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- PDB-5mmm: Structure of the 70S chloroplast ribosome -

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Basic information

Entry
Database: PDB / ID: 5mmm
TitleStructure of the 70S chloroplast ribosome
Components
  • (30S ribosomal protein ...) x 16
  • (50S ribosomal protein ...) x 17
  • (plastid ribosomal protein ...) x 22
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 4.5S ribosomal RNA
  • 5S ribosomal RNA
  • Ribosome-binding factor PSRP1, chloroplastic
  • tRNA-Phe
KeywordsRIBOSOME / chloroplast / translation / cryo-EM
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 / chloroplast stroma / plastid / 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 / chloroplast stroma / plastid / mitochondrial translation / ribosomal small subunit binding / chloroplast / DNA-templated transcription termination / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / transferase activity / negative regulation of translation / ribosome / rRNA binding / 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 / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / 30S ribosomal protein / Ribosomal protein L10 / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / Ribosomal protein S21 superfamily / 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 L11, conserved site / Ribosomal protein L10-like domain superfamily / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L10 / Ribosomal protein L10P / 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 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, RNA binding domain / Ribosomal protein L11/L12 / 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
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL24c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL24c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c / Small ribosomal subunit protein uS13c / Small ribosomal subunit protein bS6c alpha / Large ribosomal subunit protein bL31c / Large ribosomal subunit protein uL10c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein bL28c / Small ribosomal subunit protein bS21c / Large ribosomal subunit protein uL5c / Large ribosomal subunit protein bL17c / Large ribosomal subunit protein bL9c / Small ribosomal subunit protein uS17c / Large ribosomal subunit protein uL4c / Small ribosomal subunit protein uS10c / Small ribosomal subunit protein uS9c / 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 / Large ribosomal subunit protein uL11c / 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 / Large ribosomal subunit protein uL10c / 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
AuthorsBieri, P. / Leibundgut, M. / Saurer, M. / Boehringer, D. / Ban, N.
CitationJournal: EMBO J / Year: 2017
Title: The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.
Authors: Philipp Bieri / Marc Leibundgut / Martin Saurer / Daniel Boehringer / Nenad Ban /
Abstract: Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, ...Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid-specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light- and temperature-dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A-site and P-site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non-rotated state, in which the intersubunit bridges to the large subunit are stabilized.
History
DepositionDec 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Derived calculations
Category: em_software / pdbx_struct_conn_angle / struct_conn
Item: _em_software.name
Revision 1.3Dec 11, 2019Group: 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.Z_PDB

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Structure visualization

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Assembly

Deposited unit
0: 50S ribosomal protein L31
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: plastid ribosomal protein cL37, PSRP5
7: 50S ribosomal protein 6, chloroplastic
A: 23S ribosomal RNA
B: 5S ribosomal RNA
C: 50S ribosomal protein L2, chloroplastic
D: plastid ribosomal protein uL3c
E: plastid ribosomal protein uL4c
F: plastid ribosomal protein uL5c
G: plastid ribosomal protein uL6c
H: plastid ribosomal protein bL9c
I: plastid ribosomal protein uL10c
J: 50S ribosomal protein L11, chloroplastic
K: 50S ribosomal protein L13, chloroplastic
L: 50S ribosomal protein L14, chloroplastic
M: plastid ribosomal protein uL15c
N: 50S ribosomal protein L16, chloroplastic
O: plastid ribosomal protein uL14c
P: plastid ribosomal protein uL18c
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: plastid ribosomal protein uL24c
W: 4.5S ribosomal RNA
X: plastid ribosomal protein bL27c
Y: plastid ribosomal protein bL28c
Z: plastid ribosomal protein uL29c
z: tRNA-Phe
8: plastid ribosomal protein bS1c
a: 16S ribosomal RNA
b: 30S ribosomal protein S2, chloroplastic
c: 30S ribosomal protein S3, chloroplastic
d: 30S ribosomal protein S4, chloroplastic
e: 30S ribosomal protein S5, chloroplastic
f: plastid ribosomal protein bS6c
g: 30S ribosomal protein S7, chloroplastic
h: 30S ribosomal protein S8, chloroplastic
i: plastid ribosomal protein uS9c
j: plastid ribosomal protein uS10c
k: 30S ribosomal protein S11, chloroplastic
l: 30S ribosomal protein S12, chloroplastic
m: plastid ribosomal protein uS13c
n: 30S ribosomal protein S14, chloroplastic
o: 30S ribosomal protein S15, chloroplastic
p: 30S ribosomal protein S16, chloroplastic
q: plastid ribosomal protein uS17c
r: 30S ribosomal protein S18, chloroplastic
s: 30S ribosomal protein S19 alpha, chloroplastic
t: plastid ribosomal protein bS20c
u: plastid ribosomal protein bS21c
v: 30S ribosomal protein 2, chloroplastic
w: 30S ribosomal protein 3, chloroplastic
x: 30S ribosomal protein S31, chloroplastic
y: Ribosome-binding factor PSRP1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,618,916842
Polymers2,599,85161
Non-polymers19,064781
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area306490 Å2
ΔGint-2466 kcal/mol
Surface area837060 Å2
MethodPISA

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Components

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50S ribosomal protein ... , 17 types, 17 molecules 0123457CJKLNQRSTU

#1: Protein 50S ribosomal protein L31 / / plastid ribosomal protein bL31c


Mass: 14748.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R0R6, UniProt: P82249*PLUS
#2: Protein 50S ribosomal protein L32, chloroplastic / Ribosome / plastid ribosomal protein bL32c


Mass: 6650.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28804
#3: Protein 50S ribosomal protein L33, chloroplastic / Ribosome / plastid ribosomal protein bL33c


Mass: 7668.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Zn-binding protein / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28805
#4: Protein 50S ribosomal protein L34, chloroplastic / Ribosome / plastid ribosomal protein bL34c / CL34


Mass: 16126.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82244
#5: Protein 50S ribosomal protein L35, chloroplastic / Ribosome / plastid ribosomal protein bL35c / CL35


Mass: 17376.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P23326
#6: Protein/peptide 50S ribosomal protein L36, chloroplastic / Ribosome / plastid ribosomal protein bL36c


Mass: 4414.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Zn-binding protein / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12230
#8: Protein 50S ribosomal protein 6, chloroplastic / Ribosome / plastid ribosomal protein cL38 / PSRP6 / CL25 / Plastid-specific 50S ribosomal protein 6 / PSRP-6


Mass: 12080.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82411
#11: Protein 50S ribosomal protein L2, chloroplastic / Ribosome / plastid ribosomal protein uL2c / Ribosomal protein CS-L4


Mass: 29853.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06509
#18: Protein 50S ribosomal protein L11, chloroplastic / Ribosome / plastid ribosomal protein uL11c / CL11


Mass: 23689.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P31164
#19: Protein 50S ribosomal protein L13, chloroplastic / Ribosome / plastid ribosomal protein uL13c / CL13


Mass: 28211.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12629
#20: 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
#22: Protein 50S ribosomal protein L16, chloroplastic / Ribosome / plastid ribosomal protein uL15c / 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
#25: Protein 50S ribosomal protein L19, chloroplastic / Ribosome / plastid ribosomal protein bL19c / CL19


Mass: 26121.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82413
#26: Protein 50S ribosomal protein L20, chloroplastic / Ribosome / plastid ribosomal protein bL20c


Mass: 15725.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28803
#27: Protein 50S ribosomal protein L21, chloroplastic / Ribosome / plastid ribosomal protein bL21c / CL21 / CS-L7


Mass: 28441.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Residues 68-81 were built as poly-alanine and deposited as UNK.
Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P24613
#28: Protein 50S ribosomal protein L22, chloroplastic / Ribosome / plastid ribosomal protein uL22c / 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
#29: Protein 50S ribosomal protein L23, chloroplastic / Ribosome / plastid ribosomal protein uL23c / PRPL23


Mass: 21832.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9LWB5

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Plastid ribosomal protein ... , 22 types, 22 molecules 6DEFGHIMOPVXYZ8fijmqtu

#7: Protein plastid ribosomal protein cL37, PSRP5


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
#12: Protein plastid ribosomal protein uL3c


Mass: 33034.750 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 plastid ribosomal protein uL4c


Mass: 32541.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RVQ9, UniProt: O49937*PLUS
#14: Protein plastid ribosomal protein uL5c


Mass: 28182.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Residues 39-52 were built as poly-alanine and deposited as UNK.
Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RJX4, UniProt: P82192*PLUS
#15: Protein plastid ribosomal protein uL6c


Mass: 24516.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R4N9, UniProt: P82193*PLUS
#16: Protein plastid ribosomal protein bL9c


Mass: 22038.904 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 plastid ribosomal protein uL10c


Mass: 26128.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R3N5, UniProt: P82139*PLUS
#21: Protein plastid ribosomal protein uL15c


Mass: 29081.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QHT0, UniProt: P22798*PLUS
#23: Protein plastid ribosomal protein uL14c


Mass: 14577.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RLJ4, UniProt: P82194*PLUS
#24: Protein plastid ribosomal protein uL18c


Mass: 18410.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QQ60, UniProt: P82195*PLUS
#30: Protein plastid ribosomal protein uL24c


Mass: 21417.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QFU9, UniProt: P27683*PLUS
#32: Protein plastid ribosomal protein bL27c


Mass: 21366.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R4I2, UniProt: P82190*PLUS
#33: Protein plastid ribosomal protein bL28c


Mass: 16460.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RD02, UniProt: P82245*PLUS
#34: Protein plastid ribosomal protein uL29c


Mass: 19083.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R7W8, UniProt: P82248*PLUS
#36: Protein plastid ribosomal protein bS1c


Mass: 14826.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Residues 1001-1068 (OB-fold) and residues 1101-1143 and 1201-1263 (extensions) were built as poly-alanine and deposited as UNK.
Source: (natural) Spinacia oleracea (spinach)
#42: Protein plastid ribosomal protein bS6c


Mass: 23510.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R0H2, UniProt: P82403*PLUS
#45: Protein plastid ribosomal protein uS9c


Mass: 22415.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RY17, UniProt: P82278*PLUS
#46: Protein plastid ribosomal protein uS10c


Mass: 21440.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RWE7, UniProt: P82162*PLUS
#49: Protein plastid ribosomal protein uS13c


Mass: 19310.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R024, UniProt: P82163*PLUS
#53: Protein plastid ribosomal protein uS17c


Mass: 18151.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RRR0, UniProt: P82137*PLUS
#56: Protein plastid ribosomal protein bS20c


Mass: 20147.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
#57: Protein plastid ribosomal protein bS21c


Mass: 20616.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RHF9, UniProt: P82024*PLUS

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RNA chain , 5 types, 5 molecules ABWza

#9: RNA chain 23S ribosomal RNA / / plastid 23S rRNA


Mass: 911344.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 7636084
#10: RNA chain 5S ribosomal RNA / / plastid 5S rRNA


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


Mass: 34334.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 12299
#35: RNA chain tRNA-Phe


Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: An idealized full-length E-site E.coli tRNA-Phe (76 residues) from PDB 2J00 was fitted into the density and adjusted prior to minimization.
Source: (natural) Spinacia oleracea (spinach)
#37: RNA chain 16S ribosomal RNA / / plastid 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 ... , 16 types, 16 molecules bcdeghklnoprsvwx

#38: Protein 30S ribosomal protein S2, chloroplastic / Ribosome / plastid ribosomal protein uS2c


Mass: 26736.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P08242
#39: Protein 30S ribosomal protein S3, chloroplastic / Ribosome / plastid ribosomal protein uS3c


Mass: 24965.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09595
#40: Protein 30S ribosomal protein S4, chloroplastic / Ribosome / plastid ribosomal protein uS4c


Mass: 23454.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P13788
#41: Protein 30S ribosomal protein S5, chloroplastic / Ribosome / plastid ribosomal protein uS5c


Mass: 33626.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Residues 122-150 were built as poly-alanine and deposited as UNK.
Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9ST69
#43: Protein 30S ribosomal protein S7, chloroplastic / Ribosome / plastid ribosomal protein uS7c


Mass: 17378.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82129
#44: Protein 30S ribosomal protein S8, chloroplastic / Ribosome / plastid ribosomal protein uS8c


Mass: 15527.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09597
#47: Protein 30S ribosomal protein S11, chloroplastic / Ribosome / plastid ribosomal protein uS11c


Mass: 14927.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06506
#48: Protein 30S ribosomal protein S12, chloroplastic / Ribosome / plastid ribosomal protein uS12c


Mass: 13794.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P62128
#50: Protein 30S ribosomal protein S14, chloroplastic / Ribosome / plastid ribosomal protein uS14c


Mass: 11809.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06507
#51: Protein 30S ribosomal protein S15, chloroplastic / Ribosome / plastid ribosomal protein uS15c


Mass: 10778.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3I4
#52: Protein 30S ribosomal protein S16, chloroplastic / Ribosome / plastid ribosomal protein bS16c


Mass: 10454.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28807
#54: Protein 30S ribosomal protein S18, chloroplastic / Ribosome / plastid ribosomal protein bS18c


Mass: 12079.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3K7
#55: Protein 30S ribosomal protein S19 alpha, chloroplastic / Ribosome / plastid ribosomal protein uS19c / 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
#58: Protein 30S ribosomal protein 2, chloroplastic / Ribosome / plastid ribosomal protein cS22 / Plastid-specific 30S ribosomal protein 2 / PSRP-2


Mass: 28327.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82277
#59: Protein 30S ribosomal protein 3, chloroplastic / Ribosome / Pplastid ribosomal protein cS23 / plastid-specific 30S ribosomal protein 3 / PSRP-3


Mass: 20312.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82412
#60: Protein 30S ribosomal protein S31, chloroplastic / Ribosome / plastid ribosomal protein bTHXc / Plastid-specific 30S ribosomal protein 4 / PSRP-4


Mass: 10602.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P47910

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Protein , 1 types, 1 molecules y

#61: Protein Ribosome-binding factor PSRP1, chloroplastic / plastid pY / 30S ribosomal protein 1 / CS-S5 / CS5 / Plastid-specific 30S ribosomal protein 1 / ...plastid pY / 30S ribosomal protein 1 / CS-S5 / CS5 / Plastid-specific 30S ribosomal protein 1 / PSrp-1 / Ribosomal protein 1 / S22


Mass: 33799.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P19954

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Non-polymers , 2 types, 781 molecules

#62: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#63: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 779 / Source method: obtained synthetically / Formula: Mg

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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 70S ribosome / Type: RIBOSOME / Entity ID: #1-#61 / Source: NATURAL
Molecular weightValue: 2.4 MDa / Experimental value: NO
Source (natural)Organism: Spinacia oleracea (spinach) / Organelle: chloroplast / Tissue: leaf
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris hydrochlorideTris-HClTris1
225 mMPotassium chlorideKCl1
325 mMMagnesium acetateMg(CH3COO)21
42 mMDithiothreitolDTT1
50.05 mMSpermine1
62 mMSpermidine1
SpecimenConc.: 0.12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 278 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.77 sec. / Electron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 2796
Image scansMovie frames/image: 8 / Used frames/image: 2-8

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN1.9particle selectionBatchboxer
2EPUimage acquisition
4CTFFIND3CTF correctionCTF estimation
5RELION1.4CTF correctionAmplitude correction
8UCSF Chimera1.11.2model fitting
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
14PHENIX1.11.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 326094
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140583 / Symmetry type: POINT
Atomic model buildingB value: 90.8 / Protocol: OTHER / Space: RECIPROCAL

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