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Yorodumi- PDB-487d: SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MA... -
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-Basic information
Entry | Database: PDB / ID: 487d | |||||||||
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Title | SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION | |||||||||
Components | (50S ribosomal protein ...) x 7 | |||||||||
Keywords | RIBOSOME / LARGE RIBOSOMAL SUBUNIT / RIBOSOMAL PROTEIN / PROTEIN BIOSYNTHESIS / EM-RECONSTRUCTION / ATOMIC STRUCTURE / 3D ARRANGEMENT / FITTING | |||||||||
Function / homology | Function and homology information ribosomal large subunit assembly / response to radiation / regulation of translation / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding ...ribosomal large subunit assembly / response to radiation / regulation of translation / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) Geobacillus stearothermophilus (bacteria) Thermotoga maritima (bacteria) Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å | |||||||||
Authors | Brimacombe, R. / Mueller, F. | |||||||||
Citation | Journal: J Mol Biol / Year: 2000 Title: The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution. Authors: F Mueller / I Sommer / P Baranov / R Matadeen / M Stoldt / J Wöhnert / M Görlach / M van Heel / R Brimacombe / Abstract: The Escherichia coli 23 S and 5 S rRNA molecules have been fitted helix by helix to a cryo-electron microscopic (EM) reconstruction of the 50 S ribosomal subunit, using an unfiltered version of the ...The Escherichia coli 23 S and 5 S rRNA molecules have been fitted helix by helix to a cryo-electron microscopic (EM) reconstruction of the 50 S ribosomal subunit, using an unfiltered version of the recently published 50 S reconstruction at 7.5 A resolution. At this resolution, the EM density shows a well-defined network of fine structural elements, in which the major and minor grooves of the rRNA helices can be discerned at many locations. The 3D folding of the rRNA molecules within this EM density is constrained by their well-established secondary structures, and further constraints are provided by intra and inter-rRNA crosslinking data, as well as by tertiary interactions and pseudoknots. RNA-protein cross-link and foot-print sites on the 23 S and 5 S rRNA were used to position the rRNA elements concerned in relation to the known arrangement of the ribosomal proteins as determined by immuno-electron microscopy. The published X-ray or NMR structures of seven 50 S ribosomal proteins or RNA-protein complexes were incorporated into the EM density. The 3D locations of cross-link and foot-print sites to the 23 S rRNA from tRNA bound to the ribosomal A, P or E sites were correlated with the positions of the tRNA molecules directly observed in earlier reconstructions of the 70 S ribosome at 13 A or 20 A. Similarly, the positions of cross-link sites within the peptidyl transferase ring of the 23 S rRNA from the aminoacyl residue of tRNA were correlated with the locations of the CCA ends of the A and P site tRNA. Sites on the 23 S rRNA that are cross-linked to the N termini of peptides of different lengths were all found to lie within or close to the internal tunnel connecting the peptidyl transferase region with the presumed peptide exit site on the solvent side of the 50 S subunit. The post-transcriptionally modified bases in the 23 S rRNA form a cluster close to the peptidyl transferase area. The minimum conserved core elements of the secondary structure of the 23 S rRNA form a compact block within the 3D structure and, conversely, the points corresponding to the locations of expansion segments in 28 S rRNA all lie on the outside of the structure. #1: Journal: Cell(Cambridge,Mass.) / Year: 1999 Title: A Detailed View of a Ribosomal Active Site: The Structure of the Gtpase Center at 2.6 Angstroms Resolution. Authors: Wimberly, B.T. / Guymon, R. / Mc Cutcheon, J.P. / White, S. / Ramakrishnan, V. #2: Journal: Embo J. / Year: 1999 Title: The NMR Structure of the 5S Rrna E-Domain-Protein C25 Complex Shows Pre-Formed and Induced Recognition. Authors: Stoldt, M. / Woehnert, J. / Ohlenschlaeger, O. / Goerlach, M. / Brown, L.R. #3: Journal: Embo J. / Year: 1999 Title: The Three-Dimensional Structure of the RNA-Binding Domain of Ribosomal Protein L2; a Protein at the Peptidyl Transferase Center of the Ribosome. Authors: Nakagawa, A. / Nakashima, T. / Taniguchi, M. / Hosaka, H. / Kimura, M. / Tanaka, I. #4: Journal: J.Mol.Biol. / Year: 1996 Title: Ribosomal Protein L9: A Structure Determination by the Combined Use of X-Ray Crystallography and NMR Spectroscopy. Authors: Hoffman, D.W. / Cameron, C.S. / Davies, C. / White, S.W. / Ramakrishnan, V. #5: Journal: Embo J. / Year: 1996 Title: Crystal Structure of the RNA Binding Ribosomal Protein L1 from Thermus Thermophilus. Authors: Nikonov, S. / Nevskaya, N. / Eliseikina, I. / Fomenkova, N. / Nikulin, A. / Ossina, N. / Garber, M. / Jonsson, B.H. / Briand, C. / Al-Karadaghi, S. / Svensson, A. / Aevarsson, A. / Liljas, A. #6: Journal: Structure / Year: 1996 Title: The Crystal Structure of Ribosomal Protein L14 Reveals an Important Organizational Component of the Translational Apparatus. Authors: Davies, C. / White, S.W. / Ramakrishnan, V. #7: Journal: Embo J. / Year: 1993 Title: Ribosomal Protein L6: Structural Evidence of Gene Duplication from a Primitive RNA Binding Proetin. Authors: Golden, B.L. / Ramakrishnan, V. / White, S.W. #8: Journal: Structure / Year: 1999 Title: The Escherichia coli large ribosomal subunit at 7.5 A resolution Authors: Matadeen, R. / Patwardhan, A. / Gowen, B. / Orlova, E.V. / Pape, T. / Cuff, M. / Mueller, F. / Brimacombe, R. / van Heel, M. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 487d.cif.gz | 224 KB | Display | PDBx/mmCIF format |
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PDB format | pdb487d.ent.gz | 176.7 KB | Display | PDB format |
PDBx/mmJSON format | 487d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 487d_validation.pdf.gz | 396.8 KB | Display | wwPDB validaton report |
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Full document | 487d_full_validation.pdf.gz | 439.5 KB | Display | |
Data in XML | 487d_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 487d_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/87/487d ftp://data.pdbj.org/pub/pdb/validation_reports/87/487d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-50S ribosomal protein ... , 7 types, 7 molecules HIJKLMN
#1: Protein | Mass: 24331.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P27150, UniProt: Q5SLP7*PLUS |
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#2: Protein | Mass: 14759.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: P04257 |
#3: Protein | Mass: 17811.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: P02391 |
#4: Protein | Mass: 16341.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: P02417 |
#5: Protein | Mass: 14294.913 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermotoga maritima (bacteria) / References: UniProt: P29395 |
#6: Protein | Mass: 13369.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: P04450 |
#7: Protein | Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3T3H7, UniProt: P68919*PLUS |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: LARGE 50S RIBOSOMAL SUBUNIT / Type: RIBOSOME |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Crystal | Description: THE CRYST1 AND SCALE RECORDS ARE MEANINGLESS. |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200FEG / Details: from Structure 1999 citation |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 38000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN |
Image recording | Film or detector model: GENERIC FILM |
Image scans | Scanner model: IMAGE SCIENCE PATCHWORK DENSITOMETER |
-Processing
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
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3D reconstruction | Resolution: 7.5 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Num. of particles: 16000 / Symmetry type: POINT | ||||||||||||
Atomic model building | Space: REAL Details: DETAILS--OTHER REFINEMENT REMARKS- CRYO-EM RECONSTRUCTION THIS FILE HAS BEEN GENERATED BY THE USE OF ALL RELEVANT BIOCHEMICAL CONSTRAINTS AND THE CONSTRAINTS GIVEN BY THE ELECTRON DENSITY ...Details: DETAILS--OTHER REFINEMENT REMARKS- CRYO-EM RECONSTRUCTION THIS FILE HAS BEEN GENERATED BY THE USE OF ALL RELEVANT BIOCHEMICAL CONSTRAINTS AND THE CONSTRAINTS GIVEN BY THE ELECTRON DENSITY CONTOUR OF THE RIBOSOME, WHICH WAS DERIVED FROM THE CRYO-ELECTRON MICROSCOPIC RECONSTRUCTION. | ||||||||||||
Atomic model building |
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Refinement | Highest resolution: 7.5 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 7.5 Å
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