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

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Basic information

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 rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • E-site tRNA Phe
  • P-site tRNA fMet
  • messenger RNA
KeywordsRIBOSOME / 70S ribosome / dnaX / stem-loop / structured mRNA / -1 programmed frameshifting / E site
Function / homology
Function and homology information


small ribosomal subunit / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / regulation of translation / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome ...small ribosomal subunit / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / regulation of translation / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / zinc ion binding / metal ion binding
Ribosomal protein S20 / Ribosomal protein S6 superfamily / Ribosomal protein S10 domain / Ribosomal protein L31 type A / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L21-like / Ribosomal protein L25 / 30S ribosomal protein / Ribosomal protein L15 / Ribosomal protein L5, C-terminal ...Ribosomal protein S20 / Ribosomal protein S6 superfamily / Ribosomal protein S10 domain / Ribosomal protein L31 type A / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L21-like / Ribosomal protein L25 / 30S ribosomal protein / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / 30S ribosomal protein Thx / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein L36 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S18 superfamily / 30s ribosomal protein S13, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L34, conserved site / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25, beta domain / Ribosomal protein L9, C-terminal / Ribosomal protein L9, N-terminal / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein S19 conserved site / Ribosomal protein L18e/L15P / Ribosomal protein S7 domain / Ribosomal protein L35 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L5 domain superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S14, type Z / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L1, conserved site / Ribosomal protein L1-like / Ribosomal protein L13 superfamily / Ribosomal protein L10e/L16 superfamily / 30S ribosomal protein S17 / S4 domain / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal prokaryotic L21 protein / Ribosomal protein L22p/L17e / Ribosomal protein L23 / KOW motif / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal L25p family / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S2 / Ribosomal protein S3, C-terminal domain / KH domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S5, N-terminal domain / Ribosomal protein L16p/L10e / Ribosomal protein S5, C-terminal domain / Ribosomal protein S6 / Ribosomal protein S8 / Ribosomal protein S10p/S20e / Ribosomal protein S11 / Ribosomal protein S12/S23 / Ribosomal protein S13/S18 / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S16 / Ribosomal protein S17 / Ribosomal protein S18 / Ribosomal protein S19 / Ribosomal protein L17 / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L33 / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily
50S ribosomal protein L36 / 50S ribosomal protein L32 / 50S ribosomal protein L27 / 50S ribosomal protein L28 / 30S ribosomal protein S9 / 50S ribosomal protein L34 / 30S ribosomal protein S2 / 30S ribosomal protein S4 / 50S ribosomal protein L20 / 50S ribosomal protein L21 ...50S ribosomal protein L36 / 50S ribosomal protein L32 / 50S ribosomal protein L27 / 50S ribosomal protein L28 / 30S ribosomal protein S9 / 50S ribosomal protein L34 / 30S ribosomal protein S2 / 30S ribosomal protein S4 / 50S ribosomal protein L20 / 50S ribosomal protein L21 / 30S ribosomal protein S17 / 50S ribosomal protein L19 / 50S ribosomal protein L16 / 50S ribosomal protein L13 / 50S ribosomal protein L2 / 50S ribosomal protein L33 / 30S ribosomal protein S7 / 30S ribosomal protein S13 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 50S ribosomal protein L6 / 30S ribosomal protein S11 / 30S ribosomal protein S20 / 50S ribosomal protein L25 / 30S ribosomal protein S5 / 30S ribosomal protein Thx / 30S ribosomal protein S15 / 50S ribosomal protein L31 / 30S ribosomal protein S16 / 50S ribosomal protein L35 / 50S ribosomal protein L1 / 30S ribosomal protein S6 / 30S ribosomal protein S18 / 50S ribosomal protein L9 / 50S ribosomal protein L17 / gb:55771382: / gb:1126835761: / 50S ribosomal protein L15 / 50S ribosomal protein L30 / 50S ribosomal protein L18 / 30S ribosomal protein S12 / 50S ribosomal protein L6 / 30S ribosomal protein S8 / 30S ribosomal protein S14 type Z / 50S ribosomal protein L5 / 50S ribosomal protein L24 / 50S ribosomal protein L14 / 30S ribosomal protein S17 / 50S ribosomal protein L29 / 50S ribosomal protein L22 / 30S ribosomal protein S19 / 50S ribosomal protein L23 / 50S ribosomal protein L4 / 50S ribosomal protein L3 / 30S ribosomal protein S10 / 30S ribosomal protein S3
Biological speciesThermus thermophilus (bacteria)
Escherichia coli K-12 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name

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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
Polymers2,230,71756
Non-polymers7447
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area293380 Å2
ΔGint-2211 kcal/mol
Surface area720380 Å2

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Components

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RNA chain , 6 types, 6 molecules ABayzx

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


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


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


Mass: 493903.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K-12 / References: GenBank: 1126835761
#55: RNA chain E-site tRNA Phe


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


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

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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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#45: Protein/peptide 30S ribosomal protein S14 type Z / Ribosome


Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#46: Protein/peptide 30S ribosomal protein S15 /


Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#49: Protein/peptide 30S ribosomal protein S18 /


Mass: 7897.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#52: Protein/peptide 30S ribosomal protein Thx / Ribosome


Mass: 2831.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 / Zinc


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#58: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4

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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-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) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image 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
6UCSF Chimeramodel 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 buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementResolution: 3.5→384 Å / Cross valid method: FREE R-VALUE

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