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- EMDB-9572: Structure of the large subunit of the chloro-ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-9572
TitleStructure of the large subunit of the chloro-ribosome
Map dataChloro-ribosome LSU (50S)
Sample
  • Complex: Chloro-ribosome 50S
    • RNA: x 3 types
    • Protein or peptide: x 29 types
Function / homology
Function and homology information


plastid translation / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast / DNA-templated transcription termination / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit ...plastid translation / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast / DNA-templated transcription termination / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding
Similarity search - Function
Ribosomal protein L6, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / 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, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / 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 L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / 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 / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L5, conserved site / : / Ribosomal protein L5, N-terminal / Ribosomal protein L5 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein L2 signature. / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L5 / ribosomal L5P family C-terminus / Ribosomal protein L16p/L10e / Ribosomal protein L2, domain 3 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL31c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein bL28c / Large ribosomal subunit protein bL17c / Large ribosomal subunit protein bL9c ...Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL31c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein bL28c / Large ribosomal subunit protein bL17c / Large ribosomal subunit protein bL9c / Large ribosomal subunit protein uL4c / Large ribosomal subunit protein uL2cz/uL2cy / Large ribosomal subunit protein uL22c / Large ribosomal subunit protein uL14c / Large ribosomal subunit protein bL36c / Large ribosomal subunit protein uL13c / Large ribosomal subunit protein uL16c / 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 / 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 / Large ribosomal subunit protein cL38 / Large ribosomal subunit protein bL19c / Large ribosomal subunit protein uL23c
Similarity search - Component
Biological speciesSpinacia oleracea (spinach) / Spinach (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsAhmed T / Yin Z / Bhushan S
CitationJournal: Sci Rep / Year: 2016
Title: Cryo-EM structure of the large subunit of the spinach chloroplast ribosome.
Authors: Tofayel Ahmed / Zhan Yin / Shashi Bhushan /
Abstract: Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ...Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ribosome but certain differences are evident. The chloro-ribosome proteins are generally larger because of the presence of chloroplast-specific extensions in their N- and C-termini. The chloro-ribosome harbours six plastid-specific ribosomal proteins (PSRPs); four in the small subunit and two in the large subunit. Deletions and insertions occur throughout the rRNA sequence of the chloro-ribosome (except for the conserved peptidyl transferase center region) but the overall length of the rRNAs do not change significantly, compared to the E. coli. Although, recent advancements in cryo-electron microscopy (cryo-EM) have provided detailed high-resolution structures of ribosomes from many different sources, a high-resolution structure of the chloro-ribosome is still lacking. Here, we present a cryo-EM structure of the large subunit of the chloro-ribosome from spinach (Spinacia oleracea) at an average resolution of 3.5 Å. High-resolution map enabled us to localize and model chloro-ribosome proteins, chloroplast-specific protein extensions, two PSRPs (PSRP5 and 6) and three rRNA molecules present in the chloro-ribosome. Although comparable to E. coli, the polypeptide tunnel and the tunnel exit site show chloroplast-specific features.
History
DepositionOct 11, 2016-
Header (metadata) releaseFeb 1, 2017-
Map releaseFeb 1, 2017-
UpdateJun 6, 2018-
Current statusJun 6, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.132
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.132
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5h1s
  • Surface level: 0.132
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9572.png

Downloads & links

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Map

FileDownload / File: emd_9572.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChloro-ribosome LSU (50S)
Voxel sizeX=Y=Z: 1.28 Å
Density
Contour LevelBy AUTHOR: 0.132 / Movie #1: 0.132
Minimum - Maximum-0.584668 - 0.92817754
Average (Standard dev.)0.0021987308 (±0.027552119)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 399.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.281.281.28
M x/y/z312312312
origin x/y/z0.0000.0000.000
length x/y/z399.360399.360399.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS312312312
D min/max/mean-0.5850.9280.002

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Supplemental data

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Sample components

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Entire : Chloro-ribosome 50S

EntireName: Chloro-ribosome 50S
Components
  • Complex: Chloro-ribosome 50S
    • RNA: 23S rRNA23S ribosomal RNA
    • RNA: Spinach chloroplast 4.5S rRNA
    • RNA: 5S rRNA5S ribosomal RNA
    • Protein or peptide: 50S ribosomal protein L13, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L14, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L16, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L20, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L21, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L22, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L23, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L24, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L2, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L32, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L33, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L34, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L35, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L36, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L5, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L9
    • Protein or peptide: 50S ribosomal protein 5 alpha, chloroplasticRibosome
    • Protein or peptide: 50S ribosomal protein L31
    • Protein or peptide: 50S ribosomal protein 6, chloroplasticRibosome

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Supramolecule #1: Chloro-ribosome 50S

SupramoleculeName: Chloro-ribosome 50S / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 1.7 MDa

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Macromolecule #1: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 911.34425 KDa
SequenceString: UUCAAACGAG GAAAGGCUUA CGGUGGAUAC CUAGGCACCC AGAGACGAGG AAGGGCGUAU UAAUCGACGA AAUGCUUCGG GGAGUUGAA AAUAAGCAGA GAUCCGGAGA UUCCCGAAUA GGUCAACCUU UCGAACUUCU GCUGAAUCCA UGGGCAGGCA A GAGACAAC ...String:
UUCAAACGAG GAAAGGCUUA CGGUGGAUAC CUAGGCACCC AGAGACGAGG AAGGGCGUAU UAAUCGACGA AAUGCUUCGG GGAGUUGAA AAUAAGCAGA GAUCCGGAGA UUCCCGAAUA GGUCAACCUU UCGAACUUCU GCUGAAUCCA UGGGCAGGCA A GAGACAAC CUGGCGAACU GAAACAUCUU AGUAGCCAGA GGAAAAGAAA GCAAAAGCGA UUCCCGUAGU AGCGGCGAGC GA AAUGGGA GCAGCCUAAA CCGUGAAAAC GGGGUUGUGG GAGAGCAAUA CAAGCGUCGU GCUGCUAGGC GAAUCAGUGG AGU GCGGAA CCCUAGAUGG UGAAAGUCCA GUAGCCGAAA GCAUCACUAG CUUAUGCUCU GACCCGAGUA GCAUGGGGCA CGUG GAAUC CCGUGUGAAU CAGCAAGGAC CACCUUGCAA GGCUAAAUAC UCCUGGGUGA CCGAUAGCGA AGUAGUACCG UGAGG GAAG GGUGAAAAGA ACCCCCAUCG GGGAGUGAAA UAGAACAUGA AACCGUAAGC UCUCAAGCAG UGGGAGGGGG ACCAGA CCC UGACCGCGUG CCUGUUGAAG AAUGAGCCGG CGACUCAUAG GCAGUGGCUU GGUUAAGGGA ACCCACCGGA GCCGUAG CG AAAGCGAGUC UUCAUAGGGC AAUUGUCACU GCUUAUGGAC CCGAACCUGG GUGAUCUAUC CAUGACCAGG AUGAAGCU U GGGUGAAACU AAGUGGAGGU CCGAACCGAC UGAUGUUGAA GAAUCAGCGG AUGAGUUGUG GUUAGGGGUG AAAUGCCAC UCGAACCCAG AGCUAGCUGG UUCUCCCCGA AAUGCGUUGA GGCGCAGCAG UUGACUGGAC AUCUAGGGGU AAAGCACUGU UUCGGUGCG GGCCGCGAGA GCGGUACCAA AUCGAGGCAA ACUCUGAAUA CUAGAUAUGA CCUCCAAAUA ACAGGGGUCA A GGUCGGCC AGUGAGACGA UGGGGGAUAA GCUUCAUCGU CGAGAGGGAA ACAGCCCGGA UCACCAGCUA AGGCCCCUAA AU GACCGCU CAGUGAUAAA GGAGGUAGGG GUGCAGAGAC AGCCAGGAGG UUUGCCUAGA AGCAGCCACC CUUGAAAGAG UGC GUAAUA GCUCACUGAU CGAGCGCUCU UGCGCCGAAG AUGAACGGGG CUAAGCGGUC UGCCGAAGCU GUGGGAUGUA AAAA AACAU CGGUAGGGGA GCGUUCCGUG UUAGGGAGAA ACGCGUGCGU GAGCCGCGUU GGACGAAGCG GAAGCGAGAA UGUCG GCUU GAGUAACGCA AACAUUGGUG AGAAUCCAAU GCCCCGAAAA CCUAAGGGUU CCUCCGCAAG GUUCGUCCAC GGAGGG UGA GUCAGGGCCU AAGAUCAGGC CGAAAGGCGU AGUCGAUGGA CAACAGGUGA AUAUUCCUGU ACUACCCCUU GUUGGUC CC GAGGGACGGA GGAGGCUAGG UUAGCCGAAA GAUGGUUAUC GGUUCAAGGA CGCAAGGUGA CCCUGUUUUU CAGGGUAA G AAGGGGUAGA GAAAAUGCCU CGAGCCAAUG UUCGAGUACC AGGCGCUACG GCGCUGAAGU AACCGAUGCC AUACUCCCA GGAAAAGCUC GAACGACCUU CAACAAAAGG GUACCUGUAC CCGAAACCGA CACAGGUAGG UAGGUAGAGA AUACCUAGGG GCGCGAGAC AACUCUCUCU AAGGAACUCG GCAAAAUAGC CCCGUAACUU CGGGAGAAGG GGUGCCCCCU CACAAAGGGG G UCGAAGUG ACCAGGCCCG GGCGACUGUU UACCAAAAAC ACAGGUCUCC GCAAAGUCGU AAGACCAUGU AUGGGGGCUG AC GCCUGCC CAGUGCCGGA AGGUCAAGGA AGUUGGUGAC CUGAUGACAG GGGAGCCGGC GACCGAAGCC CCGGUGAACG GCG GCCGUA ACUAUAACGG UCCUAAGGUA GCGAAAUUCC UUGUCGGGUA AGUUCCGACC CGCACGAAAG GCGUAACGAU CUGG GCACU GUCUCGGAGA GAGGCUCGGU GAAAUAGACA UGUCUGUGAA GAUGCGGACU ACCUGCACCU GGACAGAAAG ACCCU AUGA AGCUUUACUG UUCCCUGGGA UUGGCUUUGG GCUUUUCCUG CGCAGCUUAG GUGGAAGGCG AAGAAGGCCC CCUUCC GGG GGGGCCCGAG CCAUCAGUGA GAUACCACUC UGGAAGAGCU AGAAUUCUAA CCUUGUGUCA GGACCUACGG GCCAAGG GA CAUUCUCAGG UAGACAGUUU CUAUGGGGCG UAGGCCUCCC AAAAGGUAAC GGAGGCGUGC AAAGGUUUCC UCGGGCCG G ACGGAGAUUG GCCCUCGAGU GCAAAGGCAG AAGGGAGCUU GACUGCAAGA CCCACCCGUC GAGCAGGGAC GAAAGUCGG CCUUAGUGAU CCGACGGUGC CGAGUGGAAG GGCCGUCGCU CAACGGAUAA AAGUUACUCU AGGGAUAACA GGCUGAUCUU CCCCAAGAG UUCACAUCGA CGGGAAGGUU UGGCACCUCG AUGUCGGCUC UUCGCCACCU GGGGCUGUAG UAUGUUCCAA G GGUUGGGC UGUUCGCCCA UUAAAGCGGU ACGUGAGCUG GGUUCAGAAC GUCGUGAGAC AGUUCGGUCC AUAUCCGGUG UG GGCGUUA GAGCAUUGAG AGGACCUUUC CCUAGUACGA GAGGACCGGG AAGGACGCAC CUCUGGUGUA CCAGUUAUCG UGC CCACGG UAAACGCUGG GUAGCCAAGU GCGGAGCGGA UAACUGCUGA AAGCAUCUAA GUAGUAAGCC CACCCCAAGA UGAG UGCUC UCCUA

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Macromolecule #2: Spinach chloroplast 4.5S rRNA

MacromoleculeName: Spinach chloroplast 4.5S rRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 34.334488 KDa
SequenceString:
AGAGAAGGUC ACGGCGAGAC GAGCCGUUUA UCAUUACGAU AGGUGUCAAG UGGAAGUGCA GUGAUGUAUG CAGCUGAGGC AUCCUAACA GACCCACAGA CUUGAAC

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Macromolecule #3: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 39.014184 KDa
SequenceString:
UAUUCUGGUG UCCUAGGCGU AGAGGAACCA CACCAAUCCA UCCCGAACUU GGUGGUUAAA CUCUACUGCG GUGACGAUAC UGUAGGGGA GGUCCUGCGG AAAAAUAGCU CGACGCCAGG AU

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Macromolecule #4: 50S ribosomal protein L13, chloroplastic

MacromoleculeName: 50S ribosomal protein L13, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 22.123639 KDa
SequenceString:
EWRQLKEAVK KEFAIPHVPL DQRWMFTLEE ATGPDIWNTT WYPKSADHVP TDKKWYVVDA TDLILGRMAS TIAIHIRGKN LASYTPSVD MGAFVIVVNA DKVAVSGKKR TQKLYRRHSG RPGGLKEETF DQLQKRIPER IIEHAVRGML PKGRLGRYLF N HLKVYKGA EHPHQAQQPI DLPLRDKRIR VEK

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Macromolecule #5: 50S ribosomal protein L14, chloroplastic

MacromoleculeName: 50S ribosomal protein L14, chloroplastic / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 13.484741 KDa
SequenceString:
MIQPQTHLNV ADNSGARELM CIRIIGASNR RYARIGDVIV AVIKEAIPNT PLERSEVIRA VVVRTCKELK RDNGMIIRYD DNAAVIIDQ EGNPKGTRIF GAIARELRQK FAKIVSLAPE VL

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Macromolecule #6: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 20.680062 KDa
SequenceString: FRLDNLGPQP GSRKKGKRKG RGHAAGQGGS CGFGMRGQKS RSGPGIMRGF EGGQMPLYRR IPKLRGIAGG MRAGLPKYVP INLRDIEVA GFKEGEEVSL ESLKAKGIIN PSGRERRLPL KILGEGELST KLQIKARAFS GSAKEKLEAA GCSVTVLPGR K KYIKESVR ...String:
FRLDNLGPQP GSRKKGKRKG RGHAAGQGGS CGFGMRGQKS RSGPGIMRGF EGGQMPLYRR IPKLRGIAGG MRAGLPKYVP INLRDIEVA GFKEGEEVSL ESLKAKGIIN PSGRERRLPL KILGEGELST KLQIKARAFS GSAKEKLEAA GCSVTVLPGR K KYIKESVR KNLARADEYF AKKRAASASE AESA

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Macromolecule #7: 50S ribosomal protein L16, chloroplastic

MacromoleculeName: 50S ribosomal protein L16, chloroplastic / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 15.328068 KDa
SequenceString:
MLSPKRTRFR KQHRGRMKGI SYRGNRICFG RYALQALEPA WITSRQIEAG RRAMTRNARR GGKIWVRIFP DKPVTVRPAE TRMGSGKGS PEYWVAVVKP GRILYEISGV AENIARRAVA IAASKMPIRT QFIISG

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Macromolecule #8: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 13.466902 KDa
SequenceString:
MKHGRKIHRL SRPADQRRAL LRGLTTQLLK HGRIKTTRAK ASAMRKYVDK MITLAKEGSL HKRRQALGFI YEKQIVHALF AEVPERYGD RNGGYTRIIR TLPRRGDNAP MAYIELV

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Macromolecule #9: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 13.801939 KDa
SequenceString:
AKAHTRREDR TARHVRIRKK VEGTPERPRL CVFRSNKHLY VQVIDDTKMH TLAAASTMQK AISENIDYSA GPTVEVAQKI GEMIAKSCL EKGITKVAFD RGGYPYHGRV KALADAAREH GLVF

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Macromolecule #10: 50S ribosomal protein L19, chloroplastic

MacromoleculeName: 50S ribosomal protein L19, chloroplastic / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 17.597373 KDa
SequenceString:
SEAEDSSDAP AESVAVVAEE ELPVESEAEA EERPPRQQRV KLGDIMGILN KKAVHAAEEL RPVPGIRTGD IVQIRLEVPE NKRRLSVYK GIVISRQNAG IHTTIRIRRI IAGVGVEIVF PLYSPNIKEI KVVSHRKVRK ARLYYLRDKL PRLSTFK

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Macromolecule #11: 50S ribosomal protein L20, chloroplastic

MacromoleculeName: 50S ribosomal protein L20, chloroplastic / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 15.594491 KDa
SequenceString:
TRVKRGYIAR RRRKKIRFFA SSFRGAHSRL TRTIAQQKIR ALVSAHRDRD RQKRDFRRLW ITRINAAIRE RGVYYNYSKF IHDLYKRQL LLNRKILAQI AILNPNCIYM IYNEIIKKED CKKYLEII

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Macromolecule #12: 50S ribosomal protein L21, chloroplastic

MacromoleculeName: 50S ribosomal protein L21, chloroplastic / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 22.793986 KDa
SequenceString: AKRRRFQEIP EELKAEFEEF QRPPNQKPQL SDVLPDDFQA PEPGTPEYND IINQFLPKKG PPPPREEIFA VVVIGSRQYI VIPGRWIYT QRLKGATVND KIVLNKVLLV GTKASTYIGT PIVTNAAVHA VVEEQLLDDK VIVFKYKKKK NYRRNIGHRQ P ITRIKITG ...String:
AKRRRFQEIP EELKAEFEEF QRPPNQKPQL SDVLPDDFQA PEPGTPEYND IINQFLPKKG PPPPREEIFA VVVIGSRQYI VIPGRWIYT QRLKGATVND KIVLNKVLLV GTKASTYIGT PIVTNAAVHA VVEEQLLDDK VIVFKYKKKK NYRRNIGHRQ P ITRIKITG ITGYEDYPAS TLEAEVEAKE EAEAEAEAEA VPV

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Macromolecule #13: 50S ribosomal protein L22, chloroplastic

MacromoleculeName: 50S ribosomal protein L22, chloroplastic / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 23.292676 KDa
SequenceString: MGFFKKKEKK AEFDVFRLYG LHHPEPGKCD EITTRGYSIS MSVDKARRVI DQIRGRSYAE TLMILELMPY RACYPIFKLI YSAAANASH NKQFNKANLI ISKAEVNKGI TLKKVKPRAR GRSYMIKRPT CHITIVLRDI THFDSYDKFL ESLTPKKLIA L LGLMSTGR ...String:
MGFFKKKEKK AEFDVFRLYG LHHPEPGKCD EITTRGYSIS MSVDKARRVI DQIRGRSYAE TLMILELMPY RACYPIFKLI YSAAANASH NKQFNKANLI ISKAEVNKGI TLKKVKPRAR GRSYMIKRPT CHITIVLRDI THFDSYDKFL ESLTPKKLIA L LGLMSTGR RRELLCGRFR ENHKIKSFLY KIALFKRYEV M

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Macromolecule #14: 50S ribosomal protein L23, chloroplastic

MacromoleculeName: 50S ribosomal protein L23, chloroplastic / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 13.575806 KDa
SequenceString:
ATEAVAPTTE EAATSQPKTS KKAKKLKYPR RILDVYQILQ SPIITEAAIK NIADENSLLF TVDVRADKKM IREAISNFFG VKVRKVNTL IRPDGTKKAY IMLNKEYNAS ELAKKIGIFP GGN

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Macromolecule #15: 50S ribosomal protein L24, chloroplastic

MacromoleculeName: 50S ribosomal protein L24, chloroplastic / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 16.552316 KDa
SequenceString:
RIKRWERKDC KPNSLPKLHK RHVKVGDTVK VISGGEKGKI GEISKIHKHN STVIIKDLNF KTKHVKSKEE GEQGQIIKIE AAIHSSNVM LILKEQEVAD RVGHKILEDV RKVRYLIKTG EIVDTPDRWK EIQNKKESET AVAVAA

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Macromolecule #16: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 15.326538 KDa
SequenceString:
AHKKGAGSTK NGRDSKGQRL GVKIYGDQVA KPGAIIIRQR GTKFHPGKNV GIGKDHTIFA LIDGLVKFEK YGPDKKKVSV YPREIQPEN PNSYRARKRE NFRLQREKKK ARREGYSFQP QLILASAATD NADESAVC

+
Macromolecule #17: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 9.016668 KDa
SequenceString:
RRICPFTGKK SNKANRVSHS NHKTKRLQFV NLQYKRVWWE AGKRFVKLRL STKALKTIEK NGLDAVAKKA GIDLRKE

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Macromolecule #18: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 12.903116 KDa
SequenceString:
KKEDELKELR TKTNEQLNEE ILQLKGELFM LRLQRSAREN FKPSDFGRMR KRVARMLTVK REREIEQGVG KRLSRKLDKA WKRSIVVRP PPSLKKLQEK ATAEAEAEKA

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Macromolecule #19: 50S ribosomal protein L2, chloroplastic

MacromoleculeName: 50S ribosomal protein L2, chloroplastic / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 29.722424 KDa
SequenceString: AIHLYKTSTS STRNGAVQVK SNPRNNLISG QRRCGKGRNA RGIITARHRG GGHKRLYRKI DFRRNEKDIY GKIVTIEYDP NRNAYICLI HYGDGEKRYI LHPRGAIIGD TIVSGTEVPI KMGNALPLTD MPLGTAIHNI EITLGRGGQL ARAAGAVAKL I AKEGKSAT ...String:
AIHLYKTSTS STRNGAVQVK SNPRNNLISG QRRCGKGRNA RGIITARHRG GGHKRLYRKI DFRRNEKDIY GKIVTIEYDP NRNAYICLI HYGDGEKRYI LHPRGAIIGD TIVSGTEVPI KMGNALPLTD MPLGTAIHNI EITLGRGGQL ARAAGAVAKL I AKEGKSAT LKLPSGEVRL ISKNCSATVG QVGNVGVNQK RLGRAGSKRW LGKRPVVRGV VMNPVDHPHG GGEGRAPIGR KS PTTPWGY PALGRRSRKR NKYSDNFIIR RRSK

+
Macromolecule #20: 50S ribosomal protein L32, chloroplastic

MacromoleculeName: 50S ribosomal protein L32, chloroplastic / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 6.519773 KDa
SequenceString:
AVPKKRTSIY KKRIRKNIWK KKGYWAALKA FSLAKSLSTG NSKSFFVRKI SNQTLE

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Macromolecule #21: 50S ribosomal protein L33, chloroplastic

MacromoleculeName: 50S ribosomal protein L33, chloroplastic / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 7.536926 KDa
SequenceString:
AKGKDVRVKV ILECTGCVRK SVNKGSRGVS RYITQKNRHN TPSRLELRKF CPYCYKHTIH GEIKK

+
Macromolecule #22: 50S ribosomal protein L34, chloroplastic

MacromoleculeName: 50S ribosomal protein L34, chloroplastic / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 6.692029 KDa
SequenceString:
GKAALCLTKR SRSRKSLART HGFRLRMSTT SGRALLKRRR AKGRKILCTK TNPSSGKRAS

+
Macromolecule #23: 50S ribosomal protein L35, chloroplastic

MacromoleculeName: 50S ribosomal protein L35, chloroplastic / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 8.459163 KDa
SequenceString:
AKGYKMKTHK ASAKRFRVTG KGKIVRRRAG KQHLLAKKNT KRKNRLSKLI QVDRSDYDNV IGALPYLKVN RKV

+
Macromolecule #24: 50S ribosomal protein L36, chloroplastic

MacromoleculeName: 50S ribosomal protein L36, chloroplastic / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 4.414462 KDa
SequenceString:
MKIRASVRPI CEKCRLIRRR GRIIVICSNP KHKQRQG

+
Macromolecule #25: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 24.117328 KDa
SequenceString: SVDAGIGVMG TKLGMMSFFE EDGTVVPVTV IGFKEGNIVT QVKTESTDGY NAVQVGYERL RDRKLTMPER GHLNKAGVIP MRHLQEFRL VSVDDFTPSQ KLLFEELFKE GDMVDISGTT IGKGFQGGIK RHNFKRGLMT HGSKSHRALG SIGAGTTPGH V YKGKKMPG ...String:
SVDAGIGVMG TKLGMMSFFE EDGTVVPVTV IGFKEGNIVT QVKTESTDGY NAVQVGYERL RDRKLTMPER GHLNKAGVIP MRHLQEFRL VSVDDFTPSQ KLLFEELFKE GDMVDISGTT IGKGFQGGIK RHNFKRGLMT HGSKSHRALG SIGAGTTPGH V YKGKKMPG RMGGTKTKIR KLKIMKIDTD LRVVMIKGAV PGKPGNLLRL APAKIVGKNI PKN

+
Macromolecule #26: 50S ribosomal protein L4, chloroplastic

MacromoleculeName: 50S ribosomal protein L4, chloroplastic / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 27.202697 KDa
SequenceString: ELIPLPILNF SGEKVGETFL NLKTAPPEKA RAVVHRGLIT HLQNKRRGTA STLTRAEVRG GGRKPYPQKK TGRARRGSQG SPLRPGGGV IFGPKPRDWT IKMNKKERRL ALSTAIASAV GNSFVVEEFA ENFEKPKTKD FIAAMQRWGL DPAEKSLFFL M DLVENVEK ...String:
ELIPLPILNF SGEKVGETFL NLKTAPPEKA RAVVHRGLIT HLQNKRRGTA STLTRAEVRG GGRKPYPQKK TGRARRGSQG SPLRPGGGV IFGPKPRDWT IKMNKKERRL ALSTAIASAV GNSFVVEEFA ENFEKPKTKD FIAAMQRWGL DPAEKSLFFL M DLVENVEK SGRNIRTLKL LTPRSLNLFD VLNAEKLVFT EGTIQYLNQR YGVDTLEDED EEEEEEEEGE EVDDGVEDGT PE PAE

+
Macromolecule #27: 50S ribosomal protein L5, chloroplastic

MacromoleculeName: 50S ribosomal protein L5, chloroplastic / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 24.248189 KDa
SequenceString: AAGTAVFVDK AEAETINRLK TNYIEKMVPL LKEEFSYSNI LEVPKVVKIV VNCGIGDASQ NAKGLDAAIN ELALITGQRP VKTKAKTSI AGFKVREGMT LGIAVTLRGN LMYSFLDRLI NLALPRTRDF QGVNPNSFDG HGNYSVGFRE QSVFPEIKPE I VGKARGMD ...String:
AAGTAVFVDK AEAETINRLK TNYIEKMVPL LKEEFSYSNI LEVPKVVKIV VNCGIGDASQ NAKGLDAAIN ELALITGQRP VKTKAKTSI AGFKVREGMT LGIAVTLRGN LMYSFLDRLI NLALPRTRDF QGVNPNSFDG HGNYSVGFRE QSVFPEIKPE I VGKARGMD VCITTTAKTD KEAYKLLSLM GMPFREGSGP STLVRKKKLK SHHFDAKKGR RY

+
Macromolecule #28: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 20.263604 KDa
SequenceString:
KESRIGKQPI TVPANVAIAM EGQDLKVKGP LGELSITYPR EVLVEKQESG FLRVRKAVET RRANQMHGLF RTLTDNMVVG VSKGFEKKL QLVGVGYRAT VEGKDLILSL GFSHPVRMAI PDELQVKVEE NTKVTVSGRD KSVVGQFAAT IRSWRPPEPY K GKGVRYVD EVVRRKEGKA GKKK

+
Macromolecule #29: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 17.669951 KDa
SequenceString:
QKKVKKIRKI ILKEDIPDLG KKGQLLDVRA GFLRNFLLPL GKAEVVTPLL LKEMKMEDER IEAEKKRVKE EAQQLARMFE TVGAFKVKR KGGKGKQIFG SVTAQDLVDI IKAQLQRDVD KKVVFLPDIR ETGEYIAELK LHPDVTAQVR VTVFAN

+
Macromolecule #30: 50S ribosomal protein 5 alpha, chloroplastic

MacromoleculeName: 50S ribosomal protein 5 alpha, chloroplastic / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 15.351212 KDa
SequenceString:
MALLSPLLSL SSVPPITSIA VSSSSFPIKL QNVSVALLPS FGQRLVAHGP VIAQKRGTVV AMVSAAAEET AGEDGDQSKV EEANISVQN LPLESKLQLK LEQKIKMKMA KKIRLRRTGL CAKESLRKRG AWPPSKMKKL KNV

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Macromolecule #31: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 10.801521 KDa
SequenceString:
RKSDIHPEFR EDAKVYCNGE LVMTTGGTQK DYTVEVWSGN HPFYLGNRSA LLLDADQVEK FRKKYGELTQ IMEIPVLKGE IILPPKKKS KAKKK

+
Macromolecule #32: 50S ribosomal protein 6, chloroplastic

MacromoleculeName: 50S ribosomal protein 6, chloroplastic / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 12.080688 KDa
SequenceString:
MSVSAIFGAR VVTIPSVLRT SSVDGRTVKL QPSTGGSCGG GVITIECSSR PQKKGTAHHM KTRPKKTARW DIKRGPAVYP PLPPLPAEW TIVSSAVDEA DSSSSTTSSS AEIAQSA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
Details: 20 mM Tris HCl, pH 7.6, 100 mM KCl, 10 mM MgOAc, 100 mM sucrose, 7 mM 2-mercaptoethanol, 1 unit/ml RNase inhibitor, 0.1% protease inhibitor
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.2 µm / Calibrated magnification: 109375 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 78000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-7 / Number grids imaged: 1 / Number real images: 1590 / Average electron dose: 26.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 338305
CTF correctionSoftware - Name: CTFFIND3
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationNumber classes: 200 / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final reconstructionNumber classes used: 20 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 174949

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