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- PDB-5wf0: 70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (C... -

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Basic information

Entry
Database: PDB / ID: 5wf0
Title70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C2)
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 31
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • Elongation factor Tu 2EF-Tu
  • Phe-tRNA-Phe
  • mRNAMessenger RNA
  • tRNA-fMet
KeywordsRIBOSOME / translation / GTPase
Function / homology
Function and homology information


guanosine tetraphosphate binding / translation elongation factor activity / large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome ...guanosine tetraphosphate binding / translation elongation factor activity / large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / GTPase activity / GTP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Elongation factor Tu domain 2 / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L10-like domain superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11 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 L11, N-terminal / Ribosomal protein L17 signature. / 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 L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / 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 L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L14P, bacterial-type
Similarity search - Domain/homology
N-FORMYLMETHIONINE / GUANOSINE-5'-TRIPHOSPHATE / : / PHENYLALANINE / : / : / : / : / RNA / RNA (> 10) ...N-FORMYLMETHIONINE / GUANOSINE-5'-TRIPHOSPHATE / : / PHENYLALANINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Elongation factor Tu 2 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL23
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli O139:H28 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFislage, M. / Frank, J.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM29169 United States
CitationJournal: Nucleic Acids Res / Year: 2018
Title: Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A.
Authors: Marcus Fislage / Jingji Zhang / Zuben Patrick Brown / Chandra Sekhar Mandava / Suparna Sanyal / Måns Ehrenberg / Joachim Frank /
Abstract: The GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular ...The GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular origins of the accuracy of ribosome-aided recognition of a cognate ternary complex and the accuracy-amplifying role of the monitoring bases A1492, A1493 and G530 of the 16S rRNA. We used the GTPase-deficient EF-Tu variant H84A with native GTP, rather than non-cleavable GTP analogues, to trap a near-cognate ternary complex in high-resolution ribosomal complexes of varying codon-recognition accuracy. We found that ribosome complexes trapped by GTPase-deficicent ternary complex due to the presence of EF-TuH84A or non-cleavable GTP analogues have very similar structures. We further discuss speed and accuracy of initial aa-tRNA selection in terms of conformational changes of aa-tRNA and stepwise activation of the monitoring bases at the decoding center of the ribosome.
History
DepositionJul 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / 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
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 18, 2018Group: Data collection / Experimental preparation / Category: em_sample_support / Item: _em_sample_support.grid_type
Revision 2.0Jul 3, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: 23S rRNA
B: 5S rRNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
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
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36 1
5: 50S ribosomal protein L10
6: 50S ribosomal protein L31
a: 16S rRNA
b: 30S ribosomal protein S2
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
u: 30S ribosomal protein S21
v: tRNA-fMet
w: tRNA-fMet
x: mRNA
y: Phe-tRNA-Phe
z: Elongation factor Tu 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,297,6901547
Polymers2,260,65759
Non-polymers37,0321488
Water12,178676
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area312080 Å2
ΔGint-2548 kcal/mol
Surface area823620 Å2

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Components

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RNA chain , 6 types, 7 molecules ABavwxy

#1: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 941548.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 216643
#2: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38813.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 1199817771
#34: RNA chain 16S rRNA /


Mass: 499239.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 1114191980
#55: RNA chain tRNA-fMet


Mass: 24818.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 817573384
#56: RNA chain mRNA / Messenger RNA


Mass: 3772.296 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#57: RNA chain Phe-tRNA-Phe


Mass: 24649.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600

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50S ribosomal protein ... , 31 types, 31 molecules CDEFGHIJKLMNOPQRSTUVWXYZ0123456

#3: Protein 50S ribosomal protein L2 /


Mass: 29663.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCT2
#4: Protein 50S ribosomal protein L3 /


Mass: 22146.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCT5
#5: Protein 50S ribosomal protein L4 /


Mass: 21990.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCT4
#6: 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) / Strain: MRE600 / References: UniProt: B7MCS3
#7: Protein 50S ribosomal protein L6 /


Mass: 18543.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCS0
#8: 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) / Strain: MRE600 / References: UniProt: B7MLK8
#9: Protein 50S ribosomal protein L11 /


Mass: 14763.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MIW9
#10: Protein 50S ribosomal protein L13 /


Mass: 15937.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MBZ2
#11: Protein 50S ribosomal protein L14 /


Mass: 13451.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCS5
#12: Protein 50S ribosomal protein L15 /


Mass: 14879.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A8A5A6
#13: Protein 50S ribosomal protein L16 /


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCS8
#14: 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) / Strain: MRE600 / References: UniProt: B7MCR0
#15: Protein 50S ribosomal protein L18 /


Mass: 12663.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCR9
#16: Protein 50S ribosomal protein L19 /


Mass: 13028.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MIU4
#17: Protein 50S ribosomal protein L20 /


Mass: 13212.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MAS6
#18: Protein 50S ribosomal protein L21 /


Mass: 11515.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MBV5
#19: Protein 50S ribosomal protein L22 /


Mass: 12096.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCT0
#20: Protein 50S ribosomal protein L23 /


Mass: 10415.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0ADZ2
#21: Protein 50S ribosomal protein L24 /


Mass: 11078.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7L4J5
#22: Protein 50S ribosomal protein L25 /


Mass: 10511.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7LAK9
#23: Protein 50S ribosomal protein L27 /


Mass: 8146.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MBV4
#24: Protein 50S ribosomal protein L28 /


Mass: 8896.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MFJ8
#25: Protein 50S ribosomal protein L29 /


Mass: 7087.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCS7
#26: Protein 50S ribosomal protein L30 /


Mass: 6223.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCR7
#27: Protein 50S ribosomal protein L32 /


Mass: 6203.069 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MJ76
#28: Protein 50S ribosomal protein L33 /


Mass: 5928.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MFJ7
#29: Protein/peptide 50S ribosomal protein L34 /


Mass: 5268.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MGC4
#30: Protein 50S ribosomal protein L35 /


Mass: 7181.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MAS7
#31: Protein/peptide 50S ribosomal protein L36 1 / Ribosome


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A8A5A4
#32: Protein 50S ribosomal protein L10 /


Mass: 14112.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MIX1
#33: Protein 50S ribosomal protein L31 /


Mass: 7516.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MI68

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

#35: Protein 30S ribosomal protein S2 /


Mass: 24253.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MBF0
#36: Protein 30S ribosomal protein S3 /


Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCS9
#37: 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) / Strain: MRE600 / References: UniProt: B7MCR2
#38: Protein 30S ribosomal protein S5 /


Mass: 16532.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7W3
#39: Protein 30S ribosomal protein S6 /


Mass: 11669.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7NGD4
#40: 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) / Strain: MRE600 / References: UniProt: B7MCV6
#41: 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) / Strain: MRE600 / References: UniProt: B7MCS1
#42: 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) / Strain: MRE600 / References: UniProt: B7MBZ1
#43: Protein 30S ribosomal protein S10 /


Mass: 11196.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCT6
#44: Protein 30S ribosomal protein S11 /


Mass: 12388.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCR3
#45: Protein 30S ribosomal protein S12 /


Mass: 13436.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCV7
#46: Protein 30S ribosomal protein S13 /


Mass: 12738.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7T1
#47: Protein 30S ribosomal protein S14 /


Mass: 11546.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCS2
#48: 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) / Strain: MRE600 / References: UniProt: B7MB86
#49: 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) / Strain: MRE600 / References: UniProt: B7MIU7
#50: 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) / Strain: MRE600 / References: UniProt: B7MCS6
#51: Protein 30S ribosomal protein S18 /


Mass: 7606.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MLK7
#52: Protein 30S ribosomal protein S19 /


Mass: 9057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCT1
#53: Protein 30S ribosomal protein S20 /


Mass: 9506.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MAE3
#54: Protein 30S ribosomal protein S21 /


Mass: 7763.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A8A4M2

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Protein , 1 types, 1 molecules z

#58: Protein Elongation factor Tu 2 / EF-Tu / EF-Tu 2


Mass: 43171.246 Da / Num. of mol.: 1 / Mutation: H84A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / Gene: tuf2, EcE24377A_4519 / Production host: Escherichia coli (E. coli) / References: UniProt: A7ZUJ2

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Non-polymers , 6 types, 2164 molecules

#59: Chemical ChemComp-FME / N-FORMYLMETHIONINE / N-Formylmethionine


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S
#60: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1480 / Source method: obtained synthetically / Formula: Mg
#61: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#62: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#63: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#64: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O

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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: 70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex 1)
Type: RIBOSOME / Entity ID: #1-#58 / Source: MULTIPLE SOURCES
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
11 mMpolymixPM1
25 mMpotassium phosphateKP1
314 mMmagnesium acetateMgOAc1
41.8 mMGuanosine-5'-triphosphateGuanosine triphosphateGTP1
510 mMphosphoenolpyruvatePEP1
61 mMdithioerythriolDTE1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 300 nM 70S ribosome in final mixture
Specimen supportDetails: grids were manually coated with gold and the carbon support was removed by glow discharge. gas mixture: 20% hydrogen/80% oxygen power: 15W
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: 5 second blot time, no wait time

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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 FIELDBright-field microscopy / Nominal magnification: 39000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 300 nm / Calibrated defocus max: 4000 nm / Cs: 2.26 mm / C2 aperture diameter: 30 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 67 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: 2843
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategoryDetails
2Leginonimage acquisition
4Gctf0.5CTF correctionfor ctf estimation
5RELION2CTF correctionfor ctf correction
8Coot0.88model fitting
10RELION2initial Euler assignment
11RELION2final Euler assignment
12RELION2classification
13RELION23D reconstruction
14REFMAC5.7model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 193521
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30623 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 82 / Protocol: OTHER / Space: RECIPROCAL

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