3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - PDB-487d

SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION

by single particle reconstruction, at 7.5 A resolution

Movie

Orientation:

#1: Depositted structure unit, Image by Jmol

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 487d
TitleSEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION
KeywordsRIBOSOME, LARGE RIBOSOMAL SUBUNIT, RIBOSOMAL PROTEIN, PROTEIN BIOSYNTHESIS, EM-RECONSTRUCTION, ATOMIC STRUCTURE, 3D ARRANGEMENT, FITTING
AuthorsBrimacombe, R., Mueller, F.
DateDeposition: 2000-02-23, Release: 2000-04-10
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - primary
ArticleJ. Mol. Biol., Vol. 298, Issue 1, Page 35-59, Year 2000
TitleThe 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.
AuthorsF Mueller, I Sommer, P Baranov, R Matadeen, M Stoldt, J Wöhnert, M Görlach, M van Heel, R Brimacombe
Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, Berlin, 14195, Germany.
KeywordsBase Sequence, Binding Sites, C-SAR protein, Aspergillus clavatus, Computer Simulation, Conserved Sequence (genetics), Cross-Linking Reagents, Cryoelectron Microscopy, Crystallography, X-Ray, Escherichia coli (chemistry), Fungal Proteins (metabolism), Microscopy, Immunoelectron, Models, Molecular, Molecular Sequence Data, Nuclear Magnetic Resonance, Biomolecular, Nucleic Acid Conformation, Peptide Elongation Factor Tu (metabolism, 3.6.1.-), RNA, Bacterial (chemistry), RNA, Ribosomal, 23S (chemistry), RNA, Ribosomal, 5S (chemistry), RNA, Transfer (chemistry, 9014-25-9), Ribonucleases (metabolism, 3.1.-), Ribosomal Proteins (metabolism), Ribosomes (chemistry), Ricin (metabolism, 9009-86-3), Thermodynamics, ribosomal protein L11
LinksPubMed: 10756104, DOI: 10.1006/jmbi.2000.3635, PII: S0022-2836(00)93635-0
Citation - 1
ArticleCell(Cambridge,Mass.), Vol. 97, Page: 491 - , Year: 1999,
TitleA Detailed View of a Ribosomal Active Site: The Structure of the Gtpase Center at 2.6 Angstroms Resolution.
AuthorsWimberly, B.T., Guymon, R., Mc Cutcheon, J.P., White, S., Ramakrishnan, V.
LinksDOI: 10.1016/S0092-8674(00)80759-X
Citation - 2
ArticleEmbo J., Vol. 18, Page: 6508 - , Year: 1999,
TitleThe NMR Structure of the 5S Rrna E-Domain-Protein C25 Complex Shows Pre-Formed and Induced Recognition.
AuthorsStoldt, M., Woehnert, J., Ohlenschlaeger, O., Goerlach, M., Brown, L.R.
LinksDOI: 10.1093/emboj/18.22.6508
Citation - 3
ArticleEmbo J., Vol. 18, Page: 1459 - , Year: 1999,
TitleThe Three-Dimensional Structure of the RNA-Binding Domain of Ribosomal Protein L2; a Protein at the Peptidyl Transferase Center of the Ribosome.
AuthorsNakagawa, A., Nakashima, T., Taniguchi, M., Hosaka, H., Kimura, M., Tanaka, I.
LinksDOI: 10.1093/emboj/18.6.1459
Citation - 4
ArticleJ.Mol.Biol., Vol. 264, Page: 1058 - , Year: 1996,
TitleRibosomal Protein L9: A Structure Determination by the Combined Use of X-Ray Crystallography and NMR Spectroscopy.
AuthorsHoffman, D.W., Cameron, C.S., Davies, C., White, S.W., Ramakrishnan, V.
LinksDOI: 10.1006/jmbi.1996.0696
Citation - 5
ArticleEmbo J., Vol. 15, Page: 1350 - , Year: 1996,
TitleCrystal Structure of the RNA Binding Ribosomal Protein L1 from Thermus Thermophilus.
AuthorsNikonov, 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.
Citation - 6
ArticleStructure, Vol. 4, Page: 55 - , Year: 1996,
TitleThe Crystal Structure of Ribosomal Protein L14 Reveals an Important Organizational Component of the Translational Apparatus.
AuthorsDavies, C., White, S.W., Ramakrishnan, V.
LinksDOI: 10.1016/S0969-2126(96)00115-3
Citation - 7
ArticleEmbo J., Vol. 12, Page: 4901 - , Year: 1993,
TitleRibosomal Protein L6: Structural Evidence of Gene Duplication from a Primitive RNA Binding Proetin.
AuthorsGolden, B.L., Ramakrishnan, V., White, S.W.
Components
ID 1 : PROTEIN (50S L1 RIBOSOMAL PROTEIN)
Image
DescriptionPROTEIN (50S L1 RIBOSOMAL PROTEIN)
Typepolypeptide(L)
Formula weight24331.266 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Genus: Thermus
NCBI taxonomy: ID:274
Organism scientific: Thermus thermophilus
LinksUniProt: P27150, Sequence view
ID 2 : PROTEIN (50S L2 RIBOSOMAL PROTEIN)
Image
DescriptionPROTEIN (50S L2 RIBOSOMAL PROTEIN)
Typepolypeptide(L)
Formula weight14759.799 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Genus: Geobacillus
NCBI taxonomy: ID:1422
Organism scientific: Geobacillus stearothermophilus
LinksUniProt: P04257, Sequence view
ID 3 : PROTEIN (50S L6 RIBOSOMAL PROTEIN)
Image
DescriptionPROTEIN (50S L6 RIBOSOMAL PROTEIN)
Typepolypeptide(L)
Formula weight17811.609 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Genus: Geobacillus
NCBI taxonomy: ID:1422
Organism scientific: Geobacillus stearothermophilus
LinksUniProt: P02391, Sequence view
ID 4 : PROTEIN (50S L9 RIBOSOMAL PROTEIN)
Image
DescriptionPROTEIN (50S L9 RIBOSOMAL PROTEIN)
Typepolypeptide(L)
Formula weight16341.195 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Genus: Geobacillus
NCBI taxonomy: ID:1422
Organism scientific: Geobacillus stearothermophilus
LinksUniProt: P02417, Sequence view
ID 5 : PROTEIN (50S L11 RIBOSOMAL PROTEIN)
Image
DescriptionPROTEIN (50S L11 RIBOSOMAL PROTEIN)
Typepolypeptide(L)
Formula weight14295.032 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Genus: Thermotoga
NCBI taxonomy: ID:2336
Organism scientific: Thermotoga maritima
LinksUniProt: P29395, Sequence view
ID 6 : PROTEIN (50S L14 RIBOSOMAL PROTEIN)
Image
DescriptionPROTEIN (50S L14 RIBOSOMAL PROTEIN)
Typepolypeptide(L)
Formula weight13369.729 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Genus: Geobacillus
NCBI taxonomy: ID:1422
Organism scientific: Geobacillus stearothermophilus
LinksUniProt: P04450, Sequence view
ID 7 : PROTEIN (50S L25 RIBOSOMAL PROTEIN)
Image
DescriptionPROTEIN (50S L25 RIBOSOMAL PROTEIN)
Typepolypeptide(L)
Formula weight10713.566 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli

LinksUniProt: P02426, Sequence view
ID 8 : AMINO GROUP
Image
DescriptionAMINO GROUP
Typenon-polymer
Formula weight16.022 Da
Number of molecules1
ID8
SourceMethod: Obtained synthetically
ID 9 : FORMIC ACID
Image
DescriptionFORMIC ACID
Typenon-polymer
Formula weight46.026 Da
Number of molecules1
ID9
SourceMethod: Obtained synthetically
Sample
Assembly
Aggregation statePARTICLE
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Experiment
MethodELECTRON MICROSCOPY
Crystal
DescriptionTHE CRYST1 AND SCALE RECORDS ARE MEANINGLESS.
Electron Microscopy
Processing
Single particle entity
Symmetry typeASYMMETRIC
3D fitting
DetailsOTHER 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.
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
3D fitting list
3D Fitting ID1
3D fitting list
3D Fitting ID1
Refine
Refine idELECTRON MICROSCOPY
Ls d res high7.50 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high7.50
Total atoms7825
Ligand atoms4
Protein atoms7821
Download
PDB format
Allpdb487d.ent.gz
pdb487d.ent (uncompressed file)
Header onlypdb487d.ent.gz
mmCIF format
mmCIF487d.cif.gz
XML format
All487d.xml.gz
No-atom487d-noatom.xml.gz
Ext-atom487d-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.5 MB
.webm (WebM/VP8 format), 3.4 MB