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- PDB-9tvu: Structure of the Chlamydomonas reinhardtii chlororibosome -

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Basic information

Entry
Database: PDB / ID: 9tvu
TitleStructure of the Chlamydomonas reinhardtii chlororibosome
Components
  • (30S ribosomal protein ...) x 3
  • (50S ribosomal protein ...) x 2
  • (Large ribosomal subunit protein ...) x 15
  • (Small ribosomal subunit protein ...) x 13
  • 16S rRNA
  • 23S
  • 3S rRNA
  • 5S rRNA
  • 7S RNA
  • KOW domain-containing protein
  • Plastid ribosomal protein L6
  • Plastid-specific ribosomal protein-7
  • Ribosomal protein S1 homologue
  • bL19c
  • bL21c
  • bL27c
  • bL32c
  • bL33c
  • bL34c
  • bS20c
  • bS21c
  • bS6c
  • cL38/PSRP6
  • cS26/PSRP8
  • uL10c
  • uL13c
  • uL15c
  • uL29c
  • uS13c
  • uS5c
KeywordsRIBOSOME / chloroplast / translation / chlororibosome
Function / homology
Function and homology information


mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / plastid / chloroplast / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal large subunit assembly / 5S rRNA binding ...mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / plastid / chloroplast / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal large subunit assembly / 5S rRNA binding / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / mitochondrion / RNA binding / cytoplasm
Similarity search - Function
Ribosomal protein PSRP-3/Ycf65 / PSRP-3/Ycf65 superfamily / Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) / TRAM domain / TRAM domain / TRAM domain profile. / : / : / S1 domain profile. / Ribosomal protein L11, bacterial-type ...Ribosomal protein PSRP-3/Ycf65 / PSRP-3/Ycf65 superfamily / Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) / TRAM domain / TRAM domain / TRAM domain profile. / : / : / S1 domain profile. / Ribosomal protein L11, bacterial-type / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / : / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / : / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L28 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein L9/RNase H1, N-terminal / : / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / L28p-like / : / Ribosomal protein S6 / Ribosomal protein S6
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS2c / Large ribosomal subunit protein bL9c / Large ribosomal subunit protein uL18c / Uncharacterized protein / Uncharacterized protein ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS2c / Large ribosomal subunit protein bL9c / Large ribosomal subunit protein uL18c / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein bL28c / Uncharacterized protein / 30S ribosomal protein S15 / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein bL17c / 30S ribosomal protein 3, chloroplastic / Uncharacterized protein / Large ribosomal subunit protein uL11c / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Small ribosomal subunit protein uS10 domain-containing protein / 50S ribosomal protein L31 / Large ribosomal subunit protein uL6 alpha-beta domain-containing protein / Uncharacterized protein / Uncharacterized protein / KOW domain-containing protein / Uncharacterized protein / 30S ribosomal protein S16, chloroplastic / Uncharacterized protein / Large ribosomal subunit protein uL3c / 50S ribosomal protein L35 / Small ribosomal subunit protein uS17c / Small ribosomal subunit protein uS9c / Small ribosomal subunit protein bS18c / Large ribosomal subunit protein uL16c / Large ribosomal subunit protein uL14c / Small ribosomal subunit protein uS12c / Large ribosomal subunit protein bL20c / Small ribosomal subunit protein uS7c / Small ribosomal subunit protein uS4c / Large ribosomal subunit protein bL36c / Small ribosomal subunit protein uS8c / Small ribosomal subunit protein uS19c / Small ribosomal subunit protein uS3c / Plastid-specific ribosomal protein-7 / Ribosomal protein S1 homologue / Small ribosomal subunit protein uS11c / Large ribosomal subunit protein uL22c / Large ribosomal subunit protein uL4c / Large ribosomal subunit protein uL5c / Large ribosomal subunit protein uL2c / Small ribosomal subunit protein uS14c
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsWaltz, F. / Kater, L. / Engel, B.D.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation216094 Switzerland
Swiss State Secretariat for Education, Research and InnovationM822.00045 Switzerland
CitationJournal: Biorxiv / Year: 2026
Title: Chloroplast-encoded small subunit extensions reshape the Chlamydomonas chlororibosome
Authors: Waltz, F. / Lehner, P.A. / Van der Stappen, P. / Kater, L. / Pfeffer, S. / Engel, B.D.
History
DepositionJan 13, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: cL38/PSRP6
3: 5S rRNA
5: 3S rRNA
6: bL33c
7: bL34c
8: 50S ribosomal protein L35
9: Large ribosomal subunit protein bL36c
B: Large ribosomal subunit protein uL2c
C: Large ribosomal subunit protein uL3c
D: Large ribosomal subunit protein uL4c
E: Large ribosomal subunit protein uL5c
F: Plastid ribosomal protein L6
G: Large ribosomal subunit protein bL9c
H: uL10c
I: Large ribosomal subunit protein uL11c
J: uL13c
K: Large ribosomal subunit protein uL14c
L: uL15c
M: Large ribosomal subunit protein uL16c
N: Large ribosomal subunit protein bL17c
O: Large ribosomal subunit protein uL18c
P: bL19c
Q: Large ribosomal subunit protein bL20c
R: bL21c
S: Large ribosomal subunit protein uL22c
T: Large ribosomal subunit protein uL23c
U: KOW domain-containing protein
V: bL27c
W: Large ribosomal subunit protein bL28c
X: uL29c
Z: bL32c
a: Ribosomal protein S1 homologue
d: Small ribosomal subunit protein uS4c
f: bS6c
g: Small ribosomal subunit protein uS7c
h: Small ribosomal subunit protein uS8c
j: Small ribosomal subunit protein uS10 domain-containing protein
k: Small ribosomal subunit protein uS11c
l: Small ribosomal subunit protein uS12c
m: uS13c
n: Small ribosomal subunit protein uS14c
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16, chloroplastic
q: Small ribosomal subunit protein uS17c
r: Small ribosomal subunit protein bS18c
s: Small ribosomal subunit protein uS19c
t: bS20c
u: bS21c
v: 30S ribosomal protein 3, chloroplastic
x: cS26/PSRP8
Y: 50S ribosomal protein L31
w: Plastid-specific ribosomal protein-7
1: 23S
4: 7S RNA
2: 16S rRNA
b: Small ribosomal subunit protein uS2c
c: Small ribosomal subunit protein uS3c
e: uS5c
i: Small ribosomal subunit protein uS9c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,638,966520
Polymers2,625,72059
Non-polymers13,246461
Water00
1


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

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Components

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Protein , 21 types, 21 molecules 067FHJLPRUVXZafmtuxwe

#1: Protein cL38/PSRP6


Mass: 7215.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Proper UNIPROT ID is A8IMN3 that has been sent to UniParc.
Source: (natural) Chlamydomonas reinhardtii (plant)
#4: Protein bL33c


Mass: 11431.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I1D3
#5: Protein bL34c


Mass: 12987.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HQG3
#12: Protein Plastid ribosomal protein L6


Mass: 22275.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J503
#14: Protein uL10c


Mass: 25941.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HVP7
#16: Protein uL13c


Mass: 24590.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HWZ6
#18: Protein uL15c


Mass: 25570.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Proper UNIPROT ID is A8JAL6 that has been sent to UniParc.
Source: (natural) Chlamydomonas reinhardtii (plant)
#22: Protein bL19c


Mass: 16626.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IW44
#24: Protein bL21c


Mass: 19516.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IP00
#27: Protein KOW domain-containing protein


Mass: 18307.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J9D9
#28: Protein bL27c


Mass: 17208.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8INR7
#30: Protein uL29c


Mass: 14965.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HXM1
#31: Protein bL32c


Mass: 10639.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IUC3
#32: Protein Ribosomal protein S1 homologue


Mass: 48345.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q70DX8
#34: Protein bS6c


Mass: 19096.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J5Y7
#40: Protein uS13c


Mass: 18561.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JDP6
#47: Protein bS20c


Mass: 18285.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JDN4
#48: Protein bS21c


Mass: 20793.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#50: Protein cS26/PSRP8


Mass: 12985.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I8A6
#52: Protein Plastid-specific ribosomal protein-7


Mass: 60136.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q5QEB1
#58: Protein uS5c


Mass: 72090.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J8M5

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RNA chain , 5 types, 5 molecules 35142

#2: RNA chain 5S rRNA


Mass: 38858.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#3: RNA chain 3S rRNA


Mass: 15149.069 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#53: RNA chain 23S


Mass: 769308.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#54: RNA chain 7S RNA


Mass: 88325.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#55: RNA chain 16S rRNA


Mass: 476372.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)

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50S ribosomal protein ... , 2 types, 2 molecules 8Y

#6: Protein 50S ribosomal protein L35


Mass: 12106.231 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JEP1
#51: Protein 50S ribosomal protein L31


Mass: 14777.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J3Z3

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Large ribosomal subunit protein ... , 15 types, 15 molecules 9BCDEGIKMNOQSTW

#7: Protein/peptide Large ribosomal subunit protein bL36c / 50S ribosomal protein L36 / chloroplastic


Mass: 4273.327 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P59774
#8: Protein Large ribosomal subunit protein uL2c / 50S ribosomal protein L2 / chloroplastic


Mass: 30955.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q8HTL2
#9: Protein Large ribosomal subunit protein uL3c


Mass: 27878.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JE35
#10: Protein Large ribosomal subunit protein uL4c / 50S ribosomal protein L4 / chloroplastic


Mass: 25659.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q84U22
#11: Protein Large ribosomal subunit protein uL5c / 50S ribosomal protein L5 / chloroplastic


Mass: 20267.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q8HTL1
#13: Protein Large ribosomal subunit protein bL9c / 50S ribosomal protein L9 / chloroplastic / CL9


Mass: 22043.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D5T7
#15: Protein Large ribosomal subunit protein uL11c / 50S ribosomal protein L11 / chloroplastic / CL11


Mass: 18562.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8ICE4
#17: Protein Large ribosomal subunit protein uL14c / 50S ribosomal protein L14 / chloroplastic


Mass: 13466.755 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P11094
#19: Protein Large ribosomal subunit protein uL16c / 50S ribosomal protein L16 / chloroplastic


Mass: 15500.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P05726
#20: Protein Large ribosomal subunit protein bL17c / 50S ribosomal protein L17 / chloroplastic / CL17


Mass: 19188.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I3M4
#21: Protein Large ribosomal subunit protein uL18c / CL18


Mass: 15818.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HNJ8
#23: Protein Large ribosomal subunit protein bL20c / 50S ribosomal protein L20 / chloroplastic


Mass: 13578.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P26565
#25: Protein Large ribosomal subunit protein uL22c / 50S ribosomal protein L22 / chloroplastic


Mass: 18959.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q84U21
#26: Protein Large ribosomal subunit protein uL23c


Mass: 12565.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: first aa are absent from the sequence and modeled as polyA
Source: (natural) Chlamydomonas reinhardtii (plant)
#29: Protein Large ribosomal subunit protein bL28c


Mass: 21945.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HWS8

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Small ribosomal subunit protein ... , 13 types, 13 molecules dghjklnqrsbci

#33: Protein Small ribosomal subunit protein uS4c / 30S ribosomal protein S4 / chloroplastic


Mass: 30082.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P48270
#35: Protein Small ribosomal subunit protein uS7c / 30S ribosomal protein S7 / chloroplastic


Mass: 19163.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P48267
#36: Protein Small ribosomal subunit protein uS8c / 30S ribosomal protein S8 / chloroplastic


Mass: 15916.647 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P59775
#37: Protein Small ribosomal subunit protein uS10 domain-containing protein


Mass: 18736.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IWQ1
#38: Protein Small ribosomal subunit protein uS11c / 30S ribosomal protein S11 / chloroplastic


Mass: 14260.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q7YKX3
#39: Protein Small ribosomal subunit protein uS12c / 30S ribosomal protein S12 / chloroplastic


Mass: 14637.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P14149
#41: Protein Small ribosomal subunit protein uS14c / 30S ribosomal protein S14 / chloroplastic


Mass: 11776.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q9GGE2
#44: Protein Small ribosomal subunit protein uS17c


Mass: 11767.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JGS2
#45: Protein Small ribosomal subunit protein bS18c / 30S ribosomal protein S18 / chloroplastic


Mass: 16315.782 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: O20032
#46: Protein Small ribosomal subunit protein uS19c / 30S ribosomal protein S19 / chloroplastic


Mass: 10463.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P59776
#56: Protein Small ribosomal subunit protein uS2c


Mass: 102698.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A218N8X3
#57: Protein Small ribosomal subunit protein uS3c / 30S ribosomal protein S3 / chloroplastic / ORF 712


Mass: 82015.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q08365
#59: Protein Small ribosomal subunit protein uS9c / 30S ribosomal protein S9 / chloroplastic


Mass: 21062.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: O20029

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

#42: Protein 30S ribosomal protein S15


Mass: 15817.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HWZ8
#43: Protein 30S ribosomal protein S16, chloroplastic


Mass: 14474.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JDN8
#49: Protein 30S ribosomal protein 3, chloroplastic


Mass: 33397.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I8A3

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Non-polymers , 2 types, 461 molecules

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


Mass: 24.305 Da / Num. of mol.: 323 / Source method: obtained synthetically / Formula: Mg
#61: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 138 / Source method: obtained synthetically / Formula: K

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Chloroplast ribosome / Type: RIBOSOME / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: mat3-4
Buffer solutionpH: 7.5
SpecimenConc.: 2.5 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 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
2EPUimage acquisition
4cryoSPARC4.7CTF correction
10cryoSPARC4.7initial Euler assignment
11cryoSPARC4.7final Euler assignment
12cryoSPARC4.7classification
13cryoSPARC4.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 225199 / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionMethod: Template matching / Num. of tomograms: 129 / Num. of volumes extracted: 20883
RefinementHighest resolution: 2.52 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00790118
ELECTRON MICROSCOPYf_angle_d0.847135234
ELECTRON MICROSCOPYf_dihedral_angle_d23.04251643
ELECTRON MICROSCOPYf_chiral_restr0.06417308
ELECTRON MICROSCOPYf_plane_restr0.0076922

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