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

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Entry
Database: PDB / ID: 487d
TitleSEVEN 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
KeywordsRIBOSOME / LARGE RIBOSOMAL SUBUNIT / RIBOSOMAL PROTEIN / PROTEIN BIOSYNTHESIS / EM-RECONSTRUCTION / ATOMIC STRUCTURE / 3D ARRANGEMENT / FITTING
Function / homology
Function and homology information


response to radiation / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / regulation of translation / large ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / tRNA binding ...response to radiation / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / regulation of translation / large ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L25, short-form / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type ...Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L25, short-form / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L11, N-terminal / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L14P, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L2, conserved site / Ribosomal protein L2 signature. / Ribosomal protein L2, domain 3 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L14P, conserved site / Ribosomal protein L6 / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Ribosomal protein L14 signature. / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Geobacillus stearothermophilus (bacteria)
Thermotoga maritima (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsBrimacombe, 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
DepositionFeb 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Jun 7, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_src_nat / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.details / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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Assembly

Deposited unit
H: 50S ribosomal protein L1
I: 50S ribosomal protein L2
J: 50S ribosomal protein L6
K: 50S ribosomal protein L9
L: 50S ribosomal protein L11
M: 50S ribosomal protein L14
N: 50S ribosomal protein L25


Theoretical massNumber of molelcules
Total (without water)111,6217
Polymers111,6217
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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50S ribosomal protein ... , 7 types, 7 molecules HIJKLMN

#1: Protein 50S ribosomal protein L1 /


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
#2: Protein 50S ribosomal protein L2 / / BstL2 / L3


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 50S ribosomal protein L6 / / BL10


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 50S ribosomal protein L9 / / BL17


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 50S ribosomal protein L11 /


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 50S ribosomal protein L14 /


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 50S ribosomal protein L25 /


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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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

MicroscopyModel: 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 FIELDBright-field microscopy / Nominal magnification: 38000 X / 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 (asymmetric)
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Num. of particles: 16000 / Symmetry type: POINT
Atomic model buildingSpace: 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
IDPDB-ID 3D fitting-ID
11CSV

1csv

1
21CSX

1csx

1
31CSW

1csw

1
RefinementHighest resolution: 7.5 Å
Refinement stepCycle: LAST / Highest resolution: 7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8774 0 4 0 8778

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