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

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Database: PDB / ID: 487d
TitleSEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION
DescriptorSEVEN 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
Specimen sourceThermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス
Geobacillus stearothermophilus / bacteria / thermophilic / ゲオバチルス・ステアロサーモフィルス
Thermotoga maritima / bacteria / thermophilic / サーモトガ・マリティマ
Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (7.5 Å resolution / Particle / Single particle)
AuthorsBrimacombe, R. / Mueller, F.
CitationJ. Mol. Biol., 2000, 298, 35-59

primary. J. Mol. Biol., 2000, 298, 35-59 Yorodumi Papers
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.
F Mueller / I Sommer / P Baranov / R Matadeen / M Stoldt / J Wöhnert / M Görlach / M van Heel / R Brimacombe

#1. Cell(Cambridge,Mass.), 1999, 97, 491-
A Detailed View of a Ribosomal Active Site: The Structure of the Gtpase Center at 2.6 Angstroms Resolution.
Wimberly, B.T. / Guymon, R. / Mc Cutcheon, J.P. / White, S. / Ramakrishnan, V.

#2. Embo J., 1999, 18, 6508-
The NMR Structure of the 5S Rrna E-Domain-Protein C25 Complex Shows Pre-Formed and Induced Recognition.
Stoldt, M. / Woehnert, J. / Ohlenschlaeger, O. / Goerlach, M. / Brown, L.R.

#3. Embo J., 1999, 18, 1459-
The Three-Dimensional Structure of the RNA-Binding Domain of Ribosomal Protein L2; a Protein at the Peptidyl Transferase Center of the Ribosome.
Nakagawa, A. / Nakashima, T. / Taniguchi, M. / Hosaka, H. / Kimura, M. / Tanaka, I.

#4. J.Mol.Biol., 1996, 264, 1058-
Ribosomal Protein L9: A Structure Determination by the Combined Use of X-Ray Crystallography and NMR Spectroscopy.
Hoffman, D.W. / Cameron, C.S. / Davies, C. / White, S.W. / Ramakrishnan, V.

#5. Embo J., 1996, 15, 1350-
Crystal Structure of the RNA Binding Ribosomal Protein L1 from Thermus Thermophilus.
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. Structure, 1996, 4, 55-
The Crystal Structure of Ribosomal Protein L14 Reveals an Important Organizational Component of the Translational Apparatus.
Davies, C. / White, S.W. / Ramakrishnan, V.

#7. Embo J., 1993, 12, 4901-
Ribosomal Protein L6: Structural Evidence of Gene Duplication from a Primitive RNA Binding Proetin.
Golden, B.L. / Ramakrishnan, V. / White, S.W.

#8. Structure, 1999, 7, 1575-
The Escherichia coli large ribosomal subunit at 7.5 A resolution
Matadeen, R. / Patwardhan, A. / Gowen, B. / Orlova, E.V. / Pape, T. / Cuff, M. / Mueller, F. / Brimacombe, R. / van Heel, M.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 23, 2000 / Release: Apr 10, 2000
RevisionDateData content typeGroupProviderType
1.0Apr 10, 2000Structure modelrepositoryInitial release
1.1Apr 26, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
H: PROTEIN (50S L1 RIBOSOMAL PROTEIN)
I: PROTEIN (50S L2 RIBOSOMAL PROTEIN)
J: PROTEIN (50S L6 RIBOSOMAL PROTEIN)
K: PROTEIN (50S L9 RIBOSOMAL PROTEIN)
L: PROTEIN (50S L11 RIBOSOMAL PROTEIN)
M: PROTEIN (50S L14 RIBOSOMAL PROTEIN)
N: PROTEIN (50S L25 RIBOSOMAL PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6839
Polyers111,6217
Non-polymers622
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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PROTEIN (50S ... , 7 types, 7 molecules HIJKLMN

#1: Polypeptide(L)PROTEIN (50S L1 RIBOSOMAL PROTEIN)


Mass: 24331.074 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: UniProt: P27150

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)PROTEIN (50S L2 RIBOSOMAL PROTEIN)


Mass: 14759.666 Da / Num. of mol.: 1 / Source: (natural) Geobacillus stearothermophilus / References: UniProt: P04257

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)PROTEIN (50S L6 RIBOSOMAL PROTEIN)


Mass: 17811.447 Da / Num. of mol.: 1 / Source: (natural) Geobacillus stearothermophilus / References: UniProt: P02391

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)PROTEIN (50S L9 RIBOSOMAL PROTEIN)


Mass: 16341.037 Da / Num. of mol.: 1 / Source: (natural) Geobacillus stearothermophilus / References: UniProt: P02417

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)PROTEIN (50S L11 RIBOSOMAL PROTEIN)


Mass: 14294.913 Da / Num. of mol.: 1 / Source: (natural) Thermotoga maritima / References: UniProt: P29395

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)PROTEIN (50S L14 RIBOSOMAL PROTEIN)


Mass: 13369.613 Da / Num. of mol.: 1 / Source: (natural) Geobacillus stearothermophilus / References: UniProt: P04450

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)PROTEIN (50S L25 RIBOSOMAL PROTEIN)


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P02426

Cellular component

Molecular function

Biological process

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Non-polymers , 2 types, 2 molecules

#8: ChemicalChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 1 / Formula: NH2
#9: ChemicalChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Formula: CH2O2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: LARGE 50S RIBOSOMAL SUBUNIT / Type: RIBOSOME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
CrystalDescription: THE CRYST1 AND SCALE RECORDS ARE MEANINGLESS.

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200FEG / Details: from Structure 1999 citation
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 38000 / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Image recordingFilm or detector model: GENERIC FILM
Image scansScanner model: IMAGE SCIENCE PATCHWORK DENSITOMETER

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Processing

SymmetryPoint symmetry: C1
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Number of particles: 16000 / Symmetry type: POINT
Atomic model buildingDetails: 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.
Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
11CSV1
21CSX1
31CSW1
Least-squares processHighest resolution: 7.5 Å
Refine hist #LASTHighest resolution: 7.5 Å
Number of atoms included #LASTProtein: 8774 / Nucleic acid: 0 / Ligand: 4 / Solvent: 0 / Total: 8778

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