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- PDB-9evt: Structure of the small subunit of the flowering plant mitoribosom... -

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Basic information

Entry
Database: PDB / ID: 9evt
TitleStructure of the small subunit of the flowering plant mitoribosome with the maturation factor RsgA
Components
  • (30S ribosomal protein ...) x 3
  • (Ribosomal protein ...) x 4
  • (Small ribosomal subunit protein ...) x 12
  • (rape) hypothetical protein
  • 18S rRNA
  • 40S ribosomal protein S15a
  • BnaC06g06470D protein
  • EngC GTPase domain-containing protein
  • IGR domain-containing protein
  • IMS import disulfide relay-system CHCH-CHCH-like Cx9C domain-containing protein
  • MOSC domain-containing protein
  • Mitochondrial 28S ribosomal protein S34
  • PROP1-like PPR domain-containing protein
  • RRM domain-containing protein
  • S5 DRBM domain-containing protein
  • bS6m
  • mS26
  • mS45
  • mS47
  • uS13m
  • uS7m,Small ribosomal subunit protein uS7m,Small ribosomal subunit protein uS7m
KeywordsRIBOSOME / mitochondria / mitoribosome / assembly factor / plant
Function / homology
Function and homology information


pollen tube development / plastid translation / gametophyte development / 3-hydroxyisobutyryl-CoA hydrolase / monocarboxylic acid metabolic process / embryo development ending in seed dormancy / cell communication / molybdenum ion binding / mitochondrial small ribosomal subunit / mitochondrial translation ...pollen tube development / plastid translation / gametophyte development / 3-hydroxyisobutyryl-CoA hydrolase / monocarboxylic acid metabolic process / embryo development ending in seed dormancy / cell communication / molybdenum ion binding / mitochondrial small ribosomal subunit / mitochondrial translation / mitochondrial membrane organization / plastid / catalytic activity / chloroplast / pyridoxal phosphate binding / small ribosomal subunit / small ribosomal subunit rRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / mitochondrion / RNA binding / cytoplasm
Similarity search - Function
CID8-like protein, RNA recognition motif 1 / CID8-like protein, RNA recognition motif 2 / IMS import disulfide relay-system, CHCH-CHCH-like Cx9C / CHCH-CHCH-like Cx9C, IMS import disulfide relay-system, / MOSC, N-terminal beta barrel / MOSC N-terminal beta barrel domain / Ribosomal protein S3, mitochondrial, plant / : / Molybdenum cofactor sulfurase, C-terminal / : ...CID8-like protein, RNA recognition motif 1 / CID8-like protein, RNA recognition motif 2 / IMS import disulfide relay-system, CHCH-CHCH-like Cx9C / CHCH-CHCH-like Cx9C, IMS import disulfide relay-system, / MOSC, N-terminal beta barrel / MOSC N-terminal beta barrel domain / Ribosomal protein S3, mitochondrial, plant / : / Molybdenum cofactor sulfurase, C-terminal / : / MOSC domain / MOSC domain profile. / Ataxin-2, C-terminal / Ataxin-2 C-terminal region / 30S ribosomal protein S31, plant / Ribosomal protein S31e / : / Ribosome biogenesis GTPase RsgA / RsgA GTPase domain / RsgA GTPase / EngC GTPase domain profile. / Pentacotripeptide-repeat region of PRORP / Pentacotripeptide-repeat region of PRORP / : / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Ribosomal protein MRP10, mitochondrial / Eukaryotic mitochondrial regulator protein / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase / Small ribosomal subunit protein mS41 SAM domain / IGR protein motif / IGR / Cysteine alpha-hairpin motif superfamily / Mitochondrial 28S ribosomal protein S34 / Mitochondrial 28S ribosomal protein S34 / Pentatricopeptide repeat domain / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Pyruvate kinase-like, insert domain superfamily / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / 30S ribosomal protein / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / ClpP/crotonase-like domain superfamily / Ribosomal protein S21 / Ribosomal protein S21 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Ribosomal protein S19, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / : / Ribosomal protein S2, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S13, conserved site
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein bS18c / BnaC06g06470D protein ...ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein bS18c / BnaC06g06470D protein / 30S ribosomal protein S16 / S5 DRBM domain-containing protein / Ribosomal protein S21 / Uncharacterized protein / 30S ribosomal protein S31, mitochondrial / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein uS10 domain-containing protein / Uncharacterized protein / Ribosomal protein S2 / EngC GTPase domain-containing protein / Uncharacterized protein / Small ribosomal subunit protein uS15c / Small ribosomal subunit protein mS41 SAM domain-containing protein / 40S ribosomal protein S15a / Small ribosomal subunit protein uS14m / Small ribosomal subunit protein mS23 / Ribosomal protein S11 / Small ribosomal subunit protein uS17c / MOSC domain-containing protein / Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein / RRM domain-containing protein / Small ribosomal subunit protein mS38 / PROP1-like PPR domain-containing protein / Mitochondrial 28S ribosomal protein S34 / 3-hydroxyisobutyryl-CoA hydrolase / Uncharacterized protein / (rape) hypothetical protein / IMS import disulfide relay-system CHCH-CHCH-like Cx9C domain-containing protein / Small ribosomal subunit protein uS19m / Small ribosomal subunit protein uS12m / Ribosomal protein S4
Similarity search - Component
Biological speciesBrassica oleracea var. botrytis (cauliflower)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.27 Å
AuthorsWaltz, F. / Skaltsogiannis, V. / Giege, P.
Funding support Germany, Switzerland, 2items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
Swiss National Science Foundation210561 Switzerland
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into cauliflower mitoribosome in translation state and in association with a late assembly factor.
Authors: Vasileios Skaltsogiannis / Philippe Wolff / Tan-Trung Nguyen / Nicolas Corre / David Pflieger / Todd Blevins / Yaser Hashem / Philippe Giegé / Florent Waltz /
Abstract: Ribosomes are key molecular machines that translate mRNA into proteins. Mitoribosomes are specific ribosomes found in mitochondria, which have been shown to be remarkably diverse across eukaryotic ...Ribosomes are key molecular machines that translate mRNA into proteins. Mitoribosomes are specific ribosomes found in mitochondria, which have been shown to be remarkably diverse across eukaryotic lineages. In plants, they possess unique features, including additional rRNA domains stabilized by plant-specific proteins. However, the structural specificities of plant mitoribosomes in translation state remained unknown. We used cryo-electron microscopy to provide a high-resolution structural characterization of the cauliflower mitoribosome, in translating and maturation states. The structure reveals the mitoribosome bound with a tRNA in the peptidyl site, along with a segment of mRNA and a nascent polypeptide. Moreover, using structural data, nanopore sequencing and mass spectrometry, we identify a set of 19 ribosomal RNA modifications. Additionally, we observe a late assembly intermediate of the small ribosomal subunit, in complex with the RsgA assembly factor. This reveals how a plant-specific extension of RsgA blocks the mRNA channel to prevent premature mRNA association before complete small subunit maturation. Our findings elucidate key aspects of translation in angiosperm plant mitochondria, revealing its distinct features compared to other eukaryotic lineages.
History
DepositionApr 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 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
A: Ribosomal protein S2
B: Small ribosomal subunit protein uS3m
C: Ribosomal protein S4
D: S5 DRBM domain-containing protein
E: bS6m
F: uS7m,Small ribosomal subunit protein uS7m,Small ribosomal subunit protein uS7m
G: 40S ribosomal protein S15a
H: 30S ribosomal protein S9
I: Small ribosomal subunit protein uS10 domain-containing protein
J: Ribosomal protein S11
K: Small ribosomal subunit protein uS12m
L: uS13m
M: Small ribosomal subunit protein uS14m
N: Small ribosomal subunit protein uS15c
O: 30S ribosomal protein S16
P: Small ribosomal subunit protein uS17c
Q: Small ribosomal subunit protein bS18c
R: Small ribosomal subunit protein uS19m
S: Ribosomal protein S21
T: 30S ribosomal protein S31, mitochondrial
U: Small ribosomal subunit protein mS23
V: mS26
W: Small ribosomal subunit protein mS29
X: BnaC06g06470D protein
Y: MOSC domain-containing protein
Z: Mitochondrial 28S ribosomal protein S34
7: EngC GTPase domain-containing protein
a: Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein
b: IMS import disulfide relay-system CHCH-CHCH-like Cx9C domain-containing protein
c: Small ribosomal subunit protein mS38
d: IGR domain-containing protein
e: mS45
f: mS47
h: (rape) hypothetical protein
i: PROP1-like PPR domain-containing protein
k: RRM domain-containing protein
2: 18S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,598,626135
Polymers1,595,07337
Non-polymers3,55398
Water00
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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Ribosomal protein ... , 4 types, 4 molecules ACJS

#1: Protein Ribosomal protein S2


Mass: 23743.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH046906
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3CN01
#3: Protein Ribosomal protein S4


Mass: 43438.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH000696
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: Q6YSL2
#10: Protein Ribosomal protein S11


Mass: 33108.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH051931
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A3P6EIC7
#19: Protein Ribosomal protein S21


Mass: 11541.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH012122
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3AW14

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Small ribosomal subunit protein ... , 12 types, 12 molecules BIKMNPQRUWac

#2: Protein Small ribosomal subunit protein uS3m / Ribosomal protein S3 / mitochondrial


Mass: 64731.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH000741
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A068BCX1
#9: Protein Small ribosomal subunit protein uS10 domain-containing protein


Mass: 25251.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH050210
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3CHA1
#11: Protein Small ribosomal subunit protein uS12m / Ribosomal protein S12 / mitochondrial


Mass: 14294.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS019876
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: P48857
#13: Protein Small ribosomal subunit protein uS14m / Ribosomal protein S14 / mitochondrial


Mass: 17928.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS019475
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A3P6BZM6
#14: Protein Small ribosomal subunit protein uS15c / 30S ribosomal protein S15 / chloroplastic


Mass: 47211.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH065138
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3D1Z7
#16: Protein Small ribosomal subunit protein uS17c


Mass: 12090.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH049400
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A3P6EMJ2
#17: Protein Small ribosomal subunit protein bS18c / 30S ribosomal protein S18 / chloroplastic


Mass: 27106.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH076274
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A078FCZ9
#18: Protein Small ribosomal subunit protein uS19m / 40S ribosomal protein S19 / mitochondrial


Mass: 23675.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: P39697
#21: Protein Small ribosomal subunit protein mS23


Mass: 21934.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH071753
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A3P6DYP2
#23: Protein Small ribosomal subunit protein mS29


Mass: 54288.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH054439
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3CAV8
#28: Protein Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein


Mass: 48589.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH049245
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A3P6FE97
#30: Protein Small ribosomal subunit protein mS38


Mass: 14562.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS042575
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A3P6GL56

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Protein , 17 types, 17 molecules DEFGLVXYZ7bdefhik

#4: Protein S5 DRBM domain-containing protein


Mass: 58296.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH015007
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3AS28
#5: Protein bS6m


Mass: 16011.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3CIR5
#6: Protein uS7m,Small ribosomal subunit protein uS7m,Small ribosomal subunit protein uS7m


Mass: 17955.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: ...Details: GWHPBJSH000704,GWHPBJSH000704,GWHPBJSH000704,GWHPBJSH000704,GWHPBJSH000704,GWHPBJSH000704,GWHPBJSH000704,GWHPBJSH000704,GWHPBJSH000704,GWHPBJSH000704,GWHPBJSH000704,GWHPBJSH000704,GWHPBJSH000704,GWHPBJSH000704,GWHPBJSH000704,GWHPBJSH000704
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#7: Protein 40S ribosomal protein S15a


Mass: 14874.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH002412
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A398AJL3
#12: Protein uS13m


Mass: 17398.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH064799
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3D1F0
#22: Protein mS26


Mass: 23093.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH068774
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0ABQ7YPD6
#24: Protein BnaC06g06470D protein


Mass: 53476.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH057126
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A078I5F5
#25: Protein MOSC domain-containing protein


Mass: 11631.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS036572
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A3P6ERU1
#26: Protein Mitochondrial 28S ribosomal protein S34


Mass: 16650.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH018393
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A8S9KXA0
#27: Protein EngC GTPase domain-containing protein


Mass: 55785.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH063220
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3CYN0
#29: Protein IMS import disulfide relay-system CHCH-CHCH-like Cx9C domain-containing protein


Mass: 9227.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A8MRX3
#31: Protein IGR domain-containing protein


Mass: 12498.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH068514
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3DCJ8
#32: Protein mS45


Mass: 44013.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH025481
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3BFU2
#33: Protein mS47


Mass: 45518.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH021410
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0ABQ7BUT9
#34: Protein (rape) hypothetical protein


Mass: 43364.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH050066
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0ABQ7ZIA1
#35: Protein PROP1-like PPR domain-containing protein


Mass: 82648.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A654ECT9
#36: Protein RRM domain-containing protein


Mass: 16001.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH080930
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A3P6FEP3

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30S ribosomal protein ... , 3 types, 3 molecules HOT

#8: Protein 30S ribosomal protein S9


Mass: 42328.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH080139
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#15: Protein 30S ribosomal protein S16


Mass: 15330.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH018119
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3ALM2
#20: Protein 30S ribosomal protein S31, mitochondrial


Mass: 10524.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS022287
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3C0Z4

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RNA chain , 1 types, 1 molecules 2

#37: RNA chain 18S rRNA


Mass: 504947.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)

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Non-polymers , 5 types, 98 molecules

#38: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#39: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 85 / Source method: obtained synthetically / Formula: Mg
#40: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#41: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#42: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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Details

Has ligand of interestN
Has protein modificationY

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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: Small subunit of the flowering plant mitochondrial ribosome in presence of RsgA
Type: COMPLEX / Entity ID: #1-#10, #12-#37 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Brassica oleracea var. botrytis (cauliflower)
Buffer solutionpH: 7.5
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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 magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50.96 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 931475
3D reconstructionResolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208855 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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