PDB-487d: SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICR...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 487d
Title	SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION
Keywords	RIBOSOME, LARGE RIBOSOMAL SUBUNIT, RIBOSOMAL PROTEIN, PROTEIN BIOSYNTHESIS, EM-RECONSTRUCTION, ATOMIC STRUCTURE, 3D ARRANGEMENT, FITTING
Authors	Brimacombe, R., Mueller, F.
Date	Deposition: 2000-02-23, Release: 2000-04-10
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	PDB-1c2w Cite PDB-1c2x Cite PDB-2wwq Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-2280 List of similar structure data about Omokage system

Article
Citation - primary
Article	J. Mol. Biol., Vol. 298, Issue 1, Page 35-59, 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 Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, Berlin, 14195, Germany.
Keywords	Base 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
Links	PubMed: 10756104, DOI: 10.1006/jmbi.2000.3635, PII: S0022-2836(00)93635-0
Citation - 1
Article	Cell(Cambridge,Mass.), Vol. 97, Page: 491 - , 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.
Links	DOI: 10.1016/S0092-8674(00)80759-X
Citation - 2
Article	Embo J., Vol. 18, Page: 6508 - , 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.
Links	DOI: 10.1093/emboj/18.22.6508
Citation - 3
Article	Embo J., Vol. 18, Page: 1459 - , 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.
Links	DOI: 10.1093/emboj/18.6.1459
Citation - 4
Article	J.Mol.Biol., Vol. 264, Page: 1058 - , 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.
Links	DOI: 10.1006/jmbi.1996.0696
Citation - 5
Article	Embo J., Vol. 15, Page: 1350 - , 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.
Citation - 6
Article	Structure, Vol. 4, Page: 55 - , 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.
Links	DOI: 10.1016/S0969-2126(96)00115-3
Citation - 7
Article	Embo J., Vol. 12, Page: 4901 - , 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.

Components
ID 1 : PROTEIN (50S L1 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (50S L1 RIBOSOMAL PROTEIN)
Type	polymer
Formula weight	24331.266 Da
Number of molecules	1
Source	Method: Isolated from a natural source Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	UniProt: P27150, Sequence view
ID 2 : PROTEIN (50S L2 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (50S L2 RIBOSOMAL PROTEIN)
Type	polymer
Formula weight	14759.799 Da
Number of molecules	1
Source	Method: Isolated from a natural source Genus: Geobacillus NCBI taxonomy: ID:1422 Organism scientific: Geobacillus stearothermophilus
Links	UniProt: P04257, Sequence view
ID 3 : PROTEIN (50S L6 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (50S L6 RIBOSOMAL PROTEIN)
Type	polymer
Formula weight	17811.609 Da
Number of molecules	1
Source	Method: Isolated from a natural source Genus: Geobacillus NCBI taxonomy: ID:1422 Organism scientific: Geobacillus stearothermophilus
Links	UniProt: P02391, Sequence view
ID 4 : PROTEIN (50S L9 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (50S L9 RIBOSOMAL PROTEIN)
Type	polymer
Formula weight	16341.195 Da
Number of molecules	1
Source	Method: Isolated from a natural source Genus: Geobacillus NCBI taxonomy: ID:1422 Organism scientific: Geobacillus stearothermophilus
Links	UniProt: P02417, Sequence view
ID 5 : PROTEIN (50S L11 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (50S L11 RIBOSOMAL PROTEIN)
Type	polymer
Formula weight	14295.032 Da
Number of molecules	1
Source	Method: Isolated from a natural source Genus: Thermotoga NCBI taxonomy: ID:2336 Organism scientific: Thermotoga maritima
Links	UniProt: P29395, Sequence view
ID 6 : PROTEIN (50S L14 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (50S L14 RIBOSOMAL PROTEIN)
Type	polymer
Formula weight	13369.729 Da
Number of molecules	1
Source	Method: Isolated from a natural source Genus: Geobacillus NCBI taxonomy: ID:1422 Organism scientific: Geobacillus stearothermophilus
Links	UniProt: P04450, Sequence view
ID 7 : PROTEIN (50S L25 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (50S L25 RIBOSOMAL PROTEIN)
Type	polymer
Formula weight	10713.566 Da
Number of molecules	1
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P02426, Sequence view
ID 8 : AMINO GROUP
Image
Description	AMINO GROUP
Type	non-polymer
Formula weight	16.022 Da
Number of molecules	1
Source	Method: Obtained synthetically
ID 9 : FORMIC ACID
Image
Description	FORMIC ACID
Type	non-polymer
Formula weight	46.026 Da
Number of molecules	1
Source	Method: Obtained synthetically

Sample
Assembly
Aggregation state	PARTICLE
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Crystal
Description	THE CRYST1 AND SCALE RECORDS ARE MEANINGLESS.

Electron Microscopy

Processing
Single particle entity
Symmetry type	ASYMMETRIC
3D fitting
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.
Refinement Space	REAL
Refine
Ls d res high	7.50 A
ID	1
Refine hist
D res high	7.50
Total atoms	7825
Ligand atoms	4
Protein atoms	7821