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- PDB-9q87: Principles of ion binding to RNA inferred from the analysis of a ... -

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Basic information

Entry
Database: PDB / ID: 9q87
TitlePrinciples of ion binding to RNA inferred from the analysis of a 1.55 Angstrom resolution bacterial ribosome structure - Part I: Mg2+
Components
  • (Large ribosomal subunit protein ...) x 29
  • (Small ribosomal subunit protein ...) x 20
  • 23S rRNA
  • 30S
  • 5S rRNA
  • A-site tRNA
  • P-site tRNA
  • mRNA
KeywordsRIBOSOME / Magnesium / Mg2+ / Potassium / K+
Function / homology
Function and homology information


transcription antitermination factor activity, RNA binding / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of ribosome biogenesis / four-way junction DNA binding / regulation of mRNA stability / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity ...transcription antitermination factor activity, RNA binding / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of ribosome biogenesis / four-way junction DNA binding / regulation of mRNA stability / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / response to reactive oxygen species / transcription elongation factor complex / transcription antitermination / DNA endonuclease activity / regulation of cell growth / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / large ribosomal subunit / ribosome biogenesis / transferase activity / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / ribosomal large subunit assembly / 5S rRNA binding / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / response to antibiotic / hydrolase activity / mRNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L11, bacterial-type / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S21 ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L11, bacterial-type / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / 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 L17 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal L25p family / Ribosomal protein L25 / 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, RNA binding domain / : / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L28/L24 superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L28 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / : / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L6, bacterial-type / : / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / : / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L33 superfamily / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature.
Similarity search - Domain/homology
COPPER (I) ION / : / 5-hydroxycytidine 5'-(dihydrogen phosphate) / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...COPPER (I) ION / : / 5-hydroxycytidine 5'-(dihydrogen phosphate) / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli B (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.55 Å
AuthorsLeonarski, F. / Henning-Knechtel, A. / Kirmizialtin, S. / Ennifar, E. / Auffinger, P.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure - Part I: Mg2.
Authors: Filip Leonarski / Anja Henning-Knechtel / Serdal Kirmizialtin / Eric Ennifar / Pascal Auffinger /
Abstract: The importance of Mg2+ ions for RNA structure and function cannot be overstated. Several attempts were made to establish a comprehensive Mg2+ binding site classification. However, such descriptions ...The importance of Mg2+ ions for RNA structure and function cannot be overstated. Several attempts were made to establish a comprehensive Mg2+ binding site classification. However, such descriptions were hampered by poorly modelled ion binding sites as observed in a recent cryo-EM 1.55 Å Escherichia coli ribosome structure where incomplete ion assignments blurred our understanding of their binding patterns. We revisited this model to establish general binding principles applicable to any RNA of sufficient resolution. These principles rely on the 2.9 Å distance separating two water molecules bound in cis to Mg2+. By applying these rules, we could assign all Mg2+ ions bound with 2-4 non-water oxygens. We also uncovered unanticipated motifs where up to five adjacent nucleotides wrap around a single ion. The formation of such motifs involves a hierarchical Mg2+ ion dehydration process that plays a significant role in ribosome biogenesis and in the folding of large RNAs. Besides, we established a classification of the Mg2+…Mg2+ and Mg2+…K+ ion pairs observed in this ribosome. Overall, the uncovered binding principles enhance our understanding of the roles of ions in RNA structure and will help refining the solvation shell of other RNA systems.
History
DepositionFeb 23, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 2.0Nov 12, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / audit_author / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / database_PDB_caveat / em_3d_fitting / em_software / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_ls_restr / struct_asym / struct_conf / struct_conn / struct_keywords / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _audit_author.name / _chem_comp.formula ..._audit_author.name / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _em_3d_fitting.ref_protocol / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.i_label_seq_id_1 / _ndb_struct_na_base_pair_step.i_label_seq_id_2 / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.j_auth_seq_id_1 / _ndb_struct_na_base_pair_step.j_label_seq_id_1 / _ndb_struct_na_base_pair_step.j_label_seq_id_2 / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.step_name / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _refine.B_iso_mean / _refine.pdbx_stereochemistry_target_values / _struct_keywords.text / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Model completeness
Details: * B-factors were corrected; * five potential CU1 (Cu+) positions were added; * A few Mg2+ and K+ ions were added; * Other minor corrections;
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 30S
B: Small ribosomal subunit protein uS2
C: Small ribosomal subunit protein uS3
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
F: Small ribosomal subunit protein bS6, fully modified isoform
G: Small ribosomal subunit protein uS7
H: Small ribosomal subunit protein uS8
I: Small ribosomal subunit protein uS9
J: Small ribosomal subunit protein uS10
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
M: Small ribosomal subunit protein uS13
N: Small ribosomal subunit protein uS14
O: Small ribosomal subunit protein uS15
P: Small ribosomal subunit protein bS16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18
S: Small ribosomal subunit protein uS19
T: Small ribosomal subunit protein bS20
U: Small ribosomal subunit protein bS21
X: mRNA
Z: P-site tRNA
0: Large ribosomal subunit protein bL33
1: Large ribosomal subunit protein bL34
2: Large ribosomal subunit protein bL35
3: Large ribosomal subunit protein bL36
5: Large ribosomal subunit protein uL11
6: A-site tRNA
a: 23S rRNA
b: 5S rRNA
c: Large ribosomal subunit protein uL2
d: Large ribosomal subunit protein uL3
e: Large ribosomal subunit protein uL4
f: Large ribosomal subunit protein uL5
g: Large ribosomal subunit protein uL6
h: Large ribosomal subunit protein bL9
i: Large ribosomal subunit protein uL13
j: Large ribosomal subunit protein uL14
k: Large ribosomal subunit protein uL15
l: Large ribosomal subunit protein uL16
m: Large ribosomal subunit protein bL17
n: Large ribosomal subunit protein uL18
o: Large ribosomal subunit protein bL19
p: Large ribosomal subunit protein bL20
q: Large ribosomal subunit protein bL21
r: Large ribosomal subunit protein uL22
s: Large ribosomal subunit protein uL23
t: Large ribosomal subunit protein uL24
u: Large ribosomal subunit protein bL25
v: Large ribosomal subunit protein bL27
w: Large ribosomal subunit protein bL28
x: Large ribosomal subunit protein uL29
y: Large ribosomal subunit protein uL30
z: Large ribosomal subunit protein bL32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,198,636712
Polymers2,178,63955
Non-polymers19,997657
Water385,30521388
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 6 types, 6 molecules AXZ6ab

#1: RNA chain 30S


Mass: 503775.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Three anionic nucleotides are present. Position:677 and 1086 corresponds to a negatively charged uridine; position: 741 corresponds to a negatively charged guanine;
Source: (natural) Escherichia coli B (bacteria) / References: GenBank: 991965528
#22: RNA chain mRNA


Mass: 1923.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli B (bacteria)
#23: RNA chain P-site tRNA


Mass: 24848.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: GenBank: 1173003849
#29: RNA chain A-site tRNA


Mass: 589.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The residues 75(C)-76(A) from an unknown tRNA in the A-site
Source: (natural) Escherichia coli B (bacteria)
#30: RNA chain 23S rRNA


Mass: 942834.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: The following residue is anionic: U:2316. / Source: (natural) Escherichia coli B (bacteria)
#31: RNA chain 5S rRNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: GenBank: 1815787944

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Small ribosomal subunit protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 25872.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7V0
#3: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7V3
#4: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7V8
#5: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7W1
#6: Protein Small ribosomal subunit protein bS6, fully modified isoform


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P02358
#7: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P02359
#8: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7W7
#9: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7X3
#10: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10 / Transcription termination/antitermination protein NusE


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7R5
#11: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13871.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7R9
#12: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13814.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7S3
#13: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7S9
#14: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0AG59
#15: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0ADZ4
#16: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7T3
#17: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0AG63
#18: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7T7
#19: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7U3
#20: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7U7
#21: Protein Small ribosomal subunit protein bS21 / 30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P68679

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Large ribosomal subunit protein ... , 29 types, 29 molecules 01235cdefghijklmnopqrstuvwxyz

#24: Protein Large ribosomal subunit protein bL33 / 50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7N9
#25: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7P5
#26: Protein Large ribosomal subunit protein bL35


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3T7Q2
#27: Protein/peptide Large ribosomal subunit protein bL36


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: A0A2X1PTA3
#28: Protein Large ribosomal subunit protein uL11


Mass: 14763.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SIC7
#32: Protein Large ribosomal subunit protein uL2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SQV7
#33: Protein Large ribosomal subunit protein uL3


Mass: 22291.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SQU2
#34: Protein Large ribosomal subunit protein uL4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SQU7
#35: Protein Large ribosomal subunit protein uL5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SR02
#36: Protein Large ribosomal subunit protein uL6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SR17
#37: Protein Large ribosomal subunit protein bL9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SFP2
#38: Protein Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SRX7
#39: Protein Large ribosomal subunit protein uL14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SQZ2
#40: Protein Large ribosomal subunit protein uL15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: A0A037Y8L6
#41: Protein Large ribosomal subunit protein uL16


Mass: 15196.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SQX7
#42: Protein Large ribosomal subunit protein bL17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SR72
#43: Protein Large ribosomal subunit protein uL18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SR22
#44: Protein Large ribosomal subunit protein bL19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SYQ7
#45: Protein Large ribosomal subunit protein bL20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3T7Q7
#46: Protein Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SSG2
#47: Protein Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SQW7
#48: Protein Large ribosomal subunit protein uL23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: C3SQV2
#49: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P60624
#50: Protein Large ribosomal subunit protein bL25 / 50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P68919
#51: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7L8
#52: Protein Large ribosomal subunit protein bL28 / 50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7M2
#53: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7M6
#54: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0AG51
#55: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: UniProt: P0A7N4

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Non-polymers , 6 types, 22045 molecules

#56: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 235 / Source method: obtained synthetically / Formula: K
#57: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 415 / Source method: obtained synthetically / Formula: Mg
#58: Chemical
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cu
#59: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#60: Chemical ChemComp-TKW / 5-hydroxycytidine 5'-(dihydrogen phosphate)


Mass: 339.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O9P / Feature type: SUBJECT OF INVESTIGATION
#61: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21388 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: Escherichia coli strain B ribosome / Type: RIBOSOME / Entity ID: #1-#55 / Source: NATURAL
Source (natural)Organism: Escherichia coli B (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIXdev_5505model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 1.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 506020 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 8B0X

8b0x


Accession code: 8B0X / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE

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