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- PDB-6wd1: Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA pro... -

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Basic information

Entry
Database: PDB / ID: 6wd1
TitleCryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure I-B)
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 31
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • mRNAMessenger RNA
  • tRNAfMet
KeywordsRIBOSOME / EF-Tu / tRNA
Function / homology
Function and homology information


DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / regulation of translation / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / transferase activity ...DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / regulation of translation / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L25, short-form / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein S16, conserved site ...Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L25, short-form / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 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 L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / 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 L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / 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 S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / 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 L16 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L21 / Ribosomal protein S15, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S2 signature 1. / KH domain / Ribosomal protein L2, conserved site / Ribosomal protein L2 signature. / Type-2 KH domain profile. / : / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / : / Ribosomal protein S2, conserved site / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S2
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS17 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / 30S ribosomal protein S3 / 50S ribosomal protein L1 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS2 / 30S ribosomal protein S10 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein uS15 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L29 / 50S ribosomal protein L21 / 50S ribosomal protein L13 / 50S ribosomal protein L9 / Small ribosomal subunit protein uS8 / 30S ribosomal protein S19 / 30S ribosomal protein S4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / 30S ribosomal protein S6 / 30S ribosomal protein S7 / 30S ribosomal protein S20 / 30S ribosomal protein S9 / 30S ribosomal protein S12
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLoveland, A.B. / Demo, G. / Korostelev, A.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM106105 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM107465 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127094 United States
CitationJournal: Nature / Year: 2020
Title: Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading.
Authors: Anna B Loveland / Gabriel Demo / Andrei A Korostelev /
Abstract: Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by the elongation factor EF-Tu. To understand the molecular mechanism of this proofreading step it is necessary ...Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by the elongation factor EF-Tu. To understand the molecular mechanism of this proofreading step it is necessary to visualize GTP-catalysed elongation, which has remained a challenge. Here we use time-resolved cryogenic electron microscopy to reveal 33 ribosomal states after the delivery of aminoacyl-tRNA by EF-Tu•GTP. Instead of locking cognate tRNA upon initial recognition, the ribosomal decoding centre dynamically monitors codon-anticodon interactions before and after GTP hydrolysis. GTP hydrolysis enables the GTPase domain of EF-Tu to extend away, releasing EF-Tu from tRNA. The 30S subunit then locks cognate tRNA in the decoding centre and rotates, enabling the tRNA to bypass 50S protrusions during accommodation into the peptidyl transferase centre. By contrast, the decoding centre fails to lock near-cognate tRNA, enabling the dissociation of near-cognate tRNA both during initial selection (before GTP hydrolysis) and proofreading (after GTP hydrolysis). These findings reveal structural similarity between ribosomes in initial selection states and in proofreading states, which together govern the efficient rejection of incorrect tRNA.
History
DepositionMar 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
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
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: 50S ribosomal protein L1
3: 16S ribosomal RNA
1: 23S ribosomal RNA
2: 5S ribosomal RNA
5: tRNAfMet
4: mRNA


Theoretical massNumber of molelcules
Total (without water)2,188,39356
Polymers2,188,39356
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

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

#1: Protein 50S ribosomal protein L2 / / Large ribosomal subunit protein uL2


Mass: 29663.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60422
#2: 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 / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60438
#3: Protein 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9F6
#4: Protein 50S ribosomal protein L5 /


Mass: 20073.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#5: Protein 50S ribosomal protein L6 /


Mass: 18801.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#6: Protein 50S ribosomal protein L9 /


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZI15
#7: Protein 50S ribosomal protein L10 /


Mass: 14112.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#8: Protein 50S ribosomal protein L11 /


Mass: 14763.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#9: Protein 50S ribosomal protein L13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZET0
#10: Protein 50S ribosomal protein L14 /


Mass: 13451.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#11: Protein 50S ribosomal protein L15 /


Mass: 14877.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A037Y8L6
#12: 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 / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0ADY7
#13: Protein 50S ribosomal protein L17 /


Mass: 13721.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#14: Protein 50S ribosomal protein L18 /


Mass: 12663.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#15: Protein 50S ribosomal protein L19 /


Mass: 13028.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#16: Protein 50S ribosomal protein L20 /


Mass: 13396.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#17: Protein 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZEN7
#18: Protein 50S ribosomal protein L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9G0
#19: Protein 50S ribosomal protein L23 /


Mass: 10546.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#20: Protein 50S ribosomal protein L24 /


Mass: 11078.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#21: Protein 50S ribosomal protein L25 /


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7XH79
#22: Protein 50S ribosomal protein L27 /


Mass: 8174.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#23: Protein 50S ribosomal protein L28 /


Mass: 8896.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#24: Protein 50S ribosomal protein L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9G3
#25: Protein 50S ribosomal protein L30 /


Mass: 6423.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#26: Protein 50S ribosomal protein L32 /


Mass: 6332.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#27: Protein/peptide 50S ribosomal protein L33 /


Mass: 5814.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#28: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MGC4
#29: Protein 50S ribosomal protein L35 /


Mass: 7181.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#30: Protein/peptide 50S ribosomal protein L36 /


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A0E2L017
#51: Protein 50S ribosomal protein L1 /


Mass: 23735.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A4Y8DMK0

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

#31: Protein 30S ribosomal protein S2 /


Mass: 25015.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: C3TPN2
#32: Protein 30S ribosomal protein S3 /


Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A376HTV6
#33: Protein 30S ribosomal protein S4 /


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: L3PZ69
#34: Protein 30S ribosomal protein S5 /


Mass: 16532.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#35: Protein 30S ribosomal protein S6 /


Mass: 11669.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: S1CG62
#36: Protein 30S ribosomal protein S7 /


Mass: 16861.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: S1D5F0
#37: Protein 30S ribosomal protein S8 /


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D8A1L7
#38: Protein 30S ribosomal protein S9 /


Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: T9TH92
#39: Protein 30S ribosomal protein S10 /


Mass: 11196.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7X302
#40: Protein 30S ribosomal protein S11 /


Mass: 12388.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#41: Protein 30S ribosomal protein S12 /


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: V6FZ95
#42: Protein 30S ribosomal protein S13 /


Mass: 12625.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A1X3KX08
#43: Protein 30S ribosomal protein S14 /


Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#44: Protein 30S ribosomal protein S15 /


Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7XN21
#45: Protein 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MIU7
#46: Protein 30S ribosomal protein S17 /


Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A080IK26
#47: Protein 30S ribosomal protein S18 /


Mass: 7606.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#48: Protein 30S ribosomal protein S19 /


Mass: 9057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: F4SQ43
#49: Protein 30S ribosomal protein S20 /


Mass: 9506.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: T6N332
#50: Protein 30S ribosomal protein S21 /


Mass: 7763.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600

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RNA chain , 5 types, 5 molecules 31254

#52: RNA chain 16S ribosomal RNA /


Mass: 498725.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 1338015391
#53: RNA chain 23S ribosomal RNA /


Mass: 941305.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 1036415628
#54: RNA chain 5S ribosomal RNA /


Mass: 38813.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 1370526515
#55: RNA chain tRNAfMet


Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 1384458579
#56: RNA chain mRNA / Messenger RNA


Mass: 5844.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600

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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: Map I-B / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Buffer solutionpH: 7.5
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 1 sec. / Electron dose: 35 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3218
Image scansMovie frames/image: 35 / Used frames/image: 1-35

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
8PyMOLmodel fitting
10CNSmodel refinement
11RSRefmodel refinement
12PHENIXmodel refinement
13FREALIGNinitial Euler assignment
14FREALIGNfinal Euler assignment
15FREALIGNclassification
16FREALIGN3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 678268
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22656 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
NMR ensembleConformers submitted total number: 1

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