[English] 日本語
Yorodumi
- PDB-9gyt: High resolution structure of B. oleracea mitoribosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gyt
TitleHigh resolution structure of B. oleracea mitoribosome
Components
  • (30S ribosomal protein ...) x 2
  • (50S ribosomal protein ...) x 3
  • (Large ribosomal subunit protein ...) x 6
  • (Ribosomal protein ...) x 3
  • (Small ribosomal subunit protein ...) x 7
  • 18S rRNA
  • 26S rRNA
  • 5S rRNA
  • PROP1-like PPR domain-containing protein
  • Ribosomal protein
  • S5 DRBM domain-containing protein
  • bL19m
  • bL20m
  • bL21m
  • bL25-2m
  • bL25m
  • bL28m
  • bL31m
  • bL32m
  • bL33m
  • bL35m
  • bL9m
  • bS18m
  • bS6m
  • mL101 (rPPR4)
  • mL102 (rPPR5)
  • mL104 (rPPR9)
  • mL40
  • mL41
  • mL46
  • mL53
  • mL54
  • mL59/mL64
  • mL60
  • mL80
  • mL87
  • mS23
  • mS26
  • mS31/mS46
  • mS33
  • mS34
  • mS35
  • mS37
  • mS38
  • mS41
  • mS45
  • mS47
  • mS76 (rPPR1)
  • mS83 (rPPR10)
  • mS86
  • uL10m
  • uL11m
  • uL14m
  • uL15m
  • uL23m
  • uL24m
  • uL29m
  • uL2m N-ter mitochondrial
  • uL30m
  • uL3m
  • uL4m
  • uL5m
  • uS11m
  • uS12m
  • uS13m
  • uS14m
  • uS17m
  • uS4m
  • uS7m,Small ribosomal subunit protein uS7m
  • uS8m
  • uS9m
KeywordsRIBOSOME / mitochondria / mitoribosome / assembly factor / plant
Function / homology
Function and homology information


endosperm cellularization / pollen tube development / endosperm development / regulation of starch biosynthetic process / plastid translation / pollen germination / nucleus localization / pollen development / regulation of programmed cell death / embryo development ending in seed dormancy ...endosperm cellularization / pollen tube development / endosperm development / regulation of starch biosynthetic process / plastid translation / pollen germination / nucleus localization / pollen development / regulation of programmed cell death / embryo development ending in seed dormancy / cell communication / vacuole organization / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / mitochondrial membrane organization / plastid / RNA splicing / chloroplast / regulation of gene expression / 5S rRNA binding / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding / cytoplasm
Similarity search - Function
Pentatricopeptide repeat-containing protein BIR6-like / Mitochondrial ribosomal protein S7, plants / Ribosomal protein S3, mitochondrial, plant / : / : / 30S ribosomal protein S31, plant / Ribosomal protein S31e / : / PPR repeat / Pentacotripeptide-repeat region of PRORP ...Pentatricopeptide repeat-containing protein BIR6-like / Mitochondrial ribosomal protein S7, plants / Ribosomal protein S3, mitochondrial, plant / : / : / 30S ribosomal protein S31, plant / Ribosomal protein S31e / : / PPR repeat / Pentacotripeptide-repeat region of PRORP / Pentacotripeptide-repeat region of PRORP / Eukaryotic mitochondrial regulator protein / PPR repeat family / Pentatricopeptide repeat domain / 39S ribosomal protein L40, mitochondrial / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / 39S ribosomal protein L43/54S ribosomal protein L51 / : / 30S ribosomal protein / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal L25p family / Ribosomal protein L25 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / RNA-binding domain superfamily / Ribosomal protein S19, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L16 / 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 L27 / Ribosomal L27 protein / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L2 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 L2, conserved site / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / : / Ribosomal protein S2 / K homology domain superfamily, prokaryotic type
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein uS7m / 30S ribosomal protein S16 ...ADENOSINE-5'-TRIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein uS7m / 30S ribosomal protein S16 / S5 DRBM domain-containing protein / Ribosomal protein S21 / Uncharacterized protein / 50S ribosomal protein L27 / Large ribosomal subunit protein uL2 C-terminal domain-containing protein / 50S ribosomal protein L13 / Large ribosomal subunit protein uL22c / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 30S ribosomal protein S31, mitochondrial / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein uS10 domain-containing protein / Uncharacterized protein / Large ribosomal subunit protein bL34m / Ribosomal protein S2 / Uncharacterized protein / Small ribosomal subunit protein uS15c / Large ribosomal subunit protein uL6 alpha-beta domain-containing protein / Uncharacterized protein / Ribosomal protein L18e/L15P domain-containing protein / Uncharacterized protein / Large ribosomal subunit protein mL43 / Uncharacterized protein / PROP1-like PPR domain-containing protein / 50S ribosomal protein L17 / Small ribosomal subunit protein mS80 (rPPR6) / Small ribosomal subunit protein uS19m / Small ribosomal subunit protein mS81 (rPPR8) / Ribosomal protein / Large ribosomal subunit protein uL16m
Similarity search - Component
Biological speciesBrassica oleracea var. botrytis (cauliflower)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.11 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
DepositionOct 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.1Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
3: 5S rRNA
A: Ribosomal protein S2
B: Small ribosomal subunit protein uS3m
C: uS4m
D: S5 DRBM domain-containing protein
E: bS6m
F: uS7m,Small ribosomal subunit protein uS7m
G: uS8m
H: uS9m
I: Small ribosomal subunit protein uS10 domain-containing protein
J: uS11m
K: uS12m
L: uS13m
M: uS14m
N: Small ribosomal subunit protein uS15c
O: 30S ribosomal protein S16
P: uS17m
Q: bS18m
R: Small ribosomal subunit protein uS19m
S: Ribosomal protein S21
T: 30S ribosomal protein S31, mitochondrial
U: mS23
V: mS26
W: Small ribosomal subunit protein mS29
X: mS31/mS46
Y: mS33
Z: mS34
a: mS35
b: mS37
c: mS38
d: mS41
e: mS45
f: mS47
g: Small ribosomal subunit protein mS81 (rPPR8)
h: mS83 (rPPR10)
i: PROP1-like PPR domain-containing protein
j: mS76 (rPPR1)
k: mS86
l: Small ribosomal subunit protein mS80 (rPPR6)
1B: Large ribosomal subunit protein uL2 C-terminal domain-containing protein
1C: uL2m N-ter mitochondrial
1D: uL3m
1E: uL4m
1F: uL5m
1G: Large ribosomal subunit protein uL6 alpha-beta domain-containing protein
1H: bL9m
1I: uL10m
1J: uL11m
1K: 50S ribosomal protein L13
1L: uL14m
1M: uL15m
1N: Large ribosomal subunit protein uL16m
1O: 50S ribosomal protein L17
1P: Ribosomal protein L18e/L15P domain-containing protein
1Q: bL19m
1R: bL20m
1S: bL21m
1T: Large ribosomal subunit protein uL22m
1U: uL23m
1V: uL24m
1W: bL25-2m
1X: bL25m
1Y: 50S ribosomal protein L27
1Z: bL28m
1a: uL29m
1b: uL30m
1c: bL31m
1d: bL32m
1e: bL33m
1f: Large ribosomal subunit protein bL34m
1g: bL35m
1h: Ribosomal protein
1i: mL40
1j: mL41
1k: Large ribosomal subunit protein mL43
1l: mL46
1m: mL53
1o: mL54
1p: mL59/mL64
1q: mL60
1r: mL80
1s: mL87
1t: mL101 (rPPR4)
1u: mL102 (rPPR5)
1v: mL104 (rPPR9)
1: 26S rRNA
2: 18S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,854,784523
Polymers3,842,37987
Non-polymers12,405436
Water180,99710047
1


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

-
Components

-
RNA chain , 3 types, 3 molecules 312

#1: RNA chain 5S rRNA


Mass: 37992.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: GenBank: 2283399346
#86: RNA chain 26S rRNA


Mass: 944322.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#87: RNA chain 18S rRNA


Mass: 570785.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)

-
Ribosomal protein ... , 3 types, 3 molecules AS1P

#2: 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
#20: 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
#54: Protein Ribosomal protein L18e/L15P domain-containing protein


Mass: 12654.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3DCH7

-
Small ribosomal subunit protein ... , 7 types, 7 molecules BINRWgl

#3: 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
#10: 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
#15: 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
#19: 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
#24: 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
#34: Protein Small ribosomal subunit protein mS81 (rPPR8) / Pentatricopeptide repeat-containing protein At5g15980 / mitochondrial


Mass: 75398.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: Q8LPF1
#39: Protein Small ribosomal subunit protein mS80 (rPPR6) / Pentatricopeptide repeat-containing protein At3g02650 / mitochondrial


Mass: 63912.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: P0C896

+
Protein , 63 types, 63 molecules CDEFGHJKLMPQUVXYZabcdefhijk1C1D1E...

#4: Protein uS4m


Mass: 43438.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH000696
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#5: 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
#6: 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
#7: Protein uS7m,Small ribosomal subunit protein uS7m / Ribosomal protein S7 / mitochondrial


Mass: 17955.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Extension in N-ter not present in UNIPROT,Extension in N-ter not present in UNIPROT GWHPBJSH000704,Extension in N-ter not present in UNIPROT,Extension in N-ter not present in UNIPROT GWHPBJSH000704
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A068BEX5
#8: Protein uS8m


Mass: 14874.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH002412
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#9: Protein uS9m


Mass: 42328.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH080139
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#11: Protein uS11m


Mass: 33108.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH051931
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#12: Protein uS12m


Mass: 14294.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS019876
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#13: 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
#14: Protein uS14m


Mass: 17928.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS019475
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#17: Protein uS17m


Mass: 12090.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH049400
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#18: Protein bS18m


Mass: 27106.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH076274
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#22: Protein mS23


Mass: 21903.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH071753
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#23: 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)
#25: Protein mS31/mS46


Mass: 53476.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH057126
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#26: Protein mS33


Mass: 11631.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS036572
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#27: Protein mS34


Mass: 16650.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH018393
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#28: Protein mS35


Mass: 48589.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH049245
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#29: Protein mS37


Mass: 9227.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#30: 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)
#31: Protein mS41


Mass: 12498.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH068514
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#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: Hydrolases; Acting on ester bonds; Thioester hydrolases
#35: Protein mS83 (rPPR10)


Mass: 43364.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH050066
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#36: 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
#37: Protein mS76 (rPPR1)


Mass: 45681.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS003368
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#38: Protein mS86


Mass: 16001.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH080930
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#41: Protein uL2m N-ter mitochondrial


Mass: 31657.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH056804
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#42: Protein uL3m


Mass: 35071.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH008303
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#43: Protein uL4m


Mass: 32921.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH075117
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#44: Protein uL5m


Mass: 21218.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH000742
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#46: Protein bL9m


Mass: 25173.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS006976
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#47: Protein uL10m


Mass: 18917.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS004443
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#48: Protein uL11m


Mass: 17083.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH065595
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#50: Protein uL14m


Mass: 18926.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH089764
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3D9E7
#51: Protein uL15m


Mass: 31222.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH025994
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#55: Protein bL19m


Mass: 26348.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH034513
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3B0P2
#56: Protein bL20m


Mass: 14749.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS041804
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#57: Protein bL21m


Mass: 30869.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#59: Protein uL23m


Mass: 19963.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH001034
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#60: Protein uL24m


Mass: 17547.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH068111
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#61: Protein bL25-2m


Mass: 27350.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH070969
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#62: Protein bL25m


Mass: 29945.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH022473
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3BK40
#64: Protein bL28m


Mass: 24618.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH021367
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#65: Protein uL29m


Mass: 16970.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS024649
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#66: Protein uL30m


Mass: 12322.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH092856
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#67: Protein bL31m


Mass: 15785.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH092851
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#68: Protein bL32m


Mass: 15228.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH071754
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#69: Protein bL33m


Mass: 12503.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS049973
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#71: Protein bL35m


Mass: 19035.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH013115
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#72: Protein Ribosomal protein


Mass: 11452.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: Q8W464
#73: Protein mL40


Mass: 27264.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS047948
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A3P6DV95
#74: Protein mL41


Mass: 10075.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS013782
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#76: Protein mL46


Mass: 27945.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH030844
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#77: Protein mL53


Mass: 14567.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS021933
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#78: Protein mL54


Mass: 13767.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH029436
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#79: Protein mL59/mL64


Mass: 15415.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH003404
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#80: Protein mL60


Mass: 8554.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS017065
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3BIE3
#81: Protein mL80


Mass: 18391.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS033403
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#82: Protein mL87


Mass: 20712.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH067819
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3DDW7
#83: Protein mL101 (rPPR4)


Mass: 55947.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH088794
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#84: Protein mL102 (rPPR5)


Mass: 85473.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH031757
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#85: Protein mL104 (rPPR9)


Mass: 58508.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH068020
Source: (natural) Brassica oleracea var. botrytis (cauliflower)

-
30S ribosomal protein ... , 2 types, 2 molecules OT

#16: 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
#21: 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

-
Large ribosomal subunit protein ... , 6 types, 6 molecules 1B1G1N1T1f1k

#40: Protein Large ribosomal subunit protein uL2 C-terminal domain-containing protein


Mass: 23174.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3B6N5
#45: Protein Large ribosomal subunit protein uL6 alpha-beta domain-containing protein


Mass: 11570.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH074602
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3D316
#52: Protein Large ribosomal subunit protein uL16m / 60S ribosomal protein L16 / mitochondrial


Mass: 20186.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH064047
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: Q95747
#58: Protein Large ribosomal subunit protein uL22m / 50S ribosomal protein L22 / chloroplastic


Mass: 29793.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3BFS0
#70: Protein Large ribosomal subunit protein bL34m


Mass: 16532.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH048407
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3CKG1
#75: Protein Large ribosomal subunit protein mL43


Mass: 13679.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS043571
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3DUE5

-
50S ribosomal protein ... , 3 types, 3 molecules 1K1O1Y

#49: Protein 50S ribosomal protein L13


Mass: 23166.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH029441
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3B978
#53: Protein 50S ribosomal protein L17


Mass: 18612.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH087064
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A8S9IRX0
#63: Protein 50S ribosomal protein L27


Mass: 17095.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH034173
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A0D3B184

-
Non-polymers , 5 types, 10483 molecules

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


Mass: 24.305 Da / Num. of mol.: 349 / Source method: obtained synthetically / Formula: Mg
#89: 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
#90: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 84 / Source method: obtained synthetically / Formula: K
#91: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#92: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10047 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Full flowering plant mitochondrial ribosome / Type: RIBOSOME / Entity ID: #1-#87 / 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 type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

-
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: 41.66 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
9PHENIX1.20.1_4487:model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 343753
3D reconstructionResolution: 2.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 219403 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSpace: REAL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more