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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 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsBrimacombe, R. / Mueller, F.
CitationJ. Mol. Biol., 2000, 298, 35-59

primary. J. Mol. Biol., 2000, 298, 35-59 StrPapers
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.

DateDeposition: Feb 23, 2000 / Release: Apr 10, 2000 / Last modification: Feb 24, 2009

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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)111,6849
Polyers111,6227
Non-polymers622
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Polypeptide(L) , 7 types, 7 molecules HIJKLMN

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


Mass: 24331.266 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: 14759.799 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: 17811.609 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: 16341.195 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: 14295.032 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: 13369.729 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: 10713.566 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: 16.022 Da / Num. of mol.: 1 / Formula: NH2
#9: ChemicalChemComp-FMT / FORMIC ACID


Mass: 46.026 Da / Num. of mol.: 1 / Formula: CH2O2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenAggregation state: PARTICLE
CrystalDescription: THE CRYST1 AND SCALE RECORDS ARE MEANINGLESS.

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Processing

EM single particle entitySymmetry type: ASYMMETRIC
Atomic model buildingDetails: 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
PDB-ID 3D fitting idID
487D11
487D12
487D13
Least-squares processHighest resolution: 7.5 A
Refine hist #LASTHighest resolution: 7.5 A
Number of atoms included #LASTProtein: 7821 / Nucleic acid: 0 / Ligand: 4 / Solvent: 0 / Total: 7825

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