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- PDB-6dnc: E.coli RF1 bound to E.coli 70S ribosome in response to UAU sense ... -

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Basic information

Entry
Database: PDB / ID: 6dnc
TitleE.coli RF1 bound to E.coli 70S ribosome in response to UAU sense A-site codon
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 32
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Peptide chain release factor 1
  • mRNAMessenger RNA
  • tRNA(fMet)
KeywordsRIBOSOME / RF1 / ribosome / sense codon / cryo-EM
Function / homologyRibosomal protein L20, C-terminal / Ribosomal protein L11/L12, 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 L9, C-terminal domain superfamily ...Ribosomal protein L20, C-terminal / Ribosomal protein L11/L12, 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 L9, C-terminal domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11, C-terminal domain 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 / Ribosomal protein L9, N-terminal domain superfamily / RNA-binding S4 domain superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S3, C-terminal domain / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L16p/L10e / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L28/L24 superfamily / Ribosomal protein S7p/S5e / 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 / L21-like superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L35 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L10 / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L18e/L15P / Ribosomal protein L13, conserved site / Ribosomal protein L34, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L16, conserved site / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L4 domain superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L36 superfamily / 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 S19, superfamily / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein L28/L24 / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal protein L1, conserved site / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein L3 / Ribosomal protein S15 / Ribosomal protein L11, N-terminal / Ribosomal protein S8 signature. / Ribosomal protein L11 signature. / Ribosomal protein L5 signature. / Ribosomal protein S19 signature. / Ribosomal protein S18 signature. / Ribosomal protein S17 signature. / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S7 signature. / Ribosomal protein S10 signature. / Ribosomal protein L23 signature. / Ribosomal protein L14 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / KH domain / Ribosomal protein L9, C-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein S9 signature.
Function and homology information
Specimen sourceEscherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsSvidritskiy, E. / Demo, G. / Korostelev, A.A.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Mechanism of premature translation termination on a sense codon.
Authors: Egor Svidritskiy / Gabriel Demo / Andrei A Korostelev
Abstract: Accurate translation termination by release factors (RFs) is critical for the integrity of cellular proteomes. Premature termination on sense codons, for example, results in truncated proteins, whose ...Accurate translation termination by release factors (RFs) is critical for the integrity of cellular proteomes. Premature termination on sense codons, for example, results in truncated proteins, whose accumulation could be detrimental to the cell. Nevertheless, some sense codons are prone to triggering premature termination, but the structural basis for this is unclear. To investigate premature termination, we determined a cryo-EM structure of the 70S ribosome bound with RF1 in response to a UAU (Tyr) sense codon. The structure reveals that RF1 recognizes a UAU codon similarly to a UAG stop codon, suggesting that sense codons induce premature termination because they structurally mimic a stop codon. Hydrophobic interaction between the nucleobase of U3 (the third position of the UAU codon) and conserved Ile-196 in RF1 is important for misreading the UAU codon. Analyses of RNA binding in ribonucleoprotein complexes or by amino acids reveal that Ile-U packing is a frequent protein-RNA-binding motif with key functional implications. We discuss parallels with eukaryotic translation termination by the release factor eRF1.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 6, 2018 / Release: Jul 4, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 4, 2018Structure modelrepositoryInitial release
1.1Jul 11, 2018Structure modelData collection / Database references / Experimental preparationcitation / citation_author / em_buffer / em_buffer_component_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.name / _em_buffer.details / _em_buffer.pH / _em_buffer_component.concentration
1.2Aug 22, 2018Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: 16S ribosomal RNA
B: 23S ribosomal RNA
C: 5S ribosomal RNA
D: tRNA(fMet)
E: 50S ribosomal protein L1
F: 50S ribosomal protein L2
G: 50S ribosomal protein L3
H: 50S ribosomal protein L4
I: 50S ribosomal protein L5
J: 50S ribosomal protein L6
K: 50S ribosomal protein L9
L: 50S ribosomal protein L10
M: 50S ribosomal protein L11
N: 50S ribosomal protein L13
O: 50S ribosomal protein L14
P: 50S ribosomal protein L15
Q: 50S ribosomal protein L16
R: 50S ribosomal protein L17
S: 50S ribosomal protein L18
T: 50S ribosomal protein L19
U: 50S ribosomal protein L20
V: 50S ribosomal protein L21
W: 50S ribosomal protein L22
X: 50S ribosomal protein L23
Y: 50S ribosomal protein L24
Z: 50S ribosomal protein L25
AA: 50S ribosomal protein L27
BA: 50S ribosomal protein L28
CA: 50S ribosomal protein L29
DA: 50S ribosomal protein L30
EA: 50S ribosomal protein L31
FA: 50S ribosomal protein L32
GA: 50S ribosomal protein L33
HA: 50S ribosomal protein L34
IA: 50S ribosomal protein L35
JA: 50S ribosomal protein L36
KA: mRNA
LA: tRNA(fMet)
MA: Peptide chain release factor 1
OA: 30S ribosomal protein S2
PA: 30S ribosomal protein S3
QA: 30S ribosomal protein S4
RA: 30S ribosomal protein S5
SA: 30S ribosomal protein S6
TA: 30S ribosomal protein S7
UA: 30S ribosomal protein S8
VA: 30S ribosomal protein S9
WA: 30S ribosomal protein S10
XA: 30S ribosomal protein S11
YA: 30S ribosomal protein S12
ZA: 30S ribosomal protein S13
AB: 30S ribosomal protein S14
BB: 30S ribosomal protein S15
CB: 30S ribosomal protein S16
DB: 30S ribosomal protein S17
EB: 30S ribosomal protein S18
FB: 30S ribosomal protein S19
GB: 30S ribosomal protein S20
HB: 30S ribosomal protein S21


Theoretical massNumber of molelcules
Total (without water)2,292,64959
Polyers2,292,64959
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 6 molecules ABCDLAKA

#1: RNA chain 16S ribosomal RNA /


Mass: 498725.406 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: GenBank: 1338015391
#2: RNA chain 23S ribosomal RNA /


Mass: 941321.250 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: GenBank: 1036415628
#3: RNA chain 5S ribosomal RNA /


Mass: 38813.133 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: GenBank: 1370526515
#4: RNA chain tRNA(fMet)


Mass: 24802.785 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: GenBank: 1384458579
#37: RNA chain mRNA / Messenger RNA


Mass: 8839.416 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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50S ribosomal protein ... , 32 types, 32 molecules EFGHIJKLMNOPQRSTUVWXYZAABACADAEAFAGAHAIAJA

#5: Protein/peptide 50S ribosomal protein L1 /


Mass: 24765.660 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MIX0
#6: Protein/peptide 50S ribosomal protein L2 /


Mass: 29923.619 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCT2
#7: Protein/peptide 50S ribosomal protein L3 /


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCT5
#8: Protein/peptide 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCT4
#9: Protein/peptide 50S ribosomal protein L5 /


Mass: 20333.611 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCS3
#10: Protein/peptide 50S ribosomal protein L6 /


Mass: 18932.791 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCS0
#11: Protein/peptide 50S ribosomal protein L9 /


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MLK8
#12: Protein/peptide 50S ribosomal protein L10 /


Mass: 17736.596 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MIX1
#13: Protein/peptide 50S ribosomal protein L11 /


Mass: 14894.362 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MIW9
#14: Protein/peptide 50S ribosomal protein L13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MBZ2
#15: Protein/peptide 50S ribosomal protein L14 /


Mass: 13565.067 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCS5
#16: 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) / Strain: MRE 600 / References: UniProt: P02413
#17: Protein/peptide 50S ribosomal protein L16 /


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCS8
#18: Protein/peptide 50S ribosomal protein L17 /


Mass: 14423.683 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7N179
#19: Protein/peptide 50S ribosomal protein L18 /


Mass: 12794.668 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCR9
#20: Protein/peptide 50S ribosomal protein L19 /


Mass: 13159.278 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MIU4
#21: Protein/peptide 50S ribosomal protein L20 /


Mass: 13528.024 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MAS6
#22: Protein/peptide 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MBV5
#23: Protein/peptide 50S ribosomal protein L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCT0
#24: Protein/peptide 50S ribosomal protein L23 /


Mass: 11222.160 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCT3
#25: Protein/peptide 50S ribosomal protein L24 / / Large ribosomal subunit protein uL24


Mass: 11339.250 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P60624
#26: 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) / Strain: MRE 600 / References: UniProt: P68919
#27: Protein/peptide 50S ribosomal protein L27 /


Mass: 9146.540 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MBV4
#28: Protein/peptide 50S ribosomal protein L28 /


Mass: 9027.551 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MFJ8
#29: Protein/peptide 50S ribosomal protein L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCS7
#30: Protein/peptide 50S ribosomal protein L30 /


Mass: 6554.820 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCR7
#31: Protein/peptide 50S ribosomal protein L31 /


Mass: 7887.117 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MI68
#32: Protein/peptide 50S ribosomal protein L32 /


Mass: 6463.445 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MJ76
#33: Protein/peptide 50S ribosomal protein L33 /


Mass: 6388.631 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MFJ7
#34: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MGC4
#35: Protein/peptide 50S ribosomal protein L35 /


Mass: 7313.032 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MAS7
#36: Protein/peptide 50S ribosomal protein L36 / / Large ribosomal subunit protein bL36-A / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7Q6

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Protein/peptide , 1 types, 1 molecules MA

#38: Protein/peptide Peptide chain release factor 1 / RF-1


Mass: 40815.578 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: prfA, ECS88_1279 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: B7MKB3

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

#39: Protein/peptide 30S ribosomal protein S2 /


Mass: 26781.670 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MBF0
#40: Protein/peptide 30S ribosomal protein S3 /


Mass: 26031.316 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCS9
#41: Protein/peptide 30S ribosomal protein S4 /


Mass: 23514.199 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCR2
#42: Protein/peptide 30S ribosomal protein S5 / / Small ribosomal subunit protein uS5


Mass: 17629.398 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7W1
#43: Protein/peptide 30S ribosomal protein S6 /


Mass: 15211.058 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02358
#44: Protein/peptide 30S ribosomal protein S7 /


Mass: 17637.445 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCV6
#45: Protein/peptide 30S ribosomal protein S8 /


Mass: 14146.557 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCS1
#46: Protein/peptide 30S ribosomal protein S9 /


Mass: 14886.270 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MBZ1
#47: Protein/peptide 30S ribosomal protein S10 /


Mass: 11755.597 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCT6
#48: Protein/peptide 30S ribosomal protein S11 /


Mass: 13870.975 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCR3
#49: Protein/peptide 30S ribosomal protein S12 /


Mass: 13768.157 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCV7
#50: Protein/peptide 30S ribosomal protein S13 / / Small ribosomal subunit protein uS13


Mass: 13128.467 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7S9
#51: Protein/peptide 30S ribosomal protein S14 /


Mass: 11677.637 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCS2
#52: Protein/peptide 30S ribosomal protein S15 /


Mass: 10290.816 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MB86
#53: Protein/peptide 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MIU7
#54: Protein/peptide 30S ribosomal protein S17 /


Mass: 9724.491 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCS6
#55: Protein/peptide 30S ribosomal protein S18 /


Mass: 9005.472 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MLK7
#56: Protein/peptide 30S ribosomal protein S19 /


Mass: 10455.355 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCT1
#57: Protein/peptide 30S ribosomal protein S20 /


Mass: 9708.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MAE3
#58: Protein/peptide 30S ribosomal protein S21 / / Small ribosomal subunit protein bS21


Mass: 8524.039 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P68679

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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
1RF1 bound to the 70S ribosome in response to sense UAU A-site codonRIBOSOME1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,580MULTIPLE SOURCES
2Peptide chain release factor 1COMPLEX381RECOMBINANT
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionDetails: 20 mM Tris-HCl, 100 mM NH4Cl, 20.5 mM MgCl2, 0.5 mM EDTA, 6 mM beta-mercaptoethanol
pH: 7
Buffer component
IDConc.NameFormulaBuffer ID
120 mMTris bufferTris-HCl1
2100 mMamonium chlorideNH4Cl1
320.5 mMmagnesium chlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: PELCO easiGlow glow discharge unit, negative 20 mA.
Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22000 / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 0.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 3963
Image scansMovie frames/image: 80 / Used frames/image: 3-42

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Processing

EM software
IDNameVersionCategory
1cisTEMparticle selection
4cisTEMCTF correction
7UCSF Chimeramodel fitting
9RSRefmodel refinement
10PHENIXmodel refinement
11FrealignX9.11initial Euler assignment
12FrealignX9.11final Euler assignment
13FrealignX9.11classification
14FrealignX9.113D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 1065147
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 639088 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingOverall b value: 200 / Ref protocol: OTHER / Ref space: REAL / Target criteria: Correlation coefficient

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