[English] 日本語
Yorodumi
- PDB-28jw: Structure of the Chlamydomonas reinhardtii chlororibosome with P-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 28jw
TitleStructure of the Chlamydomonas reinhardtii chlororibosome with P-site tRNA
Components
  • (30S ribosomal protein ...) x 3
  • (50S ribosomal protein ...) x 2
  • (Large ribosomal subunit protein ...) x 14
  • (Small ribosomal subunit protein ...) x 13
  • 16S rRNA
  • 23S rRNA
  • 3S rRNA
  • 5S rRNA
  • 7S RNA
  • KOW domain-containing protein
  • Nascent peptide
  • P-site tRNA
  • 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
  • mRNA
  • uL10c
  • uL13c
  • uL15c
  • uL23c,Large ribosomal subunit protein uL23c
  • 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 / 5S rRNA binding / small ribosomal subunit ...mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / plastid / chloroplast / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / 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) / Ribosomal protein L6, chloroplast / Family of unknown function (DUF5323) / TRAM domain / TRAM domain / TRAM domain profile. / : / : ...Ribosomal protein PSRP-3/Ycf65 / PSRP-3/Ycf65 superfamily / Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) / Ribosomal protein L6, chloroplast / Family of unknown function (DUF5323) / 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 L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L21 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 L16 signature 2. / Ribosomal protein L16, conserved site / 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 L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L2, bacterial/organellar-type / 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 L28/L24 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / Ribosomal protein S15, bacterial-type / Ribosomal protein L16 / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily
Similarity search - Domain/homology
CHLORAMPHENICOL / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS2c / Large ribosomal subunit protein bL9c ...CHLORAMPHENICOL / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS2c / Large ribosomal subunit protein bL9c / Uncharacterized protein / Large ribosomal subunit protein uL18c / Uncharacterized protein / 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 / Large ribosomal subunit protein uL23c / Small ribosomal subunit protein uS14c
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 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: Florent Waltz / Philippe A Lehner / Philippe Van der Stappen / Lukas Kater / Stefan Pfeffer / Benjamin D Engel /
Abstract: Chloroplast ribosomes (chlororibosomes) synthesize the core protein components of the photosynthetic apparatus, yet their structural diversity outside flowering plants remains largely unexplored. ...Chloroplast ribosomes (chlororibosomes) synthesize the core protein components of the photosynthetic apparatus, yet their structural diversity outside flowering plants remains largely unexplored. Here, we combine in situ cryo-electron tomography (cryo-ET) with single-particle cryo-electron microscopy (cryo-EM) to determine the structure of the chlororibosome from the unicellular green alga . Subtomogram averaging of chlororibosomes in their native environment, resolved to ~5 Å resolution and in distinct translational states, reveals particles both free in the stroma and loosely tethered to thylakoid membranes. These reconstructions uncover an additional "arm" domain on the small subunit. High-resolution single-particle reconstruction of isolated chlororibosomes to ~2.5 Å, in states bound either to the inhibitory translation factor pY or to a nascent chain-linked P-site tRNA, reveals that this domain is built primarily from extensive chloroplast-encoded insertions and extensions of conserved small subunit proteins, supported by chlororibosome-specific ribosomal proteins. The arm domain is located around the mRNA entry and exit channels, suggesting a role in stabilizing the mRNA trajectory through the small subunit and organizing chloroplast polysomes. Together, these data reveal unexpected structural variation of algal chlororibosomes and suggest that chloroplast translation has diversified substantially even among relatively closely related photosynthetic lineages.
History
DepositionFeb 4, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data 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
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: uL23c,Large ribosomal subunit protein uL23c
U: KOW domain-containing protein
V: bL27c
W: Large ribosomal subunit protein bL28c
X: uL29c
Z: bL32c
Y: 50S ribosomal protein L31
1: 23S rRNA
4: 7S RNA
y: P-site tRNA
xx: Nascent peptide
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
w: Plastid-specific ribosomal protein-7
2: 16S rRNA
b: Small ribosomal subunit protein uS2c
c: Small ribosomal subunit protein uS3c
e: uS5c
i: Small ribosomal subunit protein uS9c
A: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,665,710512
Polymers2,652,55162
Non-polymers13,159450
Water00
1


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

-
Components

+
Protein , 22 types, 22 molecules 067FHJLPRTUVXZafmtuxwe

#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) / References: UniProt: A0A835SZL0
#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
#26: Protein uL23c,Large ribosomal subunit protein uL23c / 50S ribosomal protein L23 / chloroplastic


Mass: 12565.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: N-ter extension not present in the Uniprot sequence,N-ter extension not present in the Uniprot sequence
Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q8HTL3
#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
#37: 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
#39: 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
#45: 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
#52: 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
#53: Protein bS21c


Mass: 20793.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HPN4
#55: 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
#56: 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
#60: 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

-
RNA chain , 8 types, 8 molecules 3514yxx2A

#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) / References: GenBank: 11422
#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)
#33: RNA chain 23S rRNA


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


Mass: 88325.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#35: RNA chain P-site tRNA


Mass: 24565.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: GenBank: 2484133353
#36: RNA chain Nascent peptide


Mass: 380.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#57: RNA chain 16S rRNA


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


Mass: 1884.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)

-
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
#32: 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

-
Large ribosomal subunit protein ... , 14 types, 14 molecules 9BCDEGIKMNOQSW

#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
#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

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

#38: 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
#40: 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
#41: 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
#42: 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
#43: 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
#44: 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
#46: 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
#49: 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
#50: 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
#51: 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
#58: 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
#59: 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
#61: 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

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

#47: 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
#48: 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
#54: 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

-
Non-polymers , 3 types, 450 molecules

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


Mass: 24.305 Da / Num. of mol.: 319 / Source method: obtained synthetically / Formula: Mg
#64: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 130 / Source method: obtained synthetically / Formula: K
#65: Chemical ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
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 %

-
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)

-
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: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49141 / Algorithm: BACK PROJECTION / Symmetry type: POINT
EM volume selectionMethod: Template matching / Num. of tomograms: 129 / Num. of volumes extracted: 20883
RefinementHighest resolution: 2.84 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00998223
ELECTRON MICROSCOPYf_angle_d0.792146776
ELECTRON MICROSCOPYf_dihedral_angle_d22.90348240
ELECTRON MICROSCOPYf_chiral_restr0.05918716
ELECTRON MICROSCOPYf_plane_restr0.0067914

+
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