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- PDB-5x8p: Structure of the 70S chloroplast ribosome from spinach -

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Basic information

Entry
Database: PDB / ID: 5x8p
TitleStructure of the 70S chloroplast ribosome from spinach
Components
  • (30S ribosomal protein ...) x 17
  • (50S ribosomal protein ...) x 18
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 4.8S rRNA
  • 5S rRNA5S ribosomal RNA
  • protein L15
  • protein L17
  • protein L18
  • protein L27
  • protein L28
  • protein L29
  • protein L3
  • protein L6
  • protein L9
  • protein S10
  • protein S17
  • protein S20
  • protein S21
  • protein bTHXc
  • protein cL37
  • protein cL38
  • protein cS22
  • protein cS23
  • protein plastid pY
KeywordsRIBOSOME / Cryo-EM / chloroplast ribosome
Function / homology
Function and homology information


plastid small ribosomal subunit / plastid translation / negative regulation of translational elongation / primary metabolic process / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / plastid / chloroplast stroma / mitochondrial translation / ribosomal small subunit binding ...plastid small ribosomal subunit / plastid translation / negative regulation of translational elongation / primary metabolic process / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / plastid / chloroplast stroma / mitochondrial translation / ribosomal small subunit binding / chloroplast / DNA-templated transcription termination / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / mitochondrion / RNA binding
Similarity search - Function
Ribosomal protein PSRP-3/Ycf65 / PSRP-3/Ycf65 superfamily / Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) / 30S ribosomal protein S31, plant / Ribosomal protein S31e / Ribosomal protein L6, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / Ribosome hibernation promoting factor, long/plastid ...Ribosomal protein PSRP-3/Ycf65 / PSRP-3/Ycf65 superfamily / Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) / 30S ribosomal protein S31, plant / Ribosomal protein S31e / Ribosomal protein L6, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosomal protein S1-like / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / 30S ribosomal protein / S1 domain profile. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Ribosomal protein S21 superfamily / S1 domain / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / 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 L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / RNA recognition motif / RNA recognition motif / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Eukaryotic RNA Recognition Motif (RRM) profile. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / RNA recognition motif domain / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L14P, bacterial-type / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / RNA-binding domain superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3c / Ribosome-binding factor PSRP1, chloroplastic / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3c / Ribosome-binding factor PSRP1, chloroplastic / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL31c / Small ribosomal subunit protein cS22 / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein cL38 / Large ribosomal subunit protein bL28c / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein cS23 / Large ribosomal subunit protein bL17c / Small ribosomal subunit protein bTHXc / Large ribosomal subunit protein bL9c / Small ribosomal subunit protein uS17c / Small ribosomal subunit protein uS10c / Large ribosomal subunit protein cL37 alpha / Large ribosomal subunit protein uL4c / Small ribosomal subunit protein uS11c / Small ribosomal subunit protein uS14c / Small ribosomal subunit protein uS19c / Large ribosomal subunit protein uL2cz/uL2cy / Small ribosomal subunit protein uS2c / Large ribosomal subunit protein uL22c / Small ribosomal subunit protein uS3c / Large ribosomal subunit protein uL14c / Small ribosomal subunit protein uS8c / Large ribosomal subunit protein bL36c / Large ribosomal subunit protein uL13c / Small ribosomal subunit protein uS4c / Large ribosomal subunit protein uL16c / Ribosome-binding factor PSRP1, chloroplastic / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein bL35c / Large ribosomal subunit protein bL21c / Large ribosomal subunit protein uL24c / Large ribosomal subunit protein cL37 alpha / Large ribosomal subunit protein bL20c / Large ribosomal subunit protein bL32c / Large ribosomal subunit protein bL33c / Small ribosomal subunit protein bS16c / Small ribosomal subunit protein bS1c / Small ribosomal subunit protein bTHXc / Small ribosomal subunit protein uS12cz/uS12cy / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein uS7cz/uS7cy / Small ribosomal subunit protein uS17c / Small ribosomal subunit protein uS10c / Small ribosomal subunit protein uS13c / Large ribosomal subunit protein bL9c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL5c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein bL17c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL34c / Large ribosomal subunit protein bL28c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein bL31c / Small ribosomal subunit protein cS22 / Small ribosomal subunit protein uS9c / Small ribosomal subunit protein bS6c alpha / Large ribosomal subunit protein cL38 / Small ribosomal subunit protein cS23 / Large ribosomal subunit protein bL19c / Large ribosomal subunit protein uL23c / Small ribosomal subunit protein uS15c / Small ribosomal subunit protein bS18c / Small ribosomal subunit protein uS5c
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsAhmed, T. / Shi, J. / Bhushan, S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
MOEAcRF Tier 1, 2014-T1-001-019 (RG32/14) Singapore
CitationJournal: Nucleic Acids Res / Year: 2017
Title: Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation.
Authors: Tofayel Ahmed / Jian Shi / Shashi Bhushan /
Abstract: Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, ...Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, cS23, bTHXc, cL37 and cL38) which have been suggested to play important regulatory roles in translation. However, their exact locations on the chloroplast ribosome remain elusive due to lack of a high-resolution structure, hindering our progress to understand their possible roles. Here we present a cryo-EM structure of the 70S chloroplast ribosome from spinach resolved to 3.4 Å and focus our discussion mainly on the architecture of the 30S small subunit (SSU) which is resolved to 3.7 Å. cS22 localizes at the SSU foot where it seems to compensate for the deletions in 16S rRNA. The mRNA exit site is highly remodeled due to the presence of cS23 suggesting an alternative mode of translation initiation. bTHXc is positioned at the SSU head and appears to stabilize the intersubunit bridge B1b during thermal fluctuations. The translation factor plastid pY binds to the SSU on the intersubunit side and interacts with the conserved nucleotide bases involved in decoding. Most of the intersubunit bridges are conserved compared to the bacteria, except for a new bridge involving uL2c and bS6c.
History
DepositionMar 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 6, 2018Group: Data collection / Category: em_image_scans / em_software
Item: _em_image_scans.dimension_height / _em_image_scans.dimension_width / _em_software.name
Revision 1.3Oct 16, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c / _cell.volume
Revision 1.4Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
1: 50S ribosomal protein L32, chloroplastic
2: 50S ribosomal protein L33, chloroplastic
3: 50S ribosomal protein L34, chloroplastic
4: 50S ribosomal protein L35, chloroplastic
5: 50S ribosomal protein L36, chloroplastic
6: protein cL37
7: protein cL38
B: 5S rRNA
C: 50S ribosomal protein L2, chloroplastic
D: protein L3
E: 50S ribosomal protein L4, chloroplastic
F: 50S ribosomal protein L5, chloroplastic
G: protein L6
H: protein L9
K: 50S ribosomal protein L13, chloroplastic
L: 50S ribosomal protein L14, chloroplastic
M: protein L15
N: 50S ribosomal protein L16, chloroplastic
O: protein L17
P: protein L18
Q: 50S ribosomal protein L19, chloroplastic
R: 50S ribosomal protein L20, chloroplastic
S: 50S ribosomal protein L21, chloroplastic
T: 50S ribosomal protein L22, chloroplastic
U: 50S ribosomal protein L23, chloroplastic
V: 50S ribosomal protein L24, chloroplastic
W: 4.8S rRNA
X: protein L27
Y: protein L28
Z: protein L29
A: 23S rRNA
0: 50S ribosomal protein L31
b: 30S ribosomal protein S2, chloroplastic
c: 30S ribosomal protein S3, chloroplastic
e: 30S ribosomal protein S5, chloroplastic
f: 30S ribosomal protein S6 alpha, chloroplastic
g: 30S ribosomal protein S7, chloroplastic
h: 30S ribosomal protein S8, chloroplastic
i: 30S ribosomal protein S9, chloroplastic
j: protein S10
k: 30S ribosomal protein S11, chloroplastic
l: 30S ribosomal protein S12, chloroplastic
m: 30S ribosomal protein S13, chloroplastic
o: 30S ribosomal protein S15, chloroplastic
p: 30S ribosomal protein S16, chloroplastic
q: protein S17
r: 30S ribosomal protein S18, chloroplastic
s: 30S ribosomal protein S19 alpha, chloroplastic
t: protein S20
u: protein S21
y: protein plastid pY
a: 16S rRNA
w: protein cS23
d: 30S ribosomal protein S4, chloroplastic
v: protein cS22
n: 30S ribosomal protein S14, chloroplastic
x: protein bTHXc
8: 30S ribosomal protein S1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)2,360,32058
Polymers2,360,32058
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area289870 Å2
ΔGint-2371 kcal/mol
Surface area808630 Å2

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Components

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50S ribosomal protein ... , 18 types, 18 molecules 12345CEFKLNQRSTUV0

#1: Protein 50S ribosomal protein L32, chloroplastic / Ribosome


Mass: 6519.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28804
#2: Protein 50S ribosomal protein L33, chloroplastic / Ribosome


Mass: 7536.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28805
#3: Protein 50S ribosomal protein L34, chloroplastic / Ribosome / CL34


Mass: 6789.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82244
#4: Protein 50S ribosomal protein L35, chloroplastic / Ribosome / CL35


Mass: 8459.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P23326
#5: Protein/peptide 50S ribosomal protein L36, chloroplastic / Ribosome


Mass: 4414.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12230
#9: Protein 50S ribosomal protein L2, chloroplastic / Ribosome / Ribosomal protein CS-L4


Mass: 29722.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06509
#11: Protein 50S ribosomal protein L4, chloroplastic / Ribosome / R-protein L4


Mass: 27202.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: O49937
#12: Protein 50S ribosomal protein L5, chloroplastic / Ribosome


Mass: 24248.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82192
#15: Protein 50S ribosomal protein L13, chloroplastic / Ribosome / CL13


Mass: 22774.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12629
#16: Protein 50S ribosomal protein L14, chloroplastic / Ribosome / Ribosomal protein CS-L29


Mass: 13484.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09596
#18: Protein 50S ribosomal protein L16, chloroplastic / Ribosome / Ribosomal protein CS-L24


Mass: 15328.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P17353
#21: Protein 50S ribosomal protein L19, chloroplastic / Ribosome / CL19


Mass: 17597.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82413
#22: Protein 50S ribosomal protein L20, chloroplastic / Ribosome


Mass: 15594.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28803
#23: Protein 50S ribosomal protein L21, chloroplastic / Ribosome / CL21 / CS-L7


Mass: 22793.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P24613
#24: Protein 50S ribosomal protein L22, chloroplastic / Ribosome / Ribosomal protein CS-L13


Mass: 23292.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09594
#25: Protein 50S ribosomal protein L23, chloroplastic / Ribosome / PRPL23


Mass: 13575.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9LWB5
#26: Protein 50S ribosomal protein L24, chloroplastic / Ribosome / CL24


Mass: 16552.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P27683
#32: Protein 50S ribosomal protein L31 /


Mass: 10801.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R0R6, UniProt: P82249*PLUS

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Protein , 18 types, 18 molecules 67DGHMOPXYZjqtuywv

#6: Protein protein cL37


Mass: 15694.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9S2M7, UniProt: P27684*PLUS
#7: Protein protein cL38


Mass: 12080.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RCH6, UniProt: P82411*PLUS
#10: Protein protein L3


Mass: 24117.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QEC7, UniProt: P82191*PLUS
#13: Protein protein L6


Mass: 20263.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R4N9, UniProt: P82193*PLUS
#14: Protein protein L9


Mass: 17669.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RQ91, UniProt: P82180*PLUS
#17: Protein protein L15


Mass: 20680.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QHT0, UniProt: P22798*PLUS
#19: Protein protein L17


Mass: 13466.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RLJ4, UniProt: P82194*PLUS
#20: Protein protein L18


Mass: 13801.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QQ60, UniProt: P82195*PLUS
#28: Protein protein L27


Mass: 15326.538 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R4I2, UniProt: P82190*PLUS
#29: Protein protein L28


Mass: 9016.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RD02, UniProt: P82245*PLUS
#30: Protein protein L29


Mass: 12903.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R7W8, UniProt: P82248*PLUS
#40: Protein protein S10


Mass: 13882.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RWE7, UniProt: P82162*PLUS
#46: Protein protein S17


Mass: 12195.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RRR0, UniProt: P82137*PLUS
#49: Protein protein S20


Mass: 12178.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
#50: Protein protein S21


Mass: 16096.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RHF9, UniProt: P82024*PLUS
#51: Protein protein plastid pY


Mass: 26851.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QHQ6, UniProt: P19954*PLUS
#53: Protein protein cS23


Mass: 13808.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RJX3, UniProt: P82412*PLUS
#55: Protein protein cS22


Mass: 21691.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R1W7, UniProt: P82277*PLUS

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RNA chain , 4 types, 4 molecules BWAa

#8: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 39014.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
#27: RNA chain 4.8S rRNA / 4.5S ribosomal RNA


Mass: 34334.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 12299
#31: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 911344.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 7636084
#52: RNA chain 16S rRNA /


Mass: 483466.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 7636084

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30S ribosomal protein ... , 17 types, 17 molecules bcefghiklmoprsdn8

#33: Protein 30S ribosomal protein S2, chloroplastic / Ribosome


Mass: 26736.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P08242
#34: Protein 30S ribosomal protein S3, chloroplastic / Ribosome


Mass: 24965.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09595
#35: Protein 30S ribosomal protein S5, chloroplastic / Ribosome


Mass: 27696.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9ST69
#36: Protein 30S ribosomal protein S6 alpha, chloroplastic / Ribosome


Mass: 16341.423 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82403
#37: Protein 30S ribosomal protein S7, chloroplastic / Ribosome


Mass: 17378.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82129
#38: Protein 30S ribosomal protein S8, chloroplastic / Ribosome


Mass: 15527.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09597
#39: Protein 30S ribosomal protein S9, chloroplastic / Ribosome


Mass: 17092.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82278
#41: Protein 30S ribosomal protein S11, chloroplastic / Ribosome


Mass: 14927.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06506
#42: Protein 30S ribosomal protein S12, chloroplastic / Ribosome


Mass: 13794.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P62128
#43: Protein 30S ribosomal protein S13, chloroplastic / Ribosome


Mass: 14418.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82163
#44: Protein 30S ribosomal protein S15, chloroplastic / Ribosome


Mass: 10778.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3I4
#45: Protein 30S ribosomal protein S16, chloroplastic / Ribosome


Mass: 10454.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28807
#47: Protein 30S ribosomal protein S18, chloroplastic / Ribosome


Mass: 12079.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3K7
#48: Protein 30S ribosomal protein S19 alpha, chloroplastic / Ribosome / CS-S23


Mass: 10632.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06508
#54: Protein 30S ribosomal protein S4, chloroplastic / Ribosome


Mass: 23454.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P13788
#56: Protein 30S ribosomal protein S14, chloroplastic / Ribosome


Mass: 11809.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06507
#58: Protein 30S ribosomal protein S1, chloroplastic / Ribosome / CS1


Mass: 40472.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P29344

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Protein/peptide , 1 types, 1 molecules x

#57: Protein/peptide protein bTHXc


Mass: 5188.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RMU8, UniProt: P47910*PLUS

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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

Component
IDNameTypeEntity IDParent-IDSource
1Chloroplast 70S ribosome from spinachRIBOSOMEall0NATURAL
2chloroplast ribosome 50S large subunitCOMPLEX#1-#30, #57-#581NATURAL
3chloroplast ribosome 30S small subunitCOMPLEX#31-#561NATURAL
Molecular weightValue: 1.7 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spinacia oleracea (spinach)3562
31Spinacia oleracea (spinach)3562
Buffer solutionpH: 7.6
Details: 20 mM Tris HCl, pH 7.6, 100 mM KCl, 10 mM MgOAc, 100 mM sucrose, 7 mM 2-mercaptoethanol, 1 unit/ml RNase inhibitor, 0.1% protease inhibitor
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Calibrated magnification: 133333 X / Nominal defocus max: 3700 nm / Nominal defocus min: 400 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 3700 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3161
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 25 / Used frames/image: 1-25

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Processing

EM software
IDNameCategory
1EMAN2particle selection
4CTFFIND3CTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 187946
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81305 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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