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- PDB-6eri: Structure of the chloroplast ribosome with chl-RRF and hibernatio... -

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Basic information

Entry
Database: PDB / ID: 6eri
TitleStructure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor
Components
  • (30S ribosomal protein ...) x 21
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 4.5S ribosomal RNA
  • 5S ribosomal RNA
  • Ribosome-binding factor PSRP1, chloroplastic
  • Ribosome-recycling factor, chloroplastic
  • bS1c
KeywordsRIBOSOME / Chloroplast / translation
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 / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / mitochondrion / RNA binding
Similarity search - Function
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 / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily ...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 / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / 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 S14, bacterial/plastid / 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 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 / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 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 S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, 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 / 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 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4c / Small ribosomal subunit protein uS11c / Small ribosomal subunit protein uS14c / Small ribosomal subunit protein uS19c ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 bTHXc / Small ribosomal subunit protein uS12cz/uS12cy / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein uS7cz/uS7cy / 30S ribosomal protein S20, chloroplastic / 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 / Ribosome-recycling factor, chloroplastic / Large ribosomal subunit protein bL34c / Large ribosomal subunit protein bL28c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein bL31c / Small ribosomal subunit protein uS9c / Small ribosomal subunit protein bS6c alpha / Large ribosomal subunit protein cL38 / 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 Å
AuthorsPerez Borema, A. / Aibara, S. / Paul, B. / Tobiasson, V. / Kimanius, D. / Forsberg, B.O. / Wallden, K. / Lindahl, E. / Amunts, A.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Foundation for Strategic ResearchFuture Leaders Grant FFL15:0325 Sweden
Ragnar Soderberg FoundationM44/16 Sweden
Swedish Research CouncilNT-2016-04107 Sweden
Swedish Research CouncilNT-2013-5901 Sweden
CitationJournal: Nat Plants / Year: 2018
Title: Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor.
Authors: Annemarie Perez Boerema / Shintaro Aibara / Bijoya Paul / Victor Tobiasson / Dari Kimanius / Björn O Forsberg / Karin Wallden / Erik Lindahl / A Amunts /
Abstract: Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions ...Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast. Chloroplasts evolved ~1.2 billion years ago from an engulfed primordial diazotrophic cyanobacterium, and chlororibosomes are responsible for synthesis of the core proteins driving photochemical reactions. Chlororibosomal activity is spatiotemporally coupled to the synthesis and incorporation of functionally essential co-factors, implying the presence of chloroplast-specific regulatory mechanisms and structural adaptation of the chlororibosome. Despite recent structural information, some of these aspects remained elusive. To provide new insights into the structural specialities and evolution, we report a comprehensive analysis of the 2.9-3.1 Å resolution electron cryo-microscopy structure of the spinach chlororibosome in complex with its recycling factor and hibernation-promoting factor. The model reveals a prominent channel extending from the exit tunnel to the chlororibosome exterior, structural re-arrangements that lead to increased surface area for translocon binding, and experimental evidence for parallel and convergent evolution of chloro- and mitoribosomes.
History
DepositionOct 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
AA: 23S ribosomal RNA
AB: 4.5S ribosomal RNA
AC: 50S ribosomal protein L2, chloroplastic
AD: 50S ribosomal protein L3, chloroplastic
AE: 50S ribosomal protein L4, chloroplastic
AF: 50S ribosomal protein L5, chloroplastic
AG: 50S ribosomal protein L6, chloroplastic
AH: 50S ribosomal protein L9, chloroplastic
AJ: 50S ribosomal protein L13, chloroplastic
AK: 50S ribosomal protein L14, chloroplastic
AL: 50S ribosomal protein L15, chloroplastic
AM: 50S ribosomal protein L16, chloroplastic
AN: 50S ribosomal protein L17, chloroplastic
AO: 50S ribosomal protein L18, chloroplastic
AP: 50S ribosomal protein L19, chloroplastic
AQ: 50S ribosomal protein L20, chloroplastic
AR: 50S ribosomal protein L21, chloroplastic
AS: 50S ribosomal protein L22, chloroplastic
AT: 50S ribosomal protein L23, chloroplastic
AU: 50S ribosomal protein L24, chloroplastic
AW: 50S ribosomal protein L27, chloroplastic
AX: 50S ribosomal protein L28, chloroplastic
AY: 50S ribosomal protein L29, chloroplastic
AZ: 50S ribosomal protein L31, chloroplastic
Aa: 50S ribosomal protein L32, chloroplastic
Ab: 50S ribosomal protein L33, chloroplastic
Ac: 50S ribosomal protein L34, chloroplastic
Ad: 50S ribosomal protein L35, chloroplastic
Ae: 50S ribosomal protein L36, chloroplastic
Af: 50S ribosomal protein 6, chloroplastic
Aw: 50S ribosomal protein 5 alpha, chloroplastic
Ax: 5S ribosomal RNA
Az: Ribosome-recycling factor, chloroplastic
BA: 16S ribosomal RNA
BB: 30S ribosomal protein S2, chloroplastic
BC: 30S ribosomal protein S3, chloroplastic
BD: 30S ribosomal protein S4, chloroplastic
BE: 30S ribosomal protein S5, chloroplastic
BF: 30S ribosomal protein S6 alpha, chloroplastic
BG: 30S ribosomal protein S7, chloroplastic
BH: 30S ribosomal protein S8, chloroplastic
BI: 30S ribosomal protein S9, chloroplastic
BJ: 30S ribosomal protein S10 alpha, chloroplastic
BK: 30S ribosomal protein S11, chloroplastic
BL: 30S ribosomal protein S12, chloroplastic
BM: 30S ribosomal protein S13, chloroplastic
BN: 30S ribosomal protein S14, chloroplastic
BO: 30S ribosomal protein S15, chloroplastic
BP: 30S ribosomal protein S16, chloroplastic
BQ: 30S ribosomal protein S17, chloroplastic
BR: 30S ribosomal protein S18, chloroplastic
BS: 30S ribosomal protein S19, chloroplastic
BT: 30S ribosomal protein S20, chloroplastic
BU: 30S ribosomal protein S21, chloroplastic
BV: Ribosome-binding factor PSRP1, chloroplastic
BW: 30S ribosomal protein S31, chloroplastic
BY: bS1c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,196,495402
Polymers2,188,02857
Non-polymers8,467345
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 4 types, 4 molecules AAABAxBA

#1: RNA chain 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
#2: RNA chain 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
#32: RNA chain 5S ribosomal RNA /


Mass: 38072.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
#34: RNA chain 16S ribosomal RNA /


Mass: 480386.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 7636084

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50S ribosomal protein ... , 29 types, 29 molecules ACADAEAFAGAHAJAKALAMANAOAPAQARASATAUAWAXAYAZAaAbAcAdAeAfAw

#3: Protein 50S ribosomal protein L2, chloroplastic / Ribosome / Chloroplastic large ribosomal subunit protein uL2c / Ribosomal protein CS-L4


Mass: 26990.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06509
#4: Protein 50S ribosomal protein L3, chloroplastic / Ribosome / Chloroplastic large ribosomal subunit protein uL3c


Mass: 24117.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82191
#5: Protein 50S ribosomal protein L4, chloroplastic / Ribosome / R-protein L4 / Chloroplastic large ribosomal subunit protein uL4c


Mass: 23802.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: O49937
#6: Protein 50S ribosomal protein L5, chloroplastic / Ribosome / Chloroplastic large ribosomal subunit protein uL5c


Mass: 23015.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82192
#7: Protein 50S ribosomal protein L6, chloroplastic / Ribosome / Chloroplastic large ribosomal subunit protein uL6c


Mass: 19132.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82193
#8: Protein/peptide 50S ribosomal protein L9, chloroplastic / Ribosome / CL9 / Chloroplastic large ribosomal subunit protein bL9c


Mass: 5212.397 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82180
#9: Protein 50S ribosomal protein L13, chloroplastic / Ribosome / CL13 / Chloroplastic large ribosomal subunit protein uL13c


Mass: 22991.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12629
#10: Protein 50S ribosomal protein L14, chloroplastic / Ribosome / Chloroplastic large ribosomal subunit 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
#11: Protein 50S ribosomal protein L15, chloroplastic / Ribosome / CL15 / Chloroplastic large ribosomal subunit protein uL15c


Mass: 20063.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P22798
#12: Protein 50S ribosomal protein L16, chloroplastic / Ribosome / Chloroplastic large ribosomal subunit protein uL16c / Ribosomal protein CS-L24


Mass: 15271.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P17353
#13: Protein 50S ribosomal protein L17, chloroplastic / Ribosome / CL17 / Chloroplastic large ribosomal subunit protein bL17c


Mass: 13466.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82194
#14: Protein 50S ribosomal protein L18, chloroplastic / Ribosome / CL18 / Chloroplastic large ribosomal subunit protein uL18c


Mass: 13601.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82195
#15: Protein 50S ribosomal protein L19, chloroplastic / Ribosome / CL19 / Chloroplastic large ribosomal subunit protein bL19c


Mass: 13544.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82413
#16: Protein 50S ribosomal protein L20, chloroplastic / Ribosome / Chloroplastic large ribosomal subunit protein bL20c


Mass: 14098.663 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28803
#17: Protein 50S ribosomal protein L21, chloroplastic / Ribosome / CL21 / CS-L7 / Chloroplastic large ribosomal subunit protein bL21c


Mass: 18752.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P24613
#18: Protein 50S ribosomal protein L22, chloroplastic / Ribosome / Chloroplastic large ribosomal subunit protein uL22c / Ribosomal protein CS-L13


Mass: 19826.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09594
#19: Protein 50S ribosomal protein L23, chloroplastic / Ribosome / Chloroplastic large ribosomal subunit protein uL23c / PRPL23


Mass: 10576.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9LWB5
#20: Protein 50S ribosomal protein L24, chloroplastic / Ribosome / CL24 / Chloroplastic large ribosomal subunit protein uL24c


Mass: 14487.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P27683
#21: Protein 50S ribosomal protein L27, chloroplastic / Ribosome / CL27 / Chloroplastic large ribosomal subunit protein bL27c


Mass: 12970.976 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82190
#22: Protein 50S ribosomal protein L28, chloroplastic / Ribosome / CL28 / Chloroplastic large ribosomal subunit protein bL28c


Mass: 8887.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82245
#23: Protein 50S ribosomal protein L29, chloroplastic / Ribosome / CL29 / Chloroplastic large ribosomal subunit protein uL29c


Mass: 11900.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82248
#24: Protein 50S ribosomal protein L31, chloroplastic / Ribosome / CL31 / Chloroplastic large ribosomal subunit protein bL31c


Mass: 7622.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82249
#25: Protein/peptide 50S ribosomal protein L32, chloroplastic / Ribosome / Chloroplastic large ribosomal subunit protein bL32c


Mass: 5604.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28804
#26: Protein 50S ribosomal protein L33, chloroplastic / Ribosome / Chloroplastic large ribosomal subunit protein bL33c


Mass: 7021.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28805
#27: Protein 50S ribosomal protein L34, chloroplastic / Ribosome / CL34 / Chloroplastic large ribosomal subunit protein bL34c


Mass: 6789.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82244
#28: Protein 50S ribosomal protein L35, chloroplastic / Ribosome / CL35 / Chloroplastic large ribosomal subunit protein bL35c


Mass: 8388.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P23326
#29: Protein/peptide 50S ribosomal protein L36, chloroplastic / Ribosome / Chloroplastic large ribosomal subunit protein bL36c


Mass: 4414.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12230
#30: Protein/peptide 50S ribosomal protein 6, chloroplastic / Ribosome / CL25 / Chloroplastic large ribosomal subunit protein cL38 / Plastid-specific 50S ribosomal protein 6 / PSRP-6


Mass: 5316.233 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82411
#31: Protein/peptide 50S ribosomal protein 5 alpha, chloroplastic / Ribosome / 50S ribosomal protein L40 / CL40 / Chloroplastic large ribosomal subunit protein cL37 / Plastid- ...50S ribosomal protein L40 / CL40 / Chloroplastic large ribosomal subunit protein cL37 / Plastid-specific 50S ribosomal protein 5 alpha / PSRP-5


Mass: 6093.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P27684

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Protein , 3 types, 3 molecules AzBVBY

#33: Protein Ribosome-recycling factor, chloroplastic / RRF / CpFrr / RRFHCP / Ribosome-releasing factor / chloroplastic


Mass: 21643.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82231
#55: Protein Ribosome-binding factor PSRP1, chloroplastic / 30S ribosomal protein 1 / CS-S5 / CS5 / Plastid-specific 30S ribosomal protein 1 / PSrp-1 / ...30S ribosomal protein 1 / CS-S5 / CS5 / Plastid-specific 30S ribosomal protein 1 / PSrp-1 / Ribosomal protein 1 / S22 / Translation factor pY


Mass: 11938.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P19954
#57: Protein bS1c


Mass: 14485.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)

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30S ribosomal protein ... , 21 types, 21 molecules BBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBW

#35: Protein 30S ribosomal protein S2, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein uS2c


Mass: 24166.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P08242
#36: Protein 30S ribosomal protein S3, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein uS3c


Mass: 24833.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09595
#37: Protein 30S ribosomal protein S4, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein uS4c


Mass: 23323.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P13788
#38: Protein 30S ribosomal protein S5, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein uS5c


Mass: 16990.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9ST69
#39: Protein 30S ribosomal protein S6 alpha, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein bS6c


Mass: 12974.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82403
#40: Protein 30S ribosomal protein S7, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein uS7c


Mass: 16804.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82129
#41: Protein 30S ribosomal protein S8, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit 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
#42: Protein 30S ribosomal protein S9, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein uS9c


Mass: 15479.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82278
#43: Protein 30S ribosomal protein S10 alpha, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein uS10c


Mass: 11355.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82162
#44: Protein 30S ribosomal protein S11, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein uS11c


Mass: 11844.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06506
#45: Protein 30S ribosomal protein S12, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein uS12c


Mass: 13663.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P62128
#46: Protein 30S ribosomal protein S13, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein uS13c


Mass: 13077.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82163
#47: Protein 30S ribosomal protein S14, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein uS14c


Mass: 11728.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06507
#48: Protein 30S ribosomal protein S15, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein uS15c


Mass: 8623.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3I4
#49: Protein 30S ribosomal protein S16, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein bS16c


Mass: 9607.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28807
#50: Protein 30S ribosomal protein S17, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein uS17c


Mass: 9686.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82137
#51: Protein 30S ribosomal protein S18, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein bS18c


Mass: 6281.497 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3K7
#52: Protein 30S ribosomal protein S19, chloroplastic / Ribosome / CS-S23 / Chloroplastic small ribosomal subunit protein uS19c


Mass: 9281.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06508
#53: Protein 30S ribosomal protein S20, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein bS20c


Mass: 11668.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82130
#54: Protein 30S ribosomal protein S21, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein bS21c


Mass: 7353.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82024
#56: Protein/peptide 30S ribosomal protein S31, chloroplastic / Ribosome / Chloroplastic small ribosomal subunit protein bTHXc / Plastid-specific 30S ribosomal protein 4 / PSRP-4


Mass: 4104.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P47910

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Non-polymers , 2 types, 345 molecules

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


Mass: 24.305 Da / Num. of mol.: 343 / Source method: obtained synthetically / Formula: Mg
#59: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Chloroplast ribosome in complex with RRFChloroplast / Type: RIBOSOME / Entity ID: #1-#57 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Spinacia oleracea (spinach)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130300 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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