[English] 日本語
Yorodumi
- PDB-9evs: Structure of the flowering plant mitoribosome with P-site tRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9evs
TitleStructure of the flowering plant mitoribosome with P-site tRNA
Components
  • 18S rRNA
  • 26S rRNA
  • 5S rRNA
  • Large ribosomal subunit protein uL2mz, N-terminal part
  • Nascent peptide
  • Small ribosomal subunit protein uS3m
  • bL17m
  • bL19m
  • bL20m
  • bL21m
  • bL25-2m
  • bL25m
  • bL27m
  • bL28m
  • bL31m
  • bL32m
  • bL33m
  • bL34m
  • bL35m
  • bL36m
  • bL9m
  • bS16m
  • bS18m
  • bS21m
  • bS6m
  • bTHXm
  • mL101 (rPPR4)
  • mL102 (rPPR5)
  • mL104 (rPPR9)
  • mL40
  • mL41
  • mL43
  • mL46
  • mL53
  • mL54
  • mL59/mL64
  • mL60
  • mL80
  • mL87
  • mRNA
  • mS23
  • mS26
  • mS29
  • mS31/mS46
  • mS33
  • mS34
  • mS35
  • mS37
  • mS38
  • mS41
  • mS45
  • mS47
  • mS76 (rPPR1)
  • mS77 (NFD5)
  • mS83 (rPPR10)
  • mS86
  • tRNA
  • uL10m
  • uL11m
  • uL13m
  • uL14m
  • uL15m
  • uL16m
  • uL18m
  • uL22m
  • uL23m
  • uL24m
  • uL29m
  • uL2m C-ter
  • uL30m
  • uL3m
  • uL4m
  • uL5m
  • uL6m
  • uS10m
  • uS11m
  • uS12m
  • uS13m
  • uS14m
  • uS15m
  • uS17m
  • uS19m
  • uS2m
  • uS4m
  • uS5m
  • uS7m,Small ribosomal subunit protein uS7m
  • uS8m
  • uS9m
KeywordsRIBOSOME / Mitochondria / tRNA / mitoribosome / plant
Function / homology
Function and homology information


endosperm cellularization / pollen tube development / endosperm development / regulation of starch biosynthetic process / pollen germination / nucleus localization / pollen development / regulation of programmed cell death / embryo development ending in seed dormancy / cell communication ...endosperm cellularization / pollen tube development / endosperm development / regulation of starch biosynthetic process / 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 membrane organization / regulation of gene expression / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding
Similarity search - Function
Mitochondrial ribosomal protein S7, plants / Ribosomal protein S3, mitochondrial, plant / : / Eukaryotic mitochondrial regulator protein / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / K homology domain superfamily, prokaryotic type / Ribosomal protein S5/S7 ...Mitochondrial ribosomal protein S7, plants / Ribosomal protein S3, mitochondrial, plant / : / Eukaryotic mitochondrial regulator protein / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / K homology domain superfamily, prokaryotic type / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding N-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / CHLORAMPHENICOL / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein uS7m / Uncharacterized protein / Large ribosomal subunit protein uL2mz, N-terminal part
Similarity search - Component
Biological speciesBrassica oleracea var. botrytis (cauliflower)
Brassica oleracea var. oleracea (plant)
Arabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 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: Structure of the flowering plant mitoribosome with P-site tRNA
Authors: Waltz, F. / Skaltsogiannis, V.
History
DepositionApr 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Small ribosomal subunit protein uS3m
C: uS4m
D: uS5m
E: bS6m
F: uS7m,Small ribosomal subunit protein uS7m
G: uS8m
H: uS9m
I: uS10m
J: uS11m
K: uS12m
L: uS13m
M: uS14m
N: uS15m
O: bS16m
P: uS17m
Q: bS18m
R: uS19m
S: bS21m
T: bTHXm
U: mS23
V: mS26
W: mS29
X: mS31/mS46
Y: mS33
Z: mS34
1: 26S rRNA
3: 5S rRNA
1B: uL2m C-ter
1C: Large ribosomal subunit protein uL2mz, N-terminal part
1D: uL3m
1E: uL4m
1F: uL5m
1G: uL6m
1H: bL9m
1I: uL10m
1J: uL11m
1K: uL13m
1L: uL14m
1M: uL15m
1N: uL16m
1O: bL17m
1P: uL18m
1Q: bL19m
1R: bL20m
1S: bL21m
1T: uL22m
1U: uL23m
1V: uL24m
1W: bL25-2m
1X: bL25m
1Y: bL27m
1Z: bL28m
1a: uL29m
1b: uL30m
1c: bL31m
1d: bL32m
1e: bL33m
1f: bL34m
1g: bL35m
1h: bL36m
1i: mL40
1j: mL41
1k: 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)
1x: Nascent peptide
5: tRNA
2: 18S rRNA
6: mRNA
a: mS35
b: mS37
c: mS38
d: mS41
e: mS45
f: mS47
h: mS83 (rPPR10)
i: mS77 (NFD5)
j: mS76 (rPPR1)
k: mS86
A: uS2m
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,686,079523
Polymers3,673,54888
Non-polymers12,531435
Water00
1


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

-
Components

+
Protein , 82 types, 82 molecules BCDEFGHIJKLMNOPQRSTUVWXYZ1B1C1D1E1F...

#1: 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
#2: 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)
#3: Protein uS5m


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


Mass: 16011.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#5: 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: GWHPBJSH000704 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
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
References: UniProt: A0A068BEX5
#6: 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)
#7: 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)
#8: Protein uS10m


Mass: 25251.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH050210
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#9: 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)
#10: Protein uS12m


Mass: 14283.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS019876
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#11: 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)
#12: 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)
#13: Protein uS15m


Mass: 47211.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH065138
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#14: Protein bS16m


Mass: 15330.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH018119
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#15: 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)
#16: 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)
#17: Protein uS19m


Mass: 23675.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#18: Protein bS21m


Mass: 11541.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH012122
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#19: Protein bTHXm


Mass: 10582.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS022287
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#20: 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)
#21: 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)
#22: 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)
#23: 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)
#24: 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)
#25: 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 uL2m C-ter


Mass: 23561.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH030998 / Source: (natural) Brassica oleracea var. oleracea (plant)
#29: Protein Large ribosomal subunit protein uL2mz, N-terminal part / 60S ribosomal protein L2 / mitochondrial


Mass: 35903.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH056804 / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P93311
#30: 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)
#31: Protein uL4m


Mass: 33050.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH075117
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#32: Protein uL5m


Mass: 21258.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH000742
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#33: Protein uL6m


Mass: 11570.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH074602
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#34: Protein bL9m


Mass: 25074.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS006976
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#35: 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)
#36: Protein uL11m


Mass: 17034.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH065595
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#37: Protein uL13m


Mass: 23166.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH029441
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#38: 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)
#39: 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)
#40: Protein uL16m


Mass: 20186.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH064047
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#41: Protein bL17m


Mass: 18612.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH087064
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#42: Protein uL18m


Mass: 12654.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#43: 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)
#44: 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)
#45: Protein bL21m


Mass: 30955.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#46: Protein uL22m


Mass: 29793.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#47: 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)
#48: 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)
#49: Protein bL25-2m


Mass: 27376.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH070969
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#50: 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)
#51: Protein bL27m


Mass: 17095.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH034173
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#52: Protein bL28m


Mass: 24112.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH021367
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#53: 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)
#54: Protein uL30m


Mass: 12347.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH092856
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#55: 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)
#56: 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)
#57: Protein bL33m


Mass: 7446.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS049973
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#58: 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)
#59: Protein bL35m


Mass: 18991.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH013115
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#60: Protein bL36m


Mass: 11452.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#61: 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)
#62: 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)
#63: 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)
#64: Protein mL46


Mass: 27178.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH030844
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#65: 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)
#66: 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)
#67: 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)
#68: Protein mL60


Mass: 8680.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPDUBS017065
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#69: 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)
#70: 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)
#71: 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)
#72: Protein mL102 (rPPR5)


Mass: 85828.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH031757
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#73: Protein mL104 (rPPR9)


Mass: 59234.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH068020
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#78: Protein mS35


Mass: 48577.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH049245
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#79: Protein mS37


Mass: 9227.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#80: 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)
#81: 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)
#82: 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
#83: 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
#84: Protein mS83 (rPPR10)


Mass: 43367.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH050066
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#85: Protein mS77 (NFD5)


Mass: 82648.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#86: 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)
#87: Protein mS86


Mass: 15967.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: GWHPBJSH080930 Full sequence: MHYMGLFSRAGNIFRQPRALQASNAMLQGNLSLTPSKIFVGGLSPSTDVELLKEAFGSFG KIVDAVVVLDRESGLSRGFGFVTYDSIEVANNAMQAMQNKELDGRIIGVHPADSGGGGGG ...Details: GWHPBJSH080930 Full sequence: MHYMGLFSRAGNIFRQPRALQASNAMLQGNLSLTPSKIFVGGLSPSTDVELLKEAFGSFG KIVDAVVVLDRESGLSRGFGFVTYDSIEVANNAMQAMQNKELDGRIIGVHPADSGGGGGG GGFARRGGYGGGRGGYARGGFGRGGFGGGGYGFVR,Full sequence: MHYMGLFSRAGNIFRQPRALQASNAMLQGNLSLTPSKIFVGGLSPSTDVELLKEAFGSFG KIVDAVVVLDRESGLSRGFGFVTYDSIEVANNAMQAMQNKELDGRIIGVHPADSGGGGGG GGFARRGGYGGGRGGYARGGFGRGGFGGGGYGFVR
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#88: Protein uS2m


Mass: 23743.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GWHPBJSH046906
Source: (natural) Brassica oleracea var. botrytis (cauliflower)

-
RNA chain , 5 types, 5 molecules 13526

#26: 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)
#27: 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)
#75: RNA chain tRNA


Mass: 24541.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#76: RNA chain 18S rRNA


Mass: 514869.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)
#77: RNA chain mRNA


Mass: 1907.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)

-
Protein/peptide , 1 types, 1 molecules 1x

#74: Protein/peptide Nascent peptide


Mass: 316.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Brassica oleracea var. botrytis (cauliflower)

-
Non-polymers , 5 types, 435 molecules

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


Mass: 24.305 Da / Num. of mol.: 357 / Source method: obtained synthetically / Formula: Mg
#90: 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
#91: Chemical ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#92: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 74 / Source method: obtained synthetically / Formula: K
#93: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
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: Flowering plant mitochondrial ribosome in presence of P-site tRNA
Type: RIBOSOME / Entity ID: #1-#88 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Brassica oleracea var. botrytis (cauliflower) / Organ: Flower / Organelle: Mitochondria
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 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34964 / 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