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- PDB-5uq7: 70S ribosome complex with dnaX mRNA stemloop and E-site tRNA ("in... -

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Entry
Database: PDB / ID: 5uq7
Title70S ribosome complex with dnaX mRNA stemloop and E-site tRNA ("in" conformation)
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • E-site tRNA Phe
  • P-site tRNA fMet
  • messenger RNA
KeywordsRIBOSOME / 70S ribosome / dnaX / stem-loop / structured mRNA / -1 programmed frameshifting / E site
Function/homologyRibosomal protein L1, bacterial-type / Ribosomal protein L25, C-terminal / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / 30S ribosomal protein Thx / Ribosomal protein L1 / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L31 type A / 30S ribosomal protein ...Ribosomal protein L1, bacterial-type / Ribosomal protein L25, C-terminal / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / 30S ribosomal protein Thx / Ribosomal protein L1 / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L31 type A / 30S ribosomal protein / Ribosomal protein L31 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S14, type Z / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1-like / Ribosomal protein L31 / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L36 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L28 / Ribosomal protein L28/L24 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L25 / Ribosomal protein L19 signature. / Ribosomal protein L19, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L33 / Ribosomal protein L18, bacterial-type / 30S ribosomal protein Thx / Ribosomal protein L20 signature. / Ribosomal protein L27 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L21 / L28p-like / Ribosomal protein L18 / Ribosomal protein L20, C-terminal / Ribosomal protein L20 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L6, bacterial-type / Ribosomal protein L30, bacterial-type / Ribosomal protein L34 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L13, bacterial-type / Ribosomal protein L19 / Ribosomal protein L27 / Ribosomal protein L15, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L1p/L10e family / Ribosomal protein L16 / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / 50S ribosomal protein uL4 / Ribosomal protein L24 / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L31 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S3, bacterial / Ribosomal protein S13, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S19, bacterial-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S6 signature. / Ribosomal protein S6, conserved site / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S4, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S15, bacterial-type / Ribosomal protein S18 superfamily / Ribosomal protein S18 / Ribosomal protein S6 superfamily
Function and homology information
Specimen sourceThermus thermophilus / bacteria / thermophilic /
Escherichia coli k-12 / bacteria / Escherichia coli in molecular biology / image: Escherichia coli
Synthetic construct
MethodElectron microscopy (3.5 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsZhang, Y. / Hong, S. / Skiniotis, G. / Dunham, C.M.
CitationJournal: Structure / Year: 2018
Title: Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel.
Authors: Yan Zhang / Samuel Hong / Ajchareeya Ruangprasert / Georgios Skiniotis / Christine M Dunham
Abstract: Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an ...Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an mRNA containing a 3' stem loop that regulates translation. Unexpectedly, the E-site tRNA adopts two distinct orientations. In the first structure, normal interactions with the 50S and 30S E site are observed. However, in the second structure, although the E-site tRNA makes normal interactions with the 50S E site, its anticodon stem loop moves ∼54 Å away from the 30S E site to interact with the 30S head domain and 50S uL5. This position of the E-site tRNA causes the uL1 stalk to adopt a more open conformation that likely represents an intermediate state during E-site tRNA dissociation. These results suggest that structured mRNAs at the entrance channel restrict 30S subunit movement required during translation to slow E-site tRNA dissociation.
Copyright: 2018 Elsevier Ltd. All rights reserved.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 7, 2017 / Release: Mar 7, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 7, 2018Structure modelrepositoryInitial release
1.1Mar 21, 2018Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
A: 23S rRNA
B: 5S rRNA
D: 50S ribosomal protein L2
E: 50S ribosomal protein L3
F: 50S ribosomal protein L4
G: 50S ribosomal protein L5
H: 50S ribosomal protein L6
I: 50S ribosomal protein L9
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
0: 50S ribosomal protein L27
1: 50S ribosomal protein L28
2: 50S ribosomal protein L29
3: 50S ribosomal protein L30
4: 50S ribosomal protein L31
5: 50S ribosomal protein L32
6: 50S ribosomal protein L33
7: 50S ribosomal protein L34
8: 50S ribosomal protein L35
9: 50S ribosomal protein L36
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 type Z
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 Thx
y: P-site tRNA fMet
C: 50S ribosomal protein L1
z: E-site tRNA Phe
x: messenger RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,231,46163
Polyers2,230,71756
Non-polymers7447
Water0
1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)293380
ΔGint (kcal/M)-2211
Surface area (Å2)720380

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Components

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RNA chain , 6 types, 6 molecules ABayzx

#1: RNA chain 23S rRNA


Mass: 948035.625 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank:55771382
#2: RNA chain 5S rRNA


Mass: 38882.207 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank:55771382
#32: RNA chain 16S rRNA


Mass: 493903.656 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank:55771382
#53: RNA chain P-site tRNA fMet


Mass: 24801.801 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / Strain: K-12 / References: GenBank:1126835761
#55: RNA chain E-site tRNA Phe


Mass: 24485.539 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / Strain: K-12 / References: GenBank:1126835761
#56: RNA chain messenger RNA


Mass: 17773.668 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct

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50S ribosomal protein ... , 30 types, 30 molecules DEFGHINOPQRSTUVWXYZ0123456789C

#3: Protein/peptide 50S ribosomal protein L2


Mass: 30401.355 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P60405
#4: Protein/peptide 50S ribosomal protein L3


Mass: 22249.953 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHN8
#5: Protein/peptide 50S ribosomal protein L4


Mass: 22512.023 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHN9
#6: Protein/peptide 50S ribosomal protein L5


Mass: 20930.400 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHQ0
#7: Protein/peptide 50S ribosomal protein L6


Mass: 18893.082 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHQ3, UniProt:A0A0M9ADP1*PLUS
#8: Protein/peptide 50S ribosomal protein L9


Mass: 16164.937 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SLQ1
#9: Protein/peptide 50S ribosomal protein L13


Mass: 15927.903 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P60488
#10: Protein/peptide 50S ribosomal protein L14


Mass: 13323.612 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHP8
#11: Protein/peptide 50S ribosomal protein L15


Mass: 16248.062 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHQ7
#12: Protein/peptide 50S ribosomal protein L16


Mass: 15993.909 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P60489
#13: Protein/peptide 50S ribosomal protein L17


Mass: 13750.148 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q9Z9H5
#14: Protein/peptide 50S ribosomal protein L18


Mass: 12437.570 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHQ4
#15: Protein/peptide 50S ribosomal protein L19


Mass: 15503.017 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P60490
#16: Protein/peptide 50S ribosomal protein L20


Mass: 13591.028 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P60491
#17: Protein/peptide 50S ribosomal protein L21


Mass: 11069.153 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P60492
#18: Protein/peptide 50S ribosomal protein L22


Mass: 12678.874 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHP3
#19: Protein/peptide 50S ribosomal protein L23


Mass: 10646.650 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHP0
#20: Protein/peptide 50S ribosomal protein L24


Mass: 11726.280 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHP9
#21: Protein/peptide 50S ribosomal protein L25


Mass: 21139.299 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHZ1
#22: Protein/peptide 50S ribosomal protein L27


Mass: 8689.006 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P60493
#23: Protein/peptide 50S ribosomal protein L28


Mass: 10872.965 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P60494
#24: Protein/peptide 50S ribosomal protein L29


Mass: 8485.077 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHP6
#25: Protein/peptide 50S ribosomal protein L30


Mass: 6667.931 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHQ6
#26: Protein/peptide 50S ribosomal protein L31


Mass: 8086.297 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SJE1
#27: Protein/peptide 50S ribosomal protein L32


Mass: 6590.854 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P80339
#28: Protein/peptide 50S ribosomal protein L33


Mass: 6501.700 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P35871
#29: Protein/peptide 50S ribosomal protein L34


Mass: 5975.255 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P80340
#30: Protein/peptide 50S ribosomal protein L35


Mass: 7374.981 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SKU1
#31: Protein/peptide 50S ribosomal protein L36


Mass: 4435.411 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHR2
#54: Protein/peptide 50S ribosomal protein L1


Mass: 24513.211 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SLP7

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

#33: Protein/peptide 30S ribosomal protein S2


Mass: 26646.852 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P80371
#34: Protein/peptide 30S ribosomal protein S3


Mass: 22862.430 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P80372
#35: Protein/peptide 30S ribosomal protein S4


Mass: 24242.254 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P80373
#36: Protein/peptide 30S ribosomal protein S5


Mass: 16144.848 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHQ5
#37: Protein/peptide 30S ribosomal protein S6


Mass: 11917.675 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SLP8
#38: Protein/peptide 30S ribosomal protein S7


Mass: 17919.775 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P17291
#39: Protein/peptide 30S ribosomal protein S8


Mass: 15737.372 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHQ2, UniProt:A0A0M9AFS9*PLUS
#40: Protein/peptide 30S ribosomal protein S9


Mass: 14122.225 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P80374
#41: Protein/peptide 30S ribosomal protein S10


Mass: 11056.838 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHN7
#42: Protein/peptide 30S ribosomal protein S11


Mass: 12032.662 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P80376
#43: Protein/peptide 30S ribosomal protein S12


Mass: 13650.211 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHN3
#44: Protein/peptide 30S ribosomal protein S13


Mass: 13067.221 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P80377
#45: Protein/peptide 30S ribosomal protein S14 type Z


Mass: 7027.529 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHQ1, UniProt:A0A0N0BLP2*PLUS
#46: Protein/peptide 30S ribosomal protein S15


Mass: 10447.213 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SJ76
#47: Protein/peptide 30S ribosomal protein S16


Mass: 9795.354 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SJH3
#48: Protein/peptide 30S ribosomal protein S17


Mass: 11722.904 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHP7, UniProt:A0A0N0BLS5*PLUS
#49: Protein/peptide 30S ribosomal protein S18


Mass: 7897.451 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SLQ0
#50: Protein/peptide 30S ribosomal protein S19


Mass: 9455.995 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SHP2
#51: Protein/peptide 30S ribosomal protein S20


Mass: 10876.067 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:P80380
#52: Protein/peptide 30S ribosomal protein Thx


Mass: 2831.295 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt:Q5SIH3

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Non-polymers , 2 types, 7 molecules

#57: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Formula: Zn / : Zinc
#58: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Formula: Fe4S4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: 70S-dnaX complex / 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
Source: MULTIPLE SOURCES
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 60

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Processing

EM software
IDNameCategory
6ChimeraMODEL FITTING
13PHENIXMODEL REFINEMENT
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Algorithm: BACK PROJECTION
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL
RefineCross valid method: FREE R-VALUE
Least-squares processHighest resolution: 3.5 Å / Lowest resolution: 384 Å

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Yorodumi

Thousand views of thousand structures

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

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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