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- PDB-486d: X-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL COMPLEXES -

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Basic information

Entry
Database: PDB / ID: 486d
TitleX-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL COMPLEXES
Components
  • 900 STEM-LOOP OF 16S RRNA IN THE 70S RIBOSOME
  • A-SITE CODON OF 70S RIBOSOME
  • A-SITE TRNA OF 70S RIBOSOME
  • E-SITE TRNA OF 70S RIBOSOME
  • P-SITE CODON OF 70S RIBOSOME
  • P-SITE TRNA OF 70S RIBOSOME
  • PENULTIMATE STEM OF 16S RRNA IN THE 70S RIBOSOME
KeywordsRIBOSOME / FUNCTIONAL MODELS OF 70S RIBOSOME / TRNA
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
Saccharomyces cerevisiae (brewer's yeast)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD PHASING / Resolution: 7.5 Å
AuthorsCate, J.H. / Yusupov, M.M. / Yusupova, G.Zh. / Earnest, T.N. / Noller, H.F.
Citation
Journal: Science / Year: 1999
Title: X-ray crystal structures of 70S ribosome functional complexes.
Authors: Cate, J.H. / Yusupov, M.M. / Yusupova, G.Z. / Earnest, T.N. / Noller, H.F.
#1: Journal: Science / Year: 1999
Title: Identification of an RNA-Protein Bridge Spanning the Ribosomal Subunit Interface
Authors: Culver, G.M. / Cate, J.H. / Yusupova, G.Z. / Yusupov, M.M. / Noller, H.F.
History
DepositionSep 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P-SITE TRNA OF 70S RIBOSOME
B: P-SITE CODON OF 70S RIBOSOME
C: A-SITE TRNA OF 70S RIBOSOME
D: A-SITE CODON OF 70S RIBOSOME
E: E-SITE TRNA OF 70S RIBOSOME
F: PENULTIMATE STEM OF 16S RRNA IN THE 70S RIBOSOME
G: 900 STEM-LOOP OF 16S RRNA IN THE 70S RIBOSOME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,50011
Polymers110,7317
Non-polymers7694
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)508.020, 508.020, 802.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Cell settingtetragonal
Space group name H-MI422

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Components

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RNA chain , 7 types, 7 molecules ABCDEFG

#1: RNA chain P-SITE TRNA OF 70S RIBOSOME


Mass: 24158.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#2: RNA chain P-SITE CODON OF 70S RIBOSOME


Mass: 873.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SEQUENCE FROM T. THERMOPHILUS
#3: RNA chain A-SITE TRNA OF 70S RIBOSOME


Mass: 23328.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#4: RNA chain A-SITE CODON OF 70S RIBOSOME


Mass: 911.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SEQUENCE FROM T. THERMOPHILUS
#5: RNA chain E-SITE TRNA OF 70S RIBOSOME


Mass: 23241.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#6: RNA chain PENULTIMATE STEM OF 16S RRNA IN THE 70S RIBOSOME / Coordinate model: P atoms only


Mass: 27506.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#7: RNA chain 900 STEM-LOOP OF 16S RRNA IN THE 70S RIBOSOME / Coordinate model: P atoms only


Mass: 10710.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)

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Non-polymers , 1 types, 4 molecules

#8: Chemical
ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ir

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

Crystal grow
*PLUS
Method: vapor diffusion, hanging, sitting drop / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mM1dropMgCl2
2100 mM1dropKCl
320 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1051, 1.1055, 1.0764, 1.1047
DetectorDetector: AREA DETECTOR
RadiationMonochromator: SI(111) DOUBLE-CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.10511
21.10551
31.07641
41.10471
ReflectionHighest resolution: 7.5 Å / Num. all: 124437 / Num. obs: 124437 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 15.8
Reflection
*PLUS

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Processing

Software
NameClassification
MLPHAREphasing
Omodel building
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD PHASING
Starting model: 4TNA, 3TRA, 1PBR, 1GID, 430D

4tna

3tra

1pbr

1gid

430d


Highest resolution: 7.5 Å
Details: THE MODEL WAS BULIT BY MANUAL FITTING OF INDIVIDUAL RNA MOLECULES INTO THE EXPERIMENTAL ELECTRON DENSITY USING THE GRAPHIC PROGRAM O. P TRNA WAS BUILT FROM 3TRA (ALL BUT ANTICODON STEM-LOOP) ...Details: THE MODEL WAS BULIT BY MANUAL FITTING OF INDIVIDUAL RNA MOLECULES INTO THE EXPERIMENTAL ELECTRON DENSITY USING THE GRAPHIC PROGRAM O. P TRNA WAS BUILT FROM 3TRA (ALL BUT ANTICODON STEM-LOOP) AND 4TRNA (ANTICODON STEM-LOOP), A TRNA WAS BUILT FROM 3TRA (ANTICODON STEM-LOOP) AND 4TRNA (ALL BUT ANTICODON STEM-LOOP). THE P CODON WAS BASED ON A-RNA, THE A-SITE CODON ON 3TRA. BOTH FRAGMENTS OF 16S RRNA (MOLECULES 6 AND 7) WERE BASED ON 1GID, 1PBR, 430D, AND A-RNA
Num. reflection% reflection
all124437 -
obs-97.7 %
Refinement stepCycle: LAST / Highest resolution: 7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4930 4 0 4934
Refinement
*PLUS
Highest resolution: 7.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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