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- PDB-9gyt: High resolution structure of B. oleracea mitoribosome -

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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. / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / 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. / Ribosomal protein L36 signature. / RNA recognition motif domain / 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 L6, bacterial-type / Ribosomal protein S19, 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 L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / 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 L27 / Ribosomal protein S6 superfamily / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / 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 / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily
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: To Be Published
Title: High resolution structure of B. oleracea mitoribosome
Authors: Waltz, F. / Skaltsogiannis, V. / Giege, P.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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)

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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

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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

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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)

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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

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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

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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

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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

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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)

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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

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