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- PDB-6osk: RF1 accommodated 70S complex at 60 ms -

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Basic information

Entry
Database: PDB / ID: 6osk
TitleRF1 accommodated 70S complex at 60 ms
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • FME-PHE-PHE
  • P-tRNA
  • Peptide chain release factor 1
  • mRNA
KeywordsRIBOSOME / Time-resolved cryo-EM / Termination / short-lived / millisecond
Function / homology
Function and homology information


translation release factor activity, codon specific / small ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit ...translation release factor activity, codon specific / small ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Peptide chain release factor 1 / 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 class I / RF-1 domain / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. ...Peptide chain release factor 1 / 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 class I / RF-1 domain / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / 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 L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / 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 L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S13, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L20 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-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 L34, conserved site / Ribosomal L28 family / Ribosomal protein L34 signature. / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L16 / Ribosomal protein S16
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L2 / 50S ribosomal protein L23 / Large ribosomal subunit protein uL15 / 30S ribosomal protein S5 / 50S ribosomal protein L31 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L2 / 50S ribosomal protein L23 / Large ribosomal subunit protein uL15 / 30S ribosomal protein S5 / 50S ribosomal protein L31 / Small ribosomal subunit protein uS17 / : / Large ribosomal subunit protein bL36 / 50S ribosomal protein L18 / 50S ribosomal protein L32 / 50S ribosomal protein L24 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17 / 30S ribosomal protein S3 / Small ribosomal subunit protein bS6 / Peptide chain release factor 1 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein uS15 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L14 / 50S ribosomal protein L21 / 50S ribosomal protein L13 / 50S ribosomal protein L9 / 30S ribosomal protein S18 / Small ribosomal subunit protein uS8 / 50S ribosomal protein L33 / 50S ribosomal protein L35 / 30S ribosomal protein S20 / 50S ribosomal protein L30 / 30S ribosomal protein S14 / 30S ribosomal protein S10 / 30S ribosomal protein S21 / 30S ribosomal protein S4 / 30S ribosomal protein S12 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL3 / 30S ribosomal protein S7 / Large ribosomal subunit protein bL20 / 30S ribosomal protein S9 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL5 / 50S ribosomal protein L28
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFu, Z. / Indrisiunaite, G. / Kaledhonkar, S. / Shah, B. / Sun, M. / Chen, B. / Grassucci, R.A. / Ehrenberg, M. / Frank, J.
Funding support United States, Sweden, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM55440 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM29169 United States
Swedish Research Council Sweden
CitationJournal: Nat Commun / Year: 2019
Title: The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy.
Authors: Ziao Fu / Gabriele Indrisiunaite / Sandip Kaledhonkar / Binita Shah / Ming Sun / Bo Chen / Robert A Grassucci / Måns Ehrenberg / Joachim Frank /
Abstract: When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in ...When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away. Surprisingly, free RF2 is compact, with only 20 Å between its codon-reading and GGQ motifs. Cryo-EM showed that ribosome-bound RFs have extended structures, suggesting that RFs are compact when entering the ribosome and then extend their structures upon stop codon recognition. Here we use time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.
History
DepositionMay 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / cell / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
1: 23S ribosomal RNA
2: 16S ribosomal RNA
3: 5S ribosomal RNA
4: mRNA
B: 50S ribosomal protein L2
C: 50S ribosomal protein L3
D: 50S ribosomal protein L4
E: 50S ribosomal protein L5
F: 50S ribosomal protein L6
G: 50S ribosomal protein L9
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
a: 50S ribosomal protein L31
b: 50S ribosomal protein L32
c: 50S ribosomal protein L33
d: 50S ribosomal protein L34
e: 50S ribosomal protein L35
f: 50S ribosomal protein L36
g: 30S ribosomal protein S2
h: 30S ribosomal protein S3
i: 30S ribosomal protein S4
j: 30S ribosomal protein S5
k: 30S ribosomal protein S6
l: 30S ribosomal protein S7
m: 30S ribosomal protein S8
n: 30S ribosomal protein S9
o: 30S ribosomal protein S10
p: 30S ribosomal protein S11
q: 30S ribosomal protein S12
r: 30S ribosomal protein S13
s: 30S ribosomal protein S14
t: 30S ribosomal protein S15
u: 30S ribosomal protein S16
v: 30S ribosomal protein S17
w: 30S ribosomal protein S18
x: 30S ribosomal protein S19
y: 30S ribosomal protein S20
z: 30S ribosomal protein S21
A: Peptide chain release factor 1
5: P-tRNA
6: FME-PHE-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,178,347365
Polymers2,170,75456
Non-polymers7,592309
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules 12345

#1: RNA chain 23S ribosomal RNA


Mass: 941526.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#2: RNA chain 16S ribosomal RNA


Mass: 497404.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: RNA chain 5S ribosomal RNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1273279017
#4: RNA chain mRNA


Mass: 2754.647 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#55: RNA chain P-tRNA


Mass: 24565.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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50S ribosomal protein ... , 29 types, 29 molecules BCDEFGJKLMNOPQRSTUVWXYZabcdef

#5: Protein 50S ribosomal protein L2


Mass: 29663.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A029IK04
#6: Protein 50S ribosomal protein L3 / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#7: Protein 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9F6
#8: Protein 50S ribosomal protein L5


Mass: 20073.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: V0AXZ0
#9: Protein 50S ribosomal protein L6


Mass: 18672.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A1X3JB47
#10: Protein 50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZI15
#11: Protein 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZET0
#12: Protein 50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9G5
#13: Protein 50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A037Y8L6
#14: Protein 50S ribosomal protein L16 / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY7
#15: Protein 50S ribosomal protein L17


Mass: 13592.823 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A2T1LEK9
#16: Protein 50S ribosomal protein L18


Mass: 12663.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A0F6C9R0
#17: Protein 50S ribosomal protein L19


Mass: 13028.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: D6IC61
#18: Protein 50S ribosomal protein L20


Mass: 13396.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: S1EK76
#19: Protein 50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZEN7
#20: Protein 50S ribosomal protein L22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9G0
#21: Protein 50S ribosomal protein L23


Mass: 10661.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A029IKB7
#22: Protein 50S ribosomal protein L24


Mass: 11208.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A0G3K7Z5
#23: 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: D7XH79
#24: Protein 50S ribosomal protein L27


Mass: 8275.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: U9XYH0
#25: Protein 50S ribosomal protein L28


Mass: 8896.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: V8F9Y0
#26: Protein 50S ribosomal protein L29


Mass: 7155.267 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A1X3JBH6
#27: Protein 50S ribosomal protein L30


Mass: 6423.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: J7R6H0
#28: Protein 50S ribosomal protein L31


Mass: 7516.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A080FR68
#29: Protein 50S ribosomal protein L32


Mass: 6332.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0G3K5Y7
#30: Protein 50S ribosomal protein L33


Mass: 6057.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: H4LIZ0
#31: Protein/peptide 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MGC4
#32: Protein 50S ribosomal protein L35


Mass: 7181.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: I2RJ64
#33: Protein/peptide 50S ribosomal protein L36


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0E2L017

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30S ribosomal protein ... , 20 types, 20 molecules ghijklmnopqrstuvwxyz

#34: Protein 30S ribosomal protein S2


Mass: 25072.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3TPN2
#35: Protein 30S ribosomal protein S3


Mass: 23248.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A376HTV6
#36: Protein 30S ribosomal protein S4


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: L3PZ69
#37: Protein 30S ribosomal protein S5


Mass: 16475.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A073FR78
#38: Protein 30S ribosomal protein S6


Mass: 12125.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A376ZL25
#39: Protein 30S ribosomal protein S7


Mass: 16861.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: S1D5F0
#40: Protein 30S ribosomal protein S8


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D8A1L7
#41: Protein 30S ribosomal protein S9


Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: T9TH92
#42: Protein 30S ribosomal protein S10


Mass: 11254.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: J7RLQ6
#43: Protein 30S ribosomal protein S11 / Small ribosomal subunit protein uS11


Mass: 12487.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9
#44: Protein 30S ribosomal protein S12


Mass: 13683.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: L4V1L2
#45: Protein 30S ribosomal protein S13


Mass: 12868.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A1X3JB38
#46: Protein 30S ribosomal protein S14


Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: J7R6H7
#47: Protein 30S ribosomal protein S15


Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7XN21
#48: Protein 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MIU7
#49: Protein 30S ribosomal protein S17


Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A080IK26
#50: Protein 30S ribosomal protein S18


Mass: 7734.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: D7ZI16
#51: Protein 30S ribosomal protein S19


Mass: 9421.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A0A8UF41
#52: Protein 30S ribosomal protein S20


Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: I4T5W9
#53: Protein 30S ribosomal protein S21


Mass: 8392.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: L3C5D9

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Protein / Protein/peptide , 2 types, 2 molecules A6

#54: Protein Peptide chain release factor 1 / RF-1


Mass: 28727.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A377MZQ1
#56: Protein/peptide FME-PHE-PHE


Mass: 471.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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Non-polymers , 2 types, 309 molecules

#57: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 307 / Source method: obtained synthetically / Formula: Mg
#58: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: Release complex 70S ribosomes / Type: RIBOSOME / Entity ID: #1-#54 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 41.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 202103 / Symmetry type: POINT

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