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- PDB-5mmi: Structure of the large subunit of the chloroplast ribosome -

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Basic information

Entry
Database: PDB / ID: 5mmi
TitleStructure of the large subunit of the chloroplast ribosome
Components
  • (50S ribosomal protein ...) x 17
  • (plastid ribosomal protein ...) x 14
  • 23S ribosomal RNA
  • 4.5S ribosomal RNA
  • 5S ribosomal RNA
  • E-site tRNA
KeywordsRIBOSOME / chloroplast / translation / cryo-EM
Function / homology
Function and homology information


DNA-templated transcription, termination / ribosome biogenesis / chloroplast / large ribosomal subunit / ribosomal large subunit assembly / transferase activity / ribosome / rRNA binding / structural constituent of ribosome / translation
Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L19 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L27 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L33 superfamily / 50S ribosomal protein 5, chloroplastic ...Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L19 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L27 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L33 superfamily / 50S ribosomal protein 5, chloroplastic / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal Protein L26/L24, KOW domain / Ribosomal protein L31 superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e / Ribosomal protein L16p/L10e / Ribosomal protein L23 / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L3 / Ribosomal protein L5, C-terminal / Ribosomal protein L5 domain superfamily / Ribosomal protein L10 / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / Ribosomal protein L21-like / Ribosomal protein L15 / Ribosomal protein L5, N-terminal / Ribosomal protein L11, C-terminal domain superfamily / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein L36 superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L5 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L22 signature. / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L9, C-terminal domain / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Family of unknown function (DUF5323) / Ribosomal protein L14 signature. / Ribosomal protein L5 signature. / Ribosomal protein L11 signature. / Ribosomal protein L2 signature. / Ribosomal protein L35 / Ribosomal protein L3 signature. / Ribosomal protein L15 signature. / Ribosomal protein L6 signature 1. / Ribosomal protein L33 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L9 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal domain / Ribosomal protein L9, N-terminal domain / Ribosomal protein L6 / Ribosomal protein L4/L1 family / Ribosomal protein L36 / Ribosomal protein L20 / Ribosomal protein L10 / KOW motif / Ribosomal protein L34 / Ribosomal protein L33 / Ribosomal protein L13 / ribosomal L5P family C-terminus / Ribosomal protein L19 / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal prokaryotic L21 protein / Ribosomal L28 family / Ribosomal L29 protein / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L27 protein / Ribosomal protein L17 / Ribosomal protein L31 / Ribosomal protein L2, conserved site / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L36 signature. / Ribosomal protein L2 / Ribosomal protein L10P / Ribosomal protein L29/L35 / Ribosomal protein L19 / Ribosomal protein L5 / Ribosomal protein L4/L1e / Ribosomal protein L31 / Ribosomal protein L6, conserved site / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L32p / Ribosomal protein L24 / Ribosomal protein L18, bacterial-type / Ribosomal protein L18 / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L15, bacterial-type / Ribosomal protein L21
50S ribosomal protein L5, chloroplastic / 50S ribosomal protein 5 alpha, chloroplastic / 50S ribosomal protein L20, chloroplastic / 50S ribosomal protein L32, chloroplastic / 50S ribosomal protein L33, chloroplastic / 50S ribosomal protein L11, chloroplastic / 50S ribosomal protein L10, chloroplastic / 50S ribosomal protein L9, chloroplastic / 50S ribosomal protein L27, chloroplastic / 50S ribosomal protein L3, chloroplastic ...50S ribosomal protein L5, chloroplastic / 50S ribosomal protein 5 alpha, chloroplastic / 50S ribosomal protein L20, chloroplastic / 50S ribosomal protein L32, chloroplastic / 50S ribosomal protein L33, chloroplastic / 50S ribosomal protein L11, chloroplastic / 50S ribosomal protein L10, chloroplastic / 50S ribosomal protein L9, chloroplastic / 50S ribosomal protein L27, chloroplastic / 50S ribosomal protein L3, chloroplastic / 50S ribosomal protein L17, chloroplastic / 50S ribosomal protein L6, chloroplastic / 50S ribosomal protein L21, chloroplastic / 50S ribosomal protein L18, chloroplastic / 50S ribosomal protein L34, chloroplastic / 50S ribosomal protein L28, chloroplastic / 50S ribosomal protein L29, chloroplastic / 50S ribosomal protein L31, chloroplastic / 50S ribosomal protein 6, chloroplastic / 50S ribosomal protein L19, chloroplastic / 50S ribosomal protein L23, chloroplastic / gb:7636084: / 50S ribosomal protein L24, chloroplastic / 50S ribosomal protein L16, chloroplastic / 50S ribosomal protein L35, chloroplastic / 50S ribosomal protein L28, chloroplastic / 50S ribosomal protein L3, chloroplastic / 50S ribosomal protein L24, chloroplastic / 50S ribosomal protein L15, chloroplastic / 50S ribosomal protein L18, chloroplastic / 50S ribosomal protein L31, chloroplastic / 50S ribosomal protein L10, chloroplastic / 50S ribosomal protein L27, chloroplastic / 50S ribosomal protein L6, chloroplastic / 50S ribosomal protein L29, chloroplastic / 50S ribosomal protein L5, chloroplastic / 50S ribosomal protein L15, chloroplastic / 50S ribosomal protein L17, chloroplastic / 50S ribosomal protein L9, chloroplastic / 50S ribosomal protein L4, chloroplastic / 50S ribosomal protein 5 alpha, chloroplastic / 50S ribosomal protein L4, chloroplastic / 50S ribosomal protein L2, chloroplastic / 50S ribosomal protein L22, chloroplastic / 50S ribosomal protein L14, chloroplastic / 50S ribosomal protein L36, chloroplastic / 50S ribosomal protein L13, chloroplastic / gb:12299:
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionDec 10, 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 1.3Oct 17, 2018Group: Data collection / Other / Refinement description / Category: cell / refine / Item: _cell.length_a / _cell.length_b / _cell.length_c

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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 bL17c
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: E-site tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,625,172538
Polymers1,612,86435
Non-polymers12,308503
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-101 kcal/mol
Surface area31260 Å2
MethodPISA

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Components

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

#1: Protein/peptide 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/peptide 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/peptide 50S ribosomal protein L33, chloroplastic / Ribosome / plastid ribosomal protein bL33c


Mass: 7668.121 Da / Num. of mol.: 1 / Details: Zn-binding protein / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28805
#4: Protein/peptide 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/peptide 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 / Details: Zn-binding protein / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12230
#8: Protein/peptide 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/peptide 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/peptide 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/peptide 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/peptide 50S ribosomal protein L14, chloroplastic / Ribosome / plastid ribosomal protein uL14c / 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/peptide 50S ribosomal protein L16, chloroplastic / Ribosome / plastid ribosomal protein uL16c / 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/peptide 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/peptide 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/peptide 50S ribosomal protein L21, chloroplastic / Ribosome / plastid ribosomal protein bL21c / CL21 / CS-L7


Mass: 28441.730 Da / Num. of mol.: 1
Details: Residues 68-81 were built as poly-alanine and deposited as UNK.
Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P24613
#28: Protein/peptide 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/peptide 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 ... , 14 types, 14 molecules 6DEFGHIMOPVXYZ

#7: Protein/peptide 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/peptide 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/peptide 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/peptide plastid ribosomal protein uL5c


Mass: 28182.688 Da / Num. of mol.: 1
Details: Residues 39-52 were built as poly-alanine and deposited as UNK.
Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RJX4, UniProt: P82192*PLUS
#15: Protein/peptide 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/peptide 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/peptide 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/peptide 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/peptide plastid ribosomal protein bL17c


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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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

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RNA chain , 4 types, 4 molecules ABWz

#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 E-site tRNA


Mass: 589.430 Da / Num. of mol.: 1 / Details: CA-3' end of E-site tRNA / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)

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Non-polymers , 2 types, 503 molecules

#36: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 501 / Source method: obtained synthetically / Formula: Mg / Magnesium

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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, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35
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

Buffer-ID: 1

IDConc.NameFormula
125 mMTris hydrochlorideTris-HClTris
225 mMPotassium chlorideKCl
325 mMMagnesium acetateMg(CH3COO)2
42 mMDithiothreitolDTT
50.05 mMSpermine
62 mMSpermidine
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 holderModel: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron 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

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154332 / Symmetry type: POINT
Atomic model buildingB value: 56.9 / Protocol: OTHER / Space: RECIPROCAL
RefinementResolution: 3.25→212.302 Å / SU ML: 0.44 / σ(F): 1.06 / Phase error: 26.15 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2471 41351 2.5 %
Rwork0.2343 --
Obs0.2346 1650858 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.008103202
f_angle_d1.1154296
f_dihedral_angle_d16.6248326
f_chiral_restr0.04619619
f_plane_restr0.0068225
LS refinement shell

Refinement-ID: ELECTRON MICROSCOPY

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2501-3.2870.456313950.461454328100
3.287-3.32570.396613890.36953061100
3.3257-3.36620.363713600.353853815100
3.3662-3.40890.361613930.34753861100
3.4089-3.45370.354513970.335853596100
3.4537-3.5010.352614240.325853475100
3.501-3.5510.34113900.315553622100
3.551-3.60410.32813700.304353704100
3.6041-3.66040.313712880.294954345100
3.6604-3.72040.302414300.283653187100
3.7204-3.78460.292314130.270553519100
3.7846-3.85340.279712800.265153784100
3.8534-3.92750.264614170.252453678100
3.9275-4.00770.259813680.242553529100
4.0077-4.09480.243713960.234453910100
4.0948-4.19010.222913180.225253189100
4.1901-4.29490.241914020.216353886100
4.2949-4.4110.222413630.209954042100
4.411-4.54080.215714030.201653423100
4.5408-4.68740.203813560.195153684100
4.6874-4.85490.206913750.189353742100
4.8549-5.04930.199513310.18353608100
5.0493-5.27920.186314190.174753354100
5.2792-5.55750.177113550.167853915100
5.5575-5.90570.176613010.167853805100
5.9057-6.36170.178814240.164353373100
6.3617-7.0020.169414100.162553715100
7.002-8.01520.162513740.156953652100
8.0152-10.09840.173914450.161953681100
10.0984-212.7560.162713650.15725302499

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