #37: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLP8 #38: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P17291 #39: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P0DOY9 #40: Protein | Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80374 #41: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN7 #42: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80376 #43: Protein | Mass: 14683.476 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN3 #44: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80377 #45: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P0DOY6 #46: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJ76 #47: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJH3 #48: Protein | Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P0DOY7 #49: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLQ0 #50: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP2 #51: Protein | Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80380 #52: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SIH3 |
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-Non-polymers , 6 types, 7745 molecules
#56: Chemical | ChemComp-MG / #57: Chemical | ChemComp-ZN / #58: Chemical | Mass: 475.576 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H41N3O8 / Feature type: SUBJECT OF INVESTIGATION #59: Chemical | #60: Chemical | #61: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 62.51 % / Description: Long needles |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 7.6 Details: 0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.5% PEG-20K, 7-12% MPD, 0.5 mM BME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 9, 2016 / Details: S/N 60-0112-F | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→121.84 Å / Num. obs: 1483558 / % possible obs: 98.9 % / Redundancy: 3.428 % / Biso Wilson estimate: 60.724 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.151 / Rrim(I) all: 0.179 / Χ2: 1.045 / Net I/σ(I): 7.42 / Num. measured all: 5085095 / Scaling rejects: 5441 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6XHW Resolution: 2.75→121.84 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.67 Å2 / Biso mean: 61.8085 Å2 / Biso min: 11.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→121.84 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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