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- PDB-9p0e: Flavobacterium johnsoniae ZAM64 mutant 70S initiation complex wit... -

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Basic information

Entry
Database: PDB / ID: 9p0e
TitleFlavobacterium johnsoniae ZAM64 mutant 70S initiation complex with rpsU mRNA containing Shine-Dalgarno sequence.
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 30
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • fMet-tRNA
  • rpsU mRNA
KeywordsRIBOSOME / 70S / Initiation complex / translation.
Function / homology
Function and homology information


large ribosomal subunit / ribosomal small subunit assembly / transferase activity / ribosome biogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...large ribosomal subunit / ribosomal small subunit assembly / transferase activity / ribosome biogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / cytoplasm / cytosol
Similarity search - Function
Protein of unknown function DUF4295 / Domain of unknown function (DUF4295) / : / Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 signature. ...Protein of unknown function DUF4295 / Domain of unknown function (DUF4295) / : / Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 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 L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / : / Ribosomal protein S19, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / 30S ribosomal protein S17 / : / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S14/S29 / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / Ribosomal protein L16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein L20 / Ribosomal protein S12, bacterial-type / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / :
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL22 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL25 / DUF4295 domain-containing protein / 50S ribosomal protein L31 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / AURKAIP1/COX24 domain-containing protein / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsOrtega, J. / Arpin, D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structure of a specialized 70S initiation complex.
Authors: Dominic Arpin / Bappaditya Roy / Fawwaz M Naeem / Kurt Fredrick / Joaquin Ortega /
Abstract: Bacteria of class Bacteroidia lack Shine-Dalgarno (SD) sequences and instead rely on other messenger RNA (mRNA) features, including upstream adenines, for start codon selection. Bacteroidia ribosomes ...Bacteria of class Bacteroidia lack Shine-Dalgarno (SD) sequences and instead rely on other messenger RNA (mRNA) features, including upstream adenines, for start codon selection. Bacteroidia ribosomes contain the anti-SD (ASD) sequence of 16S ribosomal RNA (rRNA) but are "blind" to SD sequences. This occurs due to the sequestration of the ASD through interactions with bS21, bS18, and bS6 on the 30S platform domain. In many Bacteroidia, including Flavobacterium johnsoniae, there is one gene with an extended SD-rpsU, which encodes bS21. Ribosomes lacking bS21 exhibit high-level translation of rpsU, establishing an autoregulatory circuit in the cell. In this work, we investigate the structural basis of initiation on rpsU mRNA. We find using cryo-electron microscopy that initiation entails the formation of a 13-base pair SD-ASD helix that sterically occludes bS21. Mutations of bS21, bS18, or bS6 that compromise the platform pocket liberate the 3' tail of 16S rRNA, enable SD-ASD pairing, and enhance initiation. As initiation on rpsU mRNA depends on SD-ASD pairing, we infer that dissociation of bS21 from replete ribosomes limits their initiation rate. This work shows how a compositional change of the ribosome can govern translation of a specific gene.
History
DepositionJun 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: 23S rRNA
2: 16S rRNA
3: 5S rRNA
4: 50S ribosomal protein L38
5: 30S ribosomal protein S22
6: rpsU mRNA
A: fMet-tRNA
B: 50S ribosomal protein L2
C: 50S ribosomal protein L3
D: 50S ribosomal protein L4
E: 50S ribosomal protein L5
F: 50S ribosomal protein L6
G: 50S ribosomal protein L9
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
a: 50S ribosomal protein L31
b: 50S ribosomal protein L32
c: 50S ribosomal protein L33
d: 50S ribosomal protein L34
e: 50S ribosomal protein L35
f: 50S ribosomal protein L36
h: 30S ribosomal protein S3
i: 30S ribosomal protein S4
j: 30S ribosomal protein S5
k: 30S ribosomal protein S6
l: 30S ribosomal protein S7
m: 30S ribosomal protein S8
n: 30S ribosomal protein S9
o: 30S ribosomal protein S10
p: 30S ribosomal protein S11
q: 30S ribosomal protein S12
r: 30S ribosomal protein S13
s: 30S ribosomal protein S14
t: 30S ribosomal protein S15
u: 30S ribosomal protein S16
v: 30S ribosomal protein S17
w: 30S ribosomal protein S18
x: 30S ribosomal protein S19
y: 30S ribosomal protein S20


Theoretical massNumber of molelcules
Total (without water)2,162,16354
Polymers2,162,16354
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules 1236A

#1: RNA chain 23S rRNA


Mass: 927297.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Production host: Flavobacterium johnsoniae (bacteria) / References: GenBank: 1735479352
#2: RNA chain 16S rRNA


Mass: 491833.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Production host: Flavobacterium johnsoniae (bacteria)
#3: RNA chain 5S rRNA


Mass: 35661.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Production host: Flavobacterium johnsoniae (bacteria) / References: GenBank: 146152184
#6: RNA chain rpsU mRNA


Mass: 7445.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Production host: Flavobacterium johnsoniae (bacteria)
#7: RNA chain fMet-tRNA


Mass: 24786.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Production host: Flavobacterium johnsoniae (bacteria) / References: GenBank: 2512344223

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50S ribosomal protein ... , 30 types, 30 molecules 4BCDEFGJKLMNOPQRSTUVWXYZabcdef

#4: Protein/peptide 50S ribosomal protein L38


Mass: 5569.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: SAMN05444388_102562 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5JJE6
#8: Protein 50S ribosomal protein L2


Mass: 29991.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplB, SAMN05444388_103383 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U0Q0
#9: Protein 50S ribosomal protein L3


Mass: 21975.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplC, SAMN05444388_103386 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L9Q4
#10: Protein 50S ribosomal protein L4


Mass: 23187.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplD, SAMN05444388_103385 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M7D775
#11: Protein 50S ribosomal protein L5


Mass: 20799.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Production host: Flavobacterium johnsoniae (bacteria)
#12: Protein 50S ribosomal protein L6


Mass: 19420.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplF, SAMN05444388_103371 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L807
#13: Protein 50S ribosomal protein L9


Mass: 15968.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplI, SAMN05444388_10496 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5M9Q7
#14: Protein 50S ribosomal protein L13


Mass: 16578.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplM, SAMN05444388_101316 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5GAA6
#15: Protein 50S ribosomal protein L14


Mass: 13339.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplN, Fjoh_0387 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A5FMZ0
#16: Protein 50S ribosomal protein L15


Mass: 15994.265 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplO, SAMN05444388_103367 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M7D8T3
#17: Protein 50S ribosomal protein L16


Mass: 16075.122 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplP, SAMN05444388_103379 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U0I0
#18: Protein 50S ribosomal protein L17


Mass: 18092.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplQ, SAMN05444388_103360 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L6R0
#19: Protein 50S ribosomal protein L18


Mass: 12660.720 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplR, SAMN05444388_103370 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M7D8T4
#20: Protein 50S ribosomal protein L19


Mass: 13316.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplS, SAMN05444388_10678 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5PX52
#21: Protein 50S ribosomal protein L20


Mass: 13244.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplT, BKM63_01510, DFS20_4202, SAMN05444388_1035 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U1H3
#22: Protein 50S ribosomal protein L21


Mass: 15901.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplU, SAMN05444388_101389 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5GFZ4
#23: Protein 50S ribosomal protein L22


Mass: 15475.993 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplV, BKM63_03295, DFS20_4234, SAMN05444388_103381 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U0F3
#24: Protein 50S ribosomal protein L23


Mass: 10690.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplW, BKM63_03310, DFS20_4237, SAMN05444388_103384 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7BX85
#25: Protein 50S ribosomal protein L24


Mass: 11439.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplX, DFS20_4228, SAMN05444388_103375 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U0F5
#26: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 21891.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rplY, ctc, SAMN05444388_101814 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5HDD0
#27: Protein 50S ribosomal protein L27


Mass: 9422.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpmA, SAMN05444388_101388 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M6R2K9
#28: Protein 50S ribosomal protein L28


Mass: 8942.626 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpmB, BKM63_00965, DFS20_2513, SAMN05444388_102564 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U1R1
#29: Protein 50S ribosomal protein L29


Mass: 7189.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpmC, Fjoh_0389 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A5FMZ2
#30: Protein 50S ribosomal protein L30


Mass: 6643.993 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpmD, DFS20_4221, SAMN05444388_103368 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L7Z6
#31: Protein 50S ribosomal protein L31


Mass: 9646.128 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: DFS20_4118, SAMN05444388_10390 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5KIG2
#32: Protein 50S ribosomal protein L32


Mass: 7518.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpmF, BKM63_04440, DFS20_0146, SAMN05444388_111146 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U029
#33: Protein 50S ribosomal protein L33


Mass: 6935.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpmG, BKM63_00960, DFS20_2514, SAMN05444388_102563 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U200
#34: Protein 50S ribosomal protein L34


Mass: 6324.544 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpmH, BKM63_01870, DFS20_4126, SAMN05444388_10381 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U1E7
#35: Protein 50S ribosomal protein L35


Mass: 7522.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpmI, BKM63_01505, DFS20_4203, SAMN05444388_1034 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7BZ40
#36: Protein/peptide 50S ribosomal protein L36


Mass: 4557.577 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpmJ, Fjoh_0375 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A5FMZ9

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30S ribosomal protein ... , 19 types, 19 molecules 5hijklmnopqrstuvwxy

#5: Protein/peptide 30S ribosomal protein S22


Mass: 3696.608 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: Fjoh_1533 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A5FJQ0
#37: Protein 30S ribosomal protein S3


Mass: 27886.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsC, BKM63_03290, DFS20_4233, SAMN05444388_103380 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7CBX1
#38: Protein 30S ribosomal protein S4


Mass: 22950.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsD, SAMN05444388_103362 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U0J7
#39: Protein 30S ribosomal protein S5


Mass: 18206.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsE, SAMN05444388_103369 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U0I9
#40: Protein 30S ribosomal protein S6


Mass: 13376.448 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsF, BKM63_14855, DFS20_3370, SAMN05444388_10494 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7BSW7
#41: Protein 30S ribosomal protein S7


Mass: 18493.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsG, SAMN05444388_103389 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L9G3
#42: Protein 30S ribosomal protein S8


Mass: 14652.163 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsH, SAMN05444388_103372 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L889
#43: Protein 30S ribosomal protein S9


Mass: 14464.888 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsI, SAMN05444388_101317 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M6R974
#44: Protein 30S ribosomal protein S10


Mass: 11446.640 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsJ, BKM63_03325, DFS20_4240, SAMN05444388_103387 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7CP29
#45: Protein 30S ribosomal protein S11


Mass: 13700.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsK, BKM63_03205, DFS20_4215, SAMN05444388_103363 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7CBV3
#46: Protein 30S ribosomal protein S12


Mass: 14121.425 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsL, ASD98_02810 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A0Q8NJJ8
#47: Protein 30S ribosomal protein S13


Mass: 13734.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsM, Z4668, ECs4163 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: P0A7T1
#48: Protein 30S ribosomal protein S14


Mass: 10211.011 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsN, BKM63_03255, DFS20_4226, SAMN05444388_103373 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U0Q7
#49: Protein 30S ribosomal protein S15


Mass: 10565.339 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsO, SAMN05444388_101497 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M6QTP8
#50: Protein 30S ribosomal protein S16


Mass: 20106.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsP, SAMN05444388_101644 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M6QGN9
#51: Protein 30S ribosomal protein S17


Mass: 10108.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsQ, DFS20_4230, SAMN05444388_103377 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L8M4
#52: Protein 30S ribosomal protein S18


Mass: 11378.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsR, BKM63_14860, DFS20_3369, SAMN05444388_10495 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U6N1
#53: Protein 30S ribosomal protein S19


Mass: 10278.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsS, DFS20_4235, SAMN05444388_103382 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L8S8
#54: Protein 30S ribosomal protein S20


Mass: 9442.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: rpsT, SAMN05444388_102514 / Production host: Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U1X2

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Details

Has ligand of interestN
Has protein modificationN

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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 initiation complex / Type: RIBOSOME / Entity ID: #3-#54, #1-#2 / Source: NATURAL
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Buffer solutionpH: 7.4
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249488 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005150121
ELECTRON MICROSCOPYf_angle_d0.609224771
ELECTRON MICROSCOPYf_dihedral_angle_d14.63259435
ELECTRON MICROSCOPYf_chiral_restr0.03829019
ELECTRON MICROSCOPYf_plane_restr0.00511841

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