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Basic information

Entry
Database: PDB / ID: 9hig
TitleCryo-EM composite structure of 70S ribosome of marine cold bacterium Pseudoalteromonas translucida (P. haloplanktis)TAC125.
Components
  • (Large ribosomal subunit protein ...) x 28
  • (Small ribosomal subunit protein ...) x 20
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • P-site tRNA-fMet
  • mRNA
KeywordsRIBOSOME / Cryo-EM / Composite structure / cold bacteria / translation
Function / homology
Function and homology information


assembly of large subunit precursor of preribosome / large ribosomal subunit / transferase activity / ribosomal small subunit assembly / ribosome binding / ribosome biogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit ...assembly of large subunit precursor of preribosome / large ribosomal subunit / transferase activity / ribosomal small subunit assembly / ribosome binding / ribosome biogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / 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 / cytosol / cytoplasm
Similarity search - Function
: / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily ...: / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein L9 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / 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 L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / 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 S6, conserved site / Ribosomal protein S6 signature. / 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 S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein S5, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 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 S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal L28 family / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / 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
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS16 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12
Similarity search - Component
Biological speciesPseudoalteromonas translucida TAC125 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.36 Å
AuthorsSingh, V. / Godsora, B.K.J. / Emmerich, A.G. / Majumdar, S. / Sanyal, S.
Funding support Sweden, United States, 9items
OrganizationGrant numberCountry
Swedish Research Council2023-05237 Sweden
Swedish Research Council2018-05498 Sweden
Swedish Research Council2016-06264 Sweden
Swedish Research Council2018-05498 Sweden
Swedish Research Council2018-05946 Sweden
Wenner-Gren FoundationUPD2023-0185 United States
Wenner-Gren FoundationUPD2017:0238 United States
Wenner-Gren FoundationUPD2018-0306 United States
Knut and Alice Wallenberg FoundationKAW 2017.0055 Sweden
CitationJournal: To Be Published
Title: Cryo-EM composite structure of 70S ribosome of marine cold bacterium Pseudoalteromonas translucida (P. haloplanktis)TAC125.
Authors: Singh, V. / Godsora, B.K.J. / Emmerich, A.G. / Majumdar, S. / Sanyal, S.
History
DepositionNov 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 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

Downloads & links

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Assembly

Deposited unit
A: 16S rRNA
B: Small ribosomal subunit protein uS2
C: Small ribosomal subunit protein uS3
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
F: Small ribosomal subunit protein bS6
G: Small ribosomal subunit protein uS7
H: Small ribosomal subunit protein uS8
I: Small ribosomal subunit protein uS9
J: Small ribosomal subunit protein uS10
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
M: Small ribosomal subunit protein uS13
N: Small ribosomal subunit protein uS14
O: Small ribosomal subunit protein uS15
P: Small ribosomal subunit protein bS16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18
S: Small ribosomal subunit protein uS19
T: Small ribosomal subunit protein bS20
U: Small ribosomal subunit protein bS21
W: P-site tRNA-fMet
X: mRNA
a: 23S rRNA
b: 5S rRNA
0: Large ribosomal subunit protein bL33
1: Large ribosomal subunit protein bL34
2: Large ribosomal subunit protein bL35
3: Large ribosomal subunit protein bL36
c: Large ribosomal subunit protein uL2
d: Large ribosomal subunit protein uL3
e: Large ribosomal subunit protein uL4
g: Large ribosomal subunit protein uL6
h: Large ribosomal subunit protein bL9
i: Large ribosomal subunit protein uL13
j: Large ribosomal subunit protein uL14
k: Large ribosomal subunit protein uL15
l: Large ribosomal subunit protein uL16
m: Large ribosomal subunit protein bL17
n: Large ribosomal subunit protein uL18
o: Large ribosomal subunit protein bL19
p: Large ribosomal subunit protein bL20
q: Large ribosomal subunit protein bL21
r: Large ribosomal subunit protein uL22
s: Large ribosomal subunit protein uL23
t: Large ribosomal subunit protein uL24
u: Large ribosomal subunit protein bL25
v: Large ribosomal subunit protein bL27
w: Large ribosomal subunit protein bL28
x: Large ribosomal subunit protein uL29
y: Large ribosomal subunit protein uL30
z: Large ribosomal subunit protein bL32
f: Large ribosomal subunit protein uL5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,143,786342
Polymers2,136,76253
Non-polymers7,024289
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 5 types, 5 molecules AWXab

#1: RNA chain 16S rRNA


Mass: 494937.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: GenBank: 76873893
#22: RNA chain P-site tRNA-fMet


Mass: 5771.507 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
#23: RNA chain mRNA


Mass: 1264.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
#24: RNA chain 23S rRNA


Mass: 935834.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: GenBank: 76873893
#25: RNA chain 5S rRNA


Mass: 37681.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: GenBank: 507148480

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Small ribosomal subunit protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

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


Mass: 26878.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IIX4
#3: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 25780.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IF19
#4: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23525.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJJ5
#5: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17735.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJK2
#6: Protein Small ribosomal subunit protein bS6 / 30S ribosomal protein S6


Mass: 13013.841 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IIA2
#7: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 17627.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3ILP6
#8: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14082.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJJ9
#9: Protein Small ribosomal subunit protein uS9


Mass: 14638.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IG27
#10: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11752.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IF26
#11: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13718.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJK7
#12: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13699.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3ILP7
#13: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13142.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJK6
#14: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14


Mass: 11518.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJJ8
#15: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10296.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJ74
#16: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 9271.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IEC9
#17: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 9789.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IFM3
#18: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 8861.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3II81
#19: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10969.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IF21
#20: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9659.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IEA5
#21: Protein Small ribosomal subunit protein bS21 / 30S ribosomal protein S21


Mass: 8589.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IIB6

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Large ribosomal subunit protein ... , 28 types, 28 molecules 0123cdeghijklmnopqrstuvwxyzf

#26: Protein Large ribosomal subunit protein bL33 / 50S ribosomal protein L33


Mass: 6131.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IFE7
#27: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5109.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IK51
#28: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7717.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IL79
#29: Protein/peptide Large ribosomal subunit protein bL36 / 50S ribosomal protein L36


Mass: 5006.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IC33
#30: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 29956.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IF22
#31: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 22214.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IF25
#32: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 21862.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IF24
#33: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19233.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJK0
#34: Protein Large ribosomal subunit protein bL9 / 50S ribosomal protein L9


Mass: 15745.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3II82
#35: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 15972.583 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IG26
#36: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13443.841 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJL9
#37: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15012.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJK4
#38: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 15694.476 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IF18
#39: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 14875.089 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJI7
#40: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 12633.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJK1
#41: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 13356.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IEC6
#42: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13593.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IL78
#43: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11513.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IFF4
#44: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12056.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IF20
#45: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 11154.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IF23
#46: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11411.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJJ6
#47: Protein Large ribosomal subunit protein bL25 / 50S ribosomal protein L25 / General stress protein CTC


Mass: 22372.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IK85
#48: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 9270.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IFF5
#49: Protein Large ribosomal subunit protein bL28


Mass: 11106.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IFE6
#50: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7195.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IFM4
#51: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6675.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJK3
#52: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6280.132 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IHD7
#53: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20126.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pseudoalteromonas translucida TAC125 (bacteria)
References: UniProt: Q3IJJ7

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Non-polymers , 2 types, 316 molecules

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


Mass: 24.305 Da / Num. of mol.: 289 / Source method: obtained synthetically / Formula: Mg
#55: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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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 Ribosome / Type: RIBOSOME
Entity ID: #3, #14, #1, #25, #2, #4, #6, #8, #11-#13, #15, #17-#18, #20-#21, #26-#53, #22-#23, #5, #16, #7, #10, #19, #9
Source: NATURAL
Source (natural)Organism: Pseudoalteromonas translucida TAC125 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Native ribosomes purified from log phase culture of Pseudoalteromonas haloplanktis TAC125 using conventional ultracentrifugation method.
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
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: 5000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCver. v3.3.1+220118particle selection
4cryoSPARCver. v3.3.1+220118CTF correction
10cryoSPARCver. v3.3.1+220118initial Euler assignment
11cryoSPARCver. v3.3.1+220118final Euler assignment
12cryoSPARCver. v3.3.1+220118classification
13cryoSPARCver. v3.3.1+2201183D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 360324 / Algorithm: FOURIER SPACE / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 96.55 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0071144016
ELECTRON MICROSCOPYf_angle_d0.7378215707
ELECTRON MICROSCOPYf_chiral_restr0.044127708
ELECTRON MICROSCOPYf_plane_restr0.005711478
ELECTRON MICROSCOPYf_dihedral_angle_d16.426257041

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