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- PDB-5we4: 70S ribosome-EF-Tu wt complex with GppNHp -

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Entry
Database: PDB / ID: 5we4
Title70S ribosome-EF-Tu wt complex with GppNHp
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 / homologyRibosomal protein S14, bacterial/plastid / Elongation factor Tu, domain 2 / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like ...Ribosomal protein S14, bacterial/plastid / Elongation factor Tu, domain 2 / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L22/L17 superfamily / Ribosomal protein L5, C-terminal / Tr-type G domain, conserved site / Ribosomal protein L15 / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L31 type A / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein L17 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L28/L24 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L19 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein S21 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein S20 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 L11/L12, N-terminal domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S16 domain superfamily / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L25, short-form / Ribosomal protein S7, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L9, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L11, N-terminal / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L11, C-terminal / Ribosomal protein L11, conserved site / Ribosomal protein S7 domain / Ribosomal protein L2, conserved site / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L10 / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, C-terminal / Ribosomal protein L16, conserved site / 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 L5, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Elongation factor Tu GTP binding domain / Ribosomal protein S12/S23 / Ribosomal protein L9 signature. / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein S11 signature. / Ribosomal protein S8 signature. / Ribosomal protein S7 signature. / Ribosomal protein L23 signature. / Ribosomal protein L14 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / KH domain / Ribosomal protein L9, C-terminal domain
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.1 Å resolution
AuthorsFislage, M. / Brown, Z. / Frank, J.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 7, 2017 / Release: Apr 25, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 25, 2018Structure modelrepositoryInitial release
1.1May 23, 2018Structure modelData collection / Database referencescitation / citation_author_citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
1.2Jul 4, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last
1.3Jul 18, 2018Structure modelData collection / Experimental preparationem_sample_support_em_sample_support.grid_type

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Structure visualization

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Structure viewerMolecule:
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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
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)2,300,9561681
Polyers2,260,72759
Non-polymers40,2291622
Water17,943996
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)313920
ΔGint (kcal/M)-2504
Surface area (Å2)818870
MethodPISA

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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: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: GenBank: 731469900
#2: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38813.133 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: GenBank: 1174070234
#34: RNA chain 16S rRNA


Mass: 499239.000 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: GenBank: 1114169151
#55: RNA chain tRNA-fMet


Mass: 24818.893 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: GenBank: 731469900
#56: RNA chain mRNA / Messenger RNA


Mass: 3773.280 Da / Num. of mol.: 1 / Source: (synth.) Escherichia coli / Details: in vitro transcription vector pT7-TP(deltai)
#57: RNA chain Phe-tRNA-Phe


Mass: 24651.930 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600

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

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


Mass: 29663.244 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P60422
#4: Protein/peptide 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


Mass: 22146.338 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P60438
#5: Protein/peptide 50S ribosomal protein L4 / / Large ribosomal subunit protein uL4


Mass: 21990.367 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P60723
#6: 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) / Strain: MRE 600 / References: UniProt: P62399
#7: Protein/peptide 50S ribosomal protein L6 / / Large ribosomal subunit protein uL6


Mass: 18543.238 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0AG55
#8: 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) / Strain: MRE 600 / References: UniProt: P0A7R1
#9: Protein/peptide 50S ribosomal protein L11 / / Large ribosomal subunit protein uL11


Mass: 14763.165 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7J7
#10: Protein/peptide 50S ribosomal protein L13 / / Large ribosomal subunit protein uL13


Mass: 15937.448 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0AA10
#11: Protein/peptide 50S ribosomal protein L14 / / Large ribosomal subunit protein uL14


Mass: 13451.910 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0ADY3
#12: Protein/peptide 50S ribosomal protein L15 / / Large ribosomal subunit protein uL15


Mass: 14879.357 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02413
#13: 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) / Strain: MRE 600 / References: UniProt: P0ADY7
#14: 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) / Strain: MRE 600 / References: UniProt: P0AG44
#15: Protein/peptide 50S ribosomal protein L18 / / Large ribosomal subunit protein uL18


Mass: 12663.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0C018
#16: 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) / Strain: MRE 600 / References: UniProt: P0A7K6
#17: Protein/peptide 50S ribosomal protein L20 / / Large ribosomal subunit protein bL20


Mass: 13212.593 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7L3
#18: Protein/peptide 50S ribosomal protein L21 / / Large ribosomal subunit protein bL21


Mass: 11515.297 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0AG48
#19: Protein/peptide 50S ribosomal protein L22 / / Large ribosomal subunit protein uL22


Mass: 12096.166 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P61175
#20: Protein/peptide 50S ribosomal protein L23 / / Large ribosomal subunit protein uL23


Mass: 10415.276 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0ADZ0
#21: Protein/peptide 50S ribosomal protein L24 / / Large ribosomal subunit protein uL24


Mass: 11078.874 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P60624
#22: Protein/peptide 50S ribosomal protein L25 / / Large ribosomal subunit protein bL25


Mass: 10511.190 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P68919
#23: Protein/peptide 50S ribosomal protein L27 / / Large ribosomal subunit protein bL27


Mass: 8146.384 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7L8
#24: 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) / Strain: MRE 600 / References: UniProt: P0A7M2
#25: Protein/peptide 50S ribosomal protein L29 / / Large ribosomal subunit protein uL29


Mass: 7087.256 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7M6
#26: Protein/peptide 50S ribosomal protein L30 / / Large ribosomal subunit protein uL30


Mass: 6223.433 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0AG51
#27: Protein/peptide 50S ribosomal protein L32 / / Large ribosomal subunit protein bL32


Mass: 6203.069 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7N4
#28: Protein/peptide 50S ribosomal protein L33 / / Large ribosomal subunit protein bL33


Mass: 5928.000 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7N9
#29: Protein/peptide 50S ribosomal protein L34 / / Large ribosomal subunit protein bL34


Mass: 5268.283 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7P5
#30: 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) / Strain: MRE 600 / References: UniProt: P0A7Q1
#31: 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
#32: Protein/peptide 50S ribosomal protein L10 / / 50S ribosomal protein L8 / Large ribosomal subunit protein uL10


Mass: 14112.345 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7J3
#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) / Strain: MRE 600 / References: UniProt: P0A7M9

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

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


Mass: 24253.943 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7V0
#36: Protein/peptide 30S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 23078.785 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7V3
#37: 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) / Strain: MRE 600 / References: UniProt: P0A7V8
#38: Protein/peptide 30S ribosomal protein S5 / / Small ribosomal subunit protein uS5


Mass: 16532.088 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7W1
#39: Protein/peptide 30S ribosomal protein S6 / / Small ribosomal subunit protein bS6


Mass: 11669.371 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02358
#40: 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) / Strain: MRE 600 / References: UniProt: P02359
#41: 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) / Strain: MRE 600 / References: UniProt: P0A7W7
#42: Protein/peptide 30S ribosomal protein S9 / / Small ribosomal subunit protein uS9


Mass: 14554.882 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7X3
#43: Protein/peptide 30S ribosomal protein S10 / / Small ribosomal subunit protein uS10


Mass: 11196.988 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7R5
#44: Protein/peptide 30S ribosomal protein S11 / / Small ribosomal subunit protein uS11


Mass: 12388.068 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7R9
#45: Protein/peptide 30S ribosomal protein S12 / / Small ribosomal subunit protein uS12


Mass: 13436.703 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7S3
#46: Protein/peptide 30S ribosomal protein S13 / / Small ribosomal subunit protein uS13


Mass: 12738.911 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7S9
#47: Protein/peptide 30S ribosomal protein S14 / / Small ribosomal subunit protein uS14


Mass: 11546.442 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0AG59
#48: Protein/peptide 30S ribosomal protein S15 / / Small ribosomal subunit protein uS15


Mass: 10159.621 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0ADZ4
#49: Protein/peptide 30S ribosomal protein S16 / / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7T3
#50: 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) / Strain: MRE 600 / References: UniProt: P0AG63
#51: 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) / Strain: MRE 600 / References: UniProt: P0A7T7
#52: Protein/peptide 30S ribosomal protein S19 / / Small ribosomal subunit protein uS19


Mass: 9057.626 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7U3
#53: 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) / Strain: MRE 600 / References: UniProt: P0A7U7
#54: Protein/peptide 30S ribosomal protein S21 / / Small ribosomal subunit protein bS21


Mass: 7763.073 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P68679

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Protein/peptide , 1 types, 1 molecules z

#58: Protein/peptide Elongation factor Tu 2 / EF-Tu / EF-Tu 2 / Bacteriophage Q beta RNA-directed RNA polymerase subunit III / P-43


Mass: 43238.312 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE 600 / Gene: tufB, b3980, JW3943 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CE48

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Non-polymers , 6 types, 2618 molecules

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


Mass: 24.305 Da / Num. of mol.: 1618 / Formula: Mg / Magnesium
#60: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Formula: K / Potassium
#61: Chemical ChemComp-FME / N-FORMYLMETHIONINE


Mass: 177.221 Da / Num. of mol.: 1 / Formula: C6H11NO3S / N-Formylmethionine
#62: Chemical ChemComp-PHE / PHENYLALANINE


Mass: 165.189 Da / Num. of mol.: 1 / Formula: C9H11NO2 / Phenylalanine
#63: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Formula: C10H17N6O13P3
Comment: GppNHp (GMPPNP, energy-carrying molecule analogue) *YM
#64: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 996 / 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

ComponentName: 70S ribosome-EF-Tu (H84A) in complex with GppNHp / Type: RIBOSOME
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58
Source: MULTIPLE SOURCES
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer ID
11 mMpolymixPM1
25 mMpotassium phosphateKP1
314 mMmagnesium acetateMgOAc1
41.8 mM5'-Guanylyl imidodiphosphateGppNHp1
510 mMphosphoenolpyruvatePEP1
61 mMdithioerythritolDTE1
SpecimenDetails: 300 nM 70S ribosome in final mixture / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: grids were manually coated with gold and the carbon support was removed by glow discharge. gas mixture: 20% hydrogen/80% oxygen power: 15 W
Grid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 kelvins / Details: 5 second blot time, no wait time

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 / Calibrated magnification: 51020 / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 4000 nm / Cs: 2.26 mm / C2 aperture diameter: 30 microns / 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) / Number of grids imaged: 1 / Number of real images: 2844
Image scansSampling size: 5 microns / Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategoryDetails
1RELION2particle selection
2Leginonimage acquisition
4Gctf0.5CTF correctionused for CTF determination
5RELION2CTF correctionused for 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 selectionNumber of particles selected: 168315
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 56963 / Algorithm: BACK PROJECTION / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingOverall b value: 84 / Ref protocol: OTHER / Ref space: RECIPROCAL

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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