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- PDB-1ml5: Structure of the E. coli ribosomal termination complex with relea... -

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Basic information

Entry
Database: PDB / ID: 1ml5
TitleStructure of the E. coli ribosomal termination complex with release factor 2
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S RIBOSOMAL PROTEIN ...) x 19
  • 30S 16S RIBOSOMAL RNA
  • 50S 23S RIBOSOMAL RNA
  • 50S 5S RIBOSOMAL RNA
  • A- AND P-SITE MESSENGER RNA CODONS
  • Peptide chain release factor 2
  • T-RNA(PHE)
KeywordsRIBOSOME / E. coli / termination of protein synthesis / release factor / cryo-eletron microscopy / angular reconstitution
Function / homology
Function and homology information


translation release factor activity, codon specific / translational termination / response to radiation / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / cytoplasmic translation ...translation release factor activity, codon specific / translational termination / response to radiation / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Peptide chain release factor 2 / Ribosomal protein L10e, archaea / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. ...Peptide chain release factor 2 / Ribosomal protein L10e, archaea / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Ribosomal protein L24e / Peptide chain release factor class I / RF-1 domain / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal protein L1, bacterial-type / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / metallochaperone-like domain / TRASH domain / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L10e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L24e signature. / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L25, short-form / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L24e / Ribosomal protein L1p/L10e family / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L11, bacterial-type / Ribosomal protein L1e signature. / 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 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 S14/S29 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L14P, bacterial-type / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / : / Ribosomal protein L30, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L23/L25, conserved site
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL14 / Peptide chain release factor RF2 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL14 / Peptide chain release factor RF2 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 14 Å
AuthorsKlaholz, B.P. / Pape, T. / Zavialov, A.V. / Myasnikov, A.G. / Orlova, E.V. / Vestergaard, B. / Ehrenberg, M. / van Heel, M.
CitationJournal: Nature / Year: 2003
Title: Structure of the Escherichia coli ribosomal termination complex with release factor 2.
Authors: Bruno P Klaholz / Tillmann Pape / Andrey V Zavialov / Alexander G Myasnikov / Elena V Orlova / Bente Vestergaard / Måns Ehrenberg / Marin van Heel /
Abstract: Termination of protein synthesis occurs when the messenger RNA presents a stop codon in the ribosomal aminoacyl (A) site. Class I release factor proteins (RF1 or RF2) are believed to recognize stop ...Termination of protein synthesis occurs when the messenger RNA presents a stop codon in the ribosomal aminoacyl (A) site. Class I release factor proteins (RF1 or RF2) are believed to recognize stop codons via tripeptide motifs, leading to release of the completed polypeptide chain from its covalent attachment to transfer RNA in the ribosomal peptidyl (P) site. Class I RFs possess a conserved GGQ amino-acid motif that is thought to be involved directly in protein-transfer-RNA bond hydrolysis. Crystal structures of bacterial and eukaryotic class I RFs have been determined, but the mechanism of stop codon recognition and peptidyl-tRNA hydrolysis remains unclear. Here we present the structure of the Escherichia coli ribosome in a post-termination complex with RF2, obtained by single-particle cryo-electron microscopy (cryo-EM). Fitting the known 70S and RF2 structures into the electron density map reveals that RF2 adopts a different conformation on the ribosome when compared with the crystal structure of the isolated protein. The amino-terminal helical domain of RF2 contacts the factor-binding site of the ribosome, the 'SPF' loop of the protein is situated close to the mRNA, and the GGQ-containing domain of RF2 interacts with the peptidyl-transferase centre (PTC). By connecting the ribosomal decoding centre with the PTC, RF2 functionally mimics a tRNA molecule in the A site. Translational termination in eukaryotes is likely to be based on a similar mechanism.
History
DepositionAug 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 18, 2019Group: Advisory / Derived calculations / Other
Category: atom_sites / cell ...atom_sites / cell / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][3] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: 30S 16S RIBOSOMAL RNA
B: T-RNA(PHE)
C: A- AND P-SITE MESSENGER RNA CODONS
a: 50S 23S RIBOSOMAL RNA
b: 50S 5S RIBOSOMAL RNA
Z: Peptide chain release factor 2
E: 30S RIBOSOMAL PROTEIN S2
F: 30S RIBOSOMAL PROTEIN S3
G: 30S RIBOSOMAL PROTEIN S4
H: 30S RIBOSOMAL PROTEIN S5
I: 30S RIBOSOMAL PROTEIN S6
J: 30S RIBOSOMAL PROTEIN S7
K: 30S RIBOSOMAL PROTEIN S8
L: 30S RIBOSOMAL PROTEIN S9
M: 30S RIBOSOMAL PROTEIN S10
N: 30S RIBOSOMAL PROTEIN S11
O: 30S RIBOSOMAL PROTEIN S12
P: 30S RIBOSOMAL PROTEIN S13
Q: 30S RIBOSOMAL PROTEIN S14
R: 30S RIBOSOMAL PROTEIN S15
S: 30S RIBOSOMAL PROTEIN S16
T: 30S RIBOSOMAL PROTEIN S17
U: 30S RIBOSOMAL PROTEIN S18
V: 30S RIBOSOMAL PROTEIN S19
W: 30S RIBOSOMAL PROTEIN S20
X: 30S RIBOSOMAL PROTEIN THX
c: 50S RIBOSOMAL PROTEIN L1
d: 50S RIBOSOMAL PROTEIN L2
e: 50S RIBOSOMAL PROTEIN L3
f: 50S RIBOSOMAL PROTEIN L4
g: 50S RIBOSOMAL PROTEIN L5
h: 50S RIBOSOMAL PROTEIN L6
l: 50S RIBOSOMAL PROTEIN L11
m: 50S RIBOSOMAL PROTEIN L13
n: 50S RIBOSOMAL PROTEIN L14
o: 50S RIBOSOMAL PROTEIN L15
p: 50S RIBOSOMAL PROTEIN L16
q: 50S RIBOSOMAL PROTEIN L18
r: 50S RIBOSOMAL PROTEIN L19
s: 50S RIBOSOMAL PROTEIN L22
t: 50S RIBOSOMAL PROTEIN L23
u: 50S RIBOSOMAL PROTEIN L24
v: 50S RIBOSOMAL PROTEIN L25
w: 50S RIBOSOMAL PROTEIN L29
x: 50S RIBOSOMAL PROTEIN L30


Theoretical massNumber of molelcules
Total (without water)2,153,30645
Polymers2,153,30645
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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RNA chain , 5 types, 5 molecules ABCab

#1: RNA chain 30S 16S RIBOSOMAL RNA / Coordinate model: P atoms only


Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#2: RNA chain T-RNA(PHE)


Mass: 24890.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: tRNA P-SITE / Source: (natural) Escherichia coli (E. coli)
#3: RNA chain A- AND P-SITE MESSENGER RNA CODONS


Mass: 1792.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 6 NT LONG MRNA FRAGMENT / Source: (natural) Escherichia coli (E. coli)
#4: RNA chain 50S 23S RIBOSOMAL RNA / Coordinate model: P atoms only


Mass: 948280.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#5: RNA chain 50S 5S RIBOSOMAL RNA / Coordinate model: P atoms only


Mass: 39846.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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Protein , 1 types, 1 molecules Z

#6: Protein Peptide chain release factor 2 / RF-2 / translation releasing factor RF-2 / Coordinate model: Cα atoms only


Mass: 41300.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: EM reconstruction of the backbone trace of the ribosome
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: prfB/SupK / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P07012

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30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules EFGHIJKLMNOPQRSTUVWX

#7: Protein 30S RIBOSOMAL PROTEIN S2 / / Coordinate model: Cα atoms only


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P80371*PLUS
#8: Protein 30S RIBOSOMAL PROTEIN S3 / / Coordinate model: Cα atoms only


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P80372*PLUS
#9: Protein 30S RIBOSOMAL PROTEIN S4 / / Coordinate model: Cα atoms only


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P80373*PLUS
#10: Protein 30S RIBOSOMAL PROTEIN S5 / / Coordinate model: Cα atoms only


Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q5SHQ5*PLUS
#11: Protein 30S RIBOSOMAL PROTEIN S6 / / Coordinate model: Cα atoms only


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q5SLP8*PLUS
#12: Protein 30S RIBOSOMAL PROTEIN S7 / / Coordinate model: Cα atoms only


Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P17291*PLUS
#13: Protein 30S RIBOSOMAL PROTEIN S8 / / Coordinate model: Cα atoms only


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0DOY9*PLUS
#14: Protein 30S RIBOSOMAL PROTEIN S9 / / Coordinate model: Cα atoms only


Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P80374*PLUS
#15: Protein 30S RIBOSOMAL PROTEIN S10 / / Coordinate model: Cα atoms only


Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q5SHN7*PLUS
#16: Protein 30S RIBOSOMAL PROTEIN S11 / / Coordinate model: Cα atoms only


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P80376*PLUS
#17: Protein 30S RIBOSOMAL PROTEIN S12 / / Coordinate model: Cα atoms only


Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q5SHN3*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S13 / / Coordinate model: Cα atoms only


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P80377*PLUS
#19: Protein 30S RIBOSOMAL PROTEIN S14 / / Coordinate model: Cα atoms only


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0DOY6*PLUS
#20: Protein 30S RIBOSOMAL PROTEIN S15 / / Coordinate model: Cα atoms only


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q5SJ76*PLUS
#21: Protein 30S RIBOSOMAL PROTEIN S16 / / Coordinate model: Cα atoms only


Mass: 10808.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q5SJH3*PLUS
#22: Protein 30S RIBOSOMAL PROTEIN S17 / / Coordinate model: Cα atoms only


Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0DOY7*PLUS
#23: Protein 30S RIBOSOMAL PROTEIN S18 / / Coordinate model: Cα atoms only


Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q5SLQ0*PLUS
#24: Protein 30S RIBOSOMAL PROTEIN S19 / / Coordinate model: Cα atoms only


Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q5SHP2*PLUS
#25: Protein 30S RIBOSOMAL PROTEIN S20 / / Coordinate model: Cα atoms only


Mass: 11722.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P80380*PLUS
#26: Protein/peptide 30S RIBOSOMAL PROTEIN THX / Ribosome / Coordinate model: Cα atoms only


Mass: 3218.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q5SIH3*PLUS

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50S RIBOSOMAL PROTEIN ... , 19 types, 19 molecules cdefghlmnopqrstuvwx

#27: Protein 50S RIBOSOMAL PROTEIN L1 / / Coordinate model: Cα atoms only


Mass: 24736.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q5SLP7*PLUS
#28: Protein 50S RIBOSOMAL PROTEIN L2 / / Coordinate model: Cα atoms only


Mass: 19283.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q5L3Z4*PLUS
#29: Protein 50S RIBOSOMAL PROTEIN L3 / / Coordinate model: Cα atoms only


Mass: 37412.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P20279*PLUS
#30: Protein 50S RIBOSOMAL PROTEIN L4 / / Coordinate model: Cα atoms only


Mass: 26443.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P12735*PLUS
#31: Protein 50S RIBOSOMAL PROTEIN L5 / / Coordinate model: Cα atoms only


Mass: 19420.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P14124*PLUS
#32: Protein 50S RIBOSOMAL PROTEIN L6 / / Coordinate model: Cα atoms only


Mass: 19202.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02391*PLUS
#33: Protein 50S RIBOSOMAL PROTEIN L11 / / Coordinate model: Cα atoms only


Mass: 15111.923 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P29395*PLUS
#34: Protein 50S RIBOSOMAL PROTEIN L13 / / Coordinate model: Cα atoms only


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P29198*PLUS
#35: Protein 50S RIBOSOMAL PROTEIN L14 / / Coordinate model: Cα atoms only


Mass: 13369.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P04450*PLUS
#36: Protein 50S RIBOSOMAL PROTEIN L15 / / Coordinate model: Cα atoms only


Mass: 17874.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P12737*PLUS
#37: Protein 50S RIBOSOMAL PROTEIN L16 / / Coordinate model: Cα atoms only


Mass: 15313.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60617*PLUS
#38: Protein 50S RIBOSOMAL PROTEIN L18 / / Coordinate model: Cα atoms only


Mass: 20509.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P14123*PLUS
#39: Protein 50S RIBOSOMAL PROTEIN L19 / / Coordinate model: Cα atoms only


Mass: 7233.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P14116*PLUS
#40: Protein 50S RIBOSOMAL PROTEIN L22 / / Coordinate model: Cα atoms only


Mass: 12808.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q5SHP3*PLUS
#41: Protein 50S RIBOSOMAL PROTEIN L23 / / Coordinate model: Cα atoms only


Mass: 9481.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P12732*PLUS
#42: Protein 50S RIBOSOMAL PROTEIN L24 / / Coordinate model: Cα atoms only


Mass: 13539.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P10972*PLUS
#43: Protein 50S RIBOSOMAL PROTEIN L25 / / Coordinate model: Cα atoms only


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68919*PLUS
#44: Protein 50S RIBOSOMAL PROTEIN L29 / / Coordinate model: Cα atoms only


Mass: 7758.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P10971*PLUS
#45: Protein 50S RIBOSOMAL PROTEIN L30 / / Coordinate model: Cα atoms only


Mass: 6799.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q5SHQ6*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

Component
IDNameTypeDetailsParent-ID
1release factor RF2 bound to E. coli ribosomesRIBOSOMEE. coli ribosomes, paused with a UAA stop codon in the A site and a tetrapeptidyl-tRNA in the P site, added release factor RF20
2peptide release factor RF2monomer1
Buffer solutionName: polymix buffer / pH: 7.5 / Details: polymix buffer
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: holey carbon grid at 20C; flash frozen into liquid ethan
Crystal grow
*PLUS
Method: electron microscopy / Details: Electron Microscopy

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG/ST / Date: Sep 6, 2001 / Details: low dose mode
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 48000 X / Nominal defocus max: 2900 nm / Nominal defocus min: 500 nm / Cs: 2.1 mm
Specimen holderTemperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 78

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Processing

CTF correctionDetails: phase flipping CTF correction of each particle as function of position in the micrograph
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: angular reconstitution, exact filtered back-projection
Resolution: 14 Å / Num. of particles: 15800 / Nominal pixel size: 2.419 Å / Actual pixel size: 2.419 Å
Magnification calibration: scaling with respect to 70S crystal structure (PDB codes 1GIX and 1GIY)
Details: iterative refinement procedure as described in Quat. Rev. of Biophysics 33, 4 (2000), pp. 307-369
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: best visual fit using the program O
Details: REFINEMENT PROTOCOL--rigid body fit of the 70S ribosome without individual fitting of proteins or RNA fragments. Rigid body fit of three individual domains of release factor RF2 keeping the ...Details: REFINEMENT PROTOCOL--rigid body fit of the 70S ribosome without individual fitting of proteins or RNA fragments. Rigid body fit of three individual domains of release factor RF2 keeping the connectivity; linkers betweenn domains defined based on temperature factors of crystal structure, conserved Gly and Pro residues, proteolytic sites, and global domain architecture
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11GQE

1gqe

11GQE1PDBexperimental model
21GIX

1gix
PDB Unreleased entry

11GIX2PDBexperimental model
31GIY

1giy
PDB Unreleased entry

11GIY3PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms5089 6303 0 0 11392

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