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- PDB-8rd8: Cryo-EM structure of P. urativorans 70S ribosome in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8rd8
TitleCryo-EM structure of P. urativorans 70S ribosome in complex with hibernation factors Balon and RaiA (structure 1).
Components
  • (Large ribosomal subunit protein ...) x 29
  • (Small ribosomal subunit protein ...) x 20
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 30S ribosomal protein S30
  • 5S rRNA5S ribosomal RNA
  • Elongation factor TuEF-Tu
  • Methyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins
KeywordsRIBOSOME / Hibernation factor / Dormancy / Balon
Function / homology
Function and homology information


primary metabolic process / guanosine tetraphosphate binding / translation elongation factor activity / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding ...primary metabolic process / guanosine tetraphosphate binding / translation elongation factor activity / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Bacterial archaeo-eukaryotic release factor family 3 / Bacterial archaeo-eukaryotic release factor family 3 / Ribosomal protein L31 type B / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal ...Bacterial archaeo-eukaryotic release factor family 3 / Bacterial archaeo-eukaryotic release factor family 3 / Ribosomal protein L31 type B / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Elongation factor Tu domain 2 / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L9 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 L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL2 / Methyl-accepting chemotaxis protein / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL31B / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS15 / Ribosome hibernation promoting factor / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL35 / Elongation factor Tu / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL21
Similarity search - Component
Biological speciesPsychrobacter urativorans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsHelena-Bueno, K. / Rybak, M.Y. / Gagnon, M.G. / Hill, C.H. / Melnikov, S.V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal SocietyRGS/R2/202003 United Kingdom
CitationJournal: Nature / Year: 2024
Title: A new family of bacterial ribosome hibernation factors.
Authors: Karla Helena-Bueno / Mariia Yu Rybak / Chinenye L Ekemezie / Rudi Sullivan / Charlotte R Brown / Charlotte Dingwall / Arnaud Baslé / Claudia Schneider / James P R Connolly / James N Blaza / ...Authors: Karla Helena-Bueno / Mariia Yu Rybak / Chinenye L Ekemezie / Rudi Sullivan / Charlotte R Brown / Charlotte Dingwall / Arnaud Baslé / Claudia Schneider / James P R Connolly / James N Blaza / Bálint Csörgő / Patrick J Moynihan / Matthieu G Gagnon / Chris H Hill / Sergey V Melnikov /
Abstract: To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of ...To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon-EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation.
History
DepositionDec 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Methyl-accepting chemotaxis protein
F: Small ribosomal subunit protein uS9
H: Elongation factor Tu
C1: Large ribosomal subunit protein bL9
Z2: 23S rRNA
R3: Small ribosomal subunit protein bS18
A4: Small ribosomal subunit protein uS2
E5: Small ribosomal subunit protein uS5
L6: Small ribosomal subunit protein uS12
F7: Large ribosomal subunit protein uL5
D8: 5S rRNA
E9: Large ribosomal subunit protein uL4
aA: Large ribosomal subunit protein bL32
MB: Large ribosomal subunit protein bL17
UC: Large ribosomal subunit protein bL25
WD: Large ribosomal subunit protein bL28
XE: Large ribosomal subunit protein uL29
RF: Large ribosomal subunit protein uL22
FG: Small ribosomal subunit protein bS6
VH: Large ribosomal subunit protein bL27
TI: Large ribosomal subunit protein uL24
fJ: Large ribosomal subunit protein bL31B
HK: Small ribosomal subunit protein uS14
OL: Small ribosomal subunit protein uS15
MM: Small ribosomal subunit protein uS13
iN: 16S rRNA
PO: Large ribosomal subunit protein bL20
SP: Small ribosomal subunit protein uS19
BQ: Small ribosomal subunit protein uS8
GR: Large ribosomal subunit protein uL6
GS: Small ribosomal subunit protein uS7
CT: Small ribosomal subunit protein uS3
KU: Small ribosomal subunit protein uS11
NV: Small ribosomal subunit protein bS21
YW: Large ribosomal subunit protein uL30
IX: Large ribosomal subunit protein uL13
JY: Small ribosomal subunit protein uS10
QZ: Small ribosomal subunit protein uS17
Ba: Large ribosomal subunit protein bL34
Qb: Large ribosomal subunit protein bL21
Nc: Large ribosomal subunit protein uL18
Kd: Large ribosomal subunit protein uL15
Je: Large ribosomal subunit protein uL14
Af: Large ribosomal subunit protein uL3
Lg: Large ribosomal subunit protein uL16
dh: Large ribosomal subunit protein bL35
Oi: Large ribosomal subunit protein bL19
Pj: Small ribosomal subunit protein bS16
bk: Large ribosomal subunit protein bL33
Cl: Large ribosomal subunit protein uL2
Dm: Small ribosomal subunit protein uS4
Sn: Large ribosomal subunit protein uL23
To: Small ribosomal subunit protein bS20
ep: Large ribosomal subunit protein bL36
D: 30S ribosomal protein S30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,269,52157
Polymers2,269,47255
Non-polymers492
Water0
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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Protein , 3 types, 3 molecules BHD

#1: Protein Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis proteins


Mass: 41159.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter urativorans (bacteria) / Gene: AOC03_06830 / Production host: Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8U3
#3: Protein Elongation factor Tu / EF-Tu / EF-Tu


Mass: 43108.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U5B4
#55: Protein 30S ribosomal protein S30 /


Mass: 14105.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TFB0

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Small ribosomal subunit protein ... , 20 types, 20 molecules FR3A4E5L6FGHKOLMMSPBQGSCTKUNVJYQZPjDmTo

#2: Protein Small ribosomal subunit protein uS9


Mass: 14278.470 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T6M9
#6: Protein Small ribosomal subunit protein bS18


Mass: 8973.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5MK69
#7: Protein Small ribosomal subunit protein uS2


Mass: 29465.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TFJ4
#8: Protein Small ribosomal subunit protein uS5


Mass: 18192.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8J0
#9: Protein Small ribosomal subunit protein uS12


Mass: 13753.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U4C3
#19: Protein Small ribosomal subunit protein bS6


Mass: 15839.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U628
#23: Protein Small ribosomal subunit protein uS14


Mass: 11777.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8P8
#24: Protein Small ribosomal subunit protein uS15


Mass: 10218.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TF29
#25: Protein Small ribosomal subunit protein uS13


Mass: 13244.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5MJL8
#28: Protein Small ribosomal subunit protein uS19


Mass: 10336.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TUJ8
#29: Protein Small ribosomal subunit protein uS8


Mass: 14086.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U618
#31: Protein Small ribosomal subunit protein uS7


Mass: 17760.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8N5
#32: Protein Small ribosomal subunit protein uS3


Mass: 27120.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T6V9
#33: Protein Small ribosomal subunit protein uS11


Mass: 13676.589 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8P6
#34: Protein Small ribosomal subunit protein bS21


Mass: 8548.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4SY21
#37: Protein Small ribosomal subunit protein uS10


Mass: 11635.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TE68
#38: Protein Small ribosomal subunit protein uS17


Mass: 10362.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U401
#48: Protein Small ribosomal subunit protein bS16


Mass: 9955.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T275
#51: Protein Small ribosomal subunit protein uS4


Mass: 24279.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TE52
#53: Protein Small ribosomal subunit protein bS20


Mass: 9980.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T3R2

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Large ribosomal subunit protein ... , 29 types, 29 molecules C1F7E9aAMBUCWDXERFVHTIfJPOGRYWIXBaQbNcKdJeAfLgdhOibkClSnep

#4: Protein Large ribosomal subunit protein bL9


Mass: 18195.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V9E8
#10: Protein Large ribosomal subunit protein uL5


Mass: 19841.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T1L5
#12: Protein Large ribosomal subunit protein uL4


Mass: 21971.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U627
#13: Protein Large ribosomal subunit protein bL32


Mass: 7169.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4SWQ6
#14: Protein Large ribosomal subunit protein bL17


Mass: 13635.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U611
#15: Protein Large ribosomal subunit protein bL25 / General stress protein CTC


Mass: 23887.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U726
#16: Protein Large ribosomal subunit protein bL28


Mass: 9168.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T6Y7
#17: Protein Large ribosomal subunit protein uL29


Mass: 7519.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TBX9
#18: Protein Large ribosomal subunit protein uL22


Mass: 11932.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4SWS6
#20: Protein Large ribosomal subunit protein bL27


Mass: 9119.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TUE5
#21: Protein Large ribosomal subunit protein uL24


Mass: 11465.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TE60
#22: Protein Large ribosomal subunit protein bL31B


Mass: 10708.704 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4SX87
#27: Protein Large ribosomal subunit protein bL20


Mass: 13539.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5MJR6
#30: Protein Large ribosomal subunit protein uL6


Mass: 19536.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5MKV2
#35: Protein Large ribosomal subunit protein uL30


Mass: 6615.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4SWR7
#36: Protein Large ribosomal subunit protein uL13


Mass: 15802.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TBP4
#39: Protein/peptide Large ribosomal subunit protein bL34


Mass: 5292.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TEZ6
#40: Protein Large ribosomal subunit protein bL21


Mass: 11773.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5TIS3
#41: Protein Large ribosomal subunit protein uL18


Mass: 12550.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TUJ2
#42: Protein Large ribosomal subunit protein uL15


Mass: 15448.876 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T6V1
#43: Protein Large ribosomal subunit protein uL14


Mass: 13417.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5MJS2
#44: Protein Large ribosomal subunit protein uL3


Mass: 22236.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T1M3
#45: Protein Large ribosomal subunit protein uL16


Mass: 15626.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8J3
#46: Protein Large ribosomal subunit protein bL35


Mass: 7594.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U4I0
#47: Protein Large ribosomal subunit protein bL19


Mass: 14598.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TV08
#49: Protein Large ribosomal subunit protein bL33


Mass: 6053.298 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4SWV1
#50: Protein Large ribosomal subunit protein uL2


Mass: 30263.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8Q0
#52: Protein Large ribosomal subunit protein uL23


Mass: 12816.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5MJH9
#54: Protein/peptide Large ribosomal subunit protein bL36


Mass: 4330.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U3Z5

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RNA chain , 3 types, 3 molecules Z2D8iN

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


Mass: 933602.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria)
#11: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 36948.945 Da / Num. of mol.: 1 / Mutation: insertion of 85, C89A / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: GenBank: 930356181
#26: RNA chain 16S rRNA /


Mass: 514949.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter urativorans (bacteria) / Production host: Psychrobacter urativorans (bacteria) / References: GenBank: 930356181

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Non-polymers , 1 types, 2 molecules

#56: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: Ribosomes isolated from ice-treated cultures of Psychrobacter urativorans.
Type: RIBOSOME / Entity ID: #1-#55 / Source: NATURAL
Source (natural)Organism: Psychrobacter urativorans (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.75 mg/ml / Embedding 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 FIELDBright-field microscopy / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53372 / Num. of class averages: 1 / Symmetry type: POINT

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