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- PDB-6q97: Structure of tmRNA SmpB bound in A site of E. coli 70S ribosome -

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Entry
Database: PDB / ID: 6q97
TitleStructure of tmRNA SmpB bound in A site of E. coli 70S ribosome
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 31
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Nascent peptide
  • SsrA-binding protein
  • mRNAMessenger RNA
  • tRNA-Met
  • tRNA-Val
  • transfer-messenger RNA (tmRNA)
KeywordsRIBOSOME / tmRNA SmpB trans-translation translation
Function / homologyRibosomal protein L13, conserved site / Ribosomal protein S8 superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S6 superfamily ...Ribosomal protein L13, conserved site / Ribosomal protein S8 superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L31 type A / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / 30s ribosomal protein S13, C-terminal / RNA-binding S4 domain superfamily / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L19 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein S21 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain / Ribosomal protein L28/L24 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / SsrA-binding protein, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L9, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25, short-form / Ribosomal protein L6, alpha-beta domain / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L16, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S16 domain superfamily / Ribosomal protein L5 domain superfamily / Ribosomal protein S7 domain / Small protein B / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L10 / Ribosomal protein S4/S9 / Ribosomal protein L5, conserved site / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L35 / Ribosomal protein L18e/L15P / Ribosomal protein L34, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein L16 signature 2. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein S17 signature. / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S8 signature. / Ribosomal protein S7 signature. / Ribosomal protein L23 signature. / Ribosomal protein L14 signature. / KH domain / Ribosomal protein S19 signature. / Ribosomal protein L9, C-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein S5, C-terminal domain
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsRae, C.D.
Funding supportUnited Kingdom , 2 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105184332United Kingdom
Wellcome TrustWT096570United Kingdom
CitationJournal: Science / Year: 2019
Title: How a circularized tmRNA moves through the ribosome.
Authors: Christopher D Rae / Yuliya Gordiyenko / V Ramakrishnan
Abstract: During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used ...During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo-electron microscopy to determine the structures of three key states of the tmRNA-SmpB-ribosome complex during trans translation at resolutions of 3.7 to 4.4 angstroms. The results show how tmRNA and SmpB act specifically on stalled ribosomes and how the circularized complex moves through the ribosome, enabling translation to switch from the old defective message to the reading frame on tmRNA.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 17, 2018 / Release: Mar 13, 2019

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
1: 23S ribosomal RNA
2: 16S ribosomal RNA
3: 5S ribosomal RNA
5: SsrA-binding protein
6: Nascent peptide
8: tRNA-Met
9: 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
H: 50S ribosomal protein L10
I: 50S ribosomal protein L11
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
4: transfer-messenger RNA (tmRNA)
7: tRNA-Val
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,338,335501
Polyers2,327,53460
Non-polymers10,801441
Water362
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)344540
ΔGint (kcal/M)-5972
Surface area (Å2)896890
MethodPISA

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Components

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RNA chain , 7 types, 7 molecules 1238947

#1: RNA chain 23S ribosomal RNA /


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


Mass: 497405.969 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli)
#3: RNA chain 5S ribosomal RNA /


Mass: 38790.090 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli)
#6: RNA chain tRNA-Met


Mass: 24728.689 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli)
#7: RNA chain mRNA / Messenger RNA


Mass: 1892.173 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#59: RNA chain transfer-messenger RNA (tmRNA)


Mass: 117214.266 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#60: RNA chain tRNA-Val


Mass: 24823.707 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli)

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Protein/peptide , 2 types, 2 molecules 56

#4: Protein/peptide SsrA-binding protein / Small protein B


Mass: 16638.166 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: smpB, smqB, b2620, JW2601 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A832
#5: Protein/peptide Nascent peptide


Mass: 2008.194 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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50S ribosomal protein ... , 31 types, 31 molecules BCDEFGHIJKLMNOPQRSTUVWXYZabcdef

#8: Protein/peptide 50S ribosomal protein L2 /


Mass: 29592.166 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: V0A5J4
#9: Protein/peptide 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#10: Protein/peptide 50S ribosomal protein L4 / / Large ribosomal subunit protein uL4


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60723
#11: Protein/peptide 50S ribosomal protein L5 / / Large ribosomal subunit protein uL5


Mass: 20073.234 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P62399
#12: Protein/peptide 50S ribosomal protein L6 / / Large ribosomal subunit protein uL6


Mass: 18672.418 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG55
#13: Protein/peptide 50S ribosomal protein L9 / / Large ribosomal subunit protein bL9


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R1
#14: Protein/peptide 50S ribosomal protein L10 / / 50S ribosomal protein L8 / Large ribosomal subunit protein uL10


Mass: 13981.147 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J3
#15: Protein/peptide 50S ribosomal protein L11 / / Large ribosomal subunit protein uL11


Mass: 14090.395 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J7
#16: Protein/peptide 50S ribosomal protein L13 /


Mass: 15919.411 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A379XJZ2
#17: Protein/peptide 50S ribosomal protein L14 / / Large ribosomal subunit protein uL14


Mass: 13565.067 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY3
#18: Protein/peptide 50S ribosomal protein L15 / / Large ribosomal subunit protein uL15


Mass: 15008.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02413
#19: Protein/peptide 50S ribosomal protein L16 / / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY7
#20: Protein/peptide 50S ribosomal protein L17 / / Large ribosomal subunit protein bL17


Mass: 13592.823 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG44
#21: Protein/peptide 50S ribosomal protein L18 / / Large ribosomal subunit protein uL18


Mass: 12548.383 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0C018
#22: Protein/peptide 50S ribosomal protein L19 / / Large ribosomal subunit protein bL19


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7K6
#23: Protein/peptide 50S ribosomal protein L20 / / Large ribosomal subunit protein bL20


Mass: 13396.828 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L3
#24: Protein/peptide 50S ribosomal protein L21 / / Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG48
#25: Protein/peptide 50S ribosomal protein L22 /


Mass: 11993.051 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7X2Z6
#26: Protein/peptide 50S ribosomal protein L23 / / Large ribosomal subunit protein uL23


Mass: 10661.560 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#27: Protein/peptide 50S ribosomal protein L24 / / Large ribosomal subunit protein uL24


Mass: 11208.054 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60624
#28: Protein/peptide 50S ribosomal protein L25 / / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68919
#29: Protein/peptide 50S ribosomal protein L27 / / Large ribosomal subunit protein bL27


Mass: 8275.498 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L8
#30: Protein/peptide 50S ribosomal protein L28 / / Large ribosomal subunit protein bL28


Mass: 8896.354 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M2
#31: Protein/peptide 50S ribosomal protein L29 /


Mass: 6826.881 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: E3PKZ6
#32: Protein/peptide 50S ribosomal protein L30 /


Mass: 6223.367 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0E0XV41
#33: Protein/peptide 50S ribosomal protein L31 / / Large ribosomal subunit protein bL31-A


Mass: 7516.693 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M9
#34: Protein/peptide 50S ribosomal protein L32 /


Mass: 6131.992 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7XAL4
#35: Protein/peptide 50S ribosomal protein L33 / / Large ribosomal subunit protein bL33


Mass: 6057.179 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N9
#36: Protein/peptide 50S ribosomal protein L34 / / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7P5
#37: Protein/peptide 50S ribosomal protein L35 / / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#38: Protein/peptide 50S ribosomal protein L36 /


Mass: 4320.338 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli)

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

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


Mass: 25072.867 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V0
#40: Protein/peptide 30S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 23248.994 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V3
#41: Protein/peptide 30S ribosomal protein S4 / / Small ribosomal subunit protein uS4


Mass: 23383.002 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V8
#42: Protein/peptide 30S ribosomal protein S5 / / Small ribosomal subunit protein uS5


Mass: 16475.037 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W1
#43: Protein/peptide 30S ribosomal protein S6 / / Small ribosomal subunit protein bS6


Mass: 12125.993 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358
#44: Protein/peptide 30S ribosomal protein S7 / / Small ribosomal subunit protein uS7


Mass: 16861.523 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359
#45: Protein/peptide 30S ribosomal protein S8 / / Small ribosomal subunit protein uS8


Mass: 14015.361 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W7
#46: Protein/peptide 30S ribosomal protein S9 /


Mass: 14397.688 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A029HJ91
#47: Protein/peptide 30S ribosomal protein S10 / / Small ribosomal subunit protein uS10


Mass: 11254.041 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R5
#48: Protein/peptide 30S ribosomal protein S11 / / Small ribosomal subunit protein uS11


Mass: 12487.200 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9
#49: Protein/peptide 30S ribosomal protein S12 /


Mass: 13683.053 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: F5NAB8
#50: Protein/peptide 30S ribosomal protein S13 /


Mass: 12738.911 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: H4IXV7
#51: Protein/peptide 30S ribosomal protein S14 / / Small ribosomal subunit protein uS14


Mass: 11475.364 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG59
#52: Protein/peptide 30S ribosomal protein S15 / / Small ribosomal subunit protein uS15


Mass: 10072.543 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ4
#53: Protein/peptide 30S ribosomal protein S16 /


Mass: 9136.495 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: S0UHH0
#54: Protein/peptide 30S ribosomal protein S17 / / Small ribosomal subunit protein uS17


Mass: 9263.946 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG63
#55: Protein/peptide 30S ribosomal protein S18 / / Small ribosomal subunit protein bS18


Mass: 7606.768 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T7
#56: Protein/peptide 30S ribosomal protein S19 /


Mass: 9349.939 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: U9ZUL7
#57: Protein/peptide 30S ribosomal protein S20 / / Small ribosomal subunit protein bS20


Mass: 9506.190 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U7
#58: Protein/peptide 30S ribosomal protein S21 / / Small ribosomal subunit protein bS21


Mass: 8392.844 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68679

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Non-polymers , 3 types, 443 molecules

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


Mass: 24.305 Da / Num. of mol.: 439 / Formula: Mg / Magnesium
#62: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn / Zinc
#63: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Formula: H2O / Water

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1tmRNA SmpB bound in A site of E. coli 70S ribosomeRIBOSOME1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,600MULTIPLE SOURCES
270S ribosomeORGANELLE OR CELLULAR COMPONENT1,2,3,6,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,601NATURAL
3tmRNA-SmpB, nascent peptide, mRNA, P-site tRNA, E-site tRNACOMPLEX4,5,7,591RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12562Escherichia coli (E. coli)
23562Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 44 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 47776 / Symmetry type: POINT

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