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- EMDB-6710: Structure of the 30S small subunit of chloroplast ribosome from s... -

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Basic information

Entry
Database: EMDB / ID: EMD-6710
TitleStructure of the 30S small subunit of chloroplast ribosome from spinach
Map data
Sample
  • Complex: 30S small subunit of chloroplast ribosome from spinach
    • Protein or peptide: x 25 types
    • RNA: x 1 types
KeywordsCryo-EM / ribosome / chloroplast ribosome
Function / homology
Function and homology information


plastid small ribosomal subunit / plastid translation / negative regulation of translational elongation / primary metabolic process / mitochondrial small ribosomal subunit / plastid / chloroplast stroma / ribosomal small subunit binding / chloroplast / ribosomal small subunit biogenesis ...plastid small ribosomal subunit / plastid translation / negative regulation of translational elongation / primary metabolic process / mitochondrial small ribosomal subunit / plastid / chloroplast stroma / ribosomal small subunit binding / chloroplast / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / mitochondrion / RNA binding
Similarity search - Function
Ribosomal protein PSRP-3/Ycf65 / PSRP-3/Ycf65 superfamily / Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) / 30S ribosomal protein S31, plant / Ribosomal protein S31e / Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosomal protein S1-like ...Ribosomal protein PSRP-3/Ycf65 / PSRP-3/Ycf65 superfamily / Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) / 30S ribosomal protein S31, plant / Ribosomal protein S31e / Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosomal protein S1-like / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / 30S ribosomal protein / S1 domain profile. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Ribosomal protein S21 superfamily / S1 domain / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / RNA-binding domain superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S2 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S14 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Type-2 KH domain profile. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13/S18 / Ribosomal protein S4/S9 / Ribosomal protein S19 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14p/S29e / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature.
Similarity search - Domain/homology
Ribosome-binding factor PSRP1, chloroplastic / Small ribosomal subunit protein cS22 / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein cS23 / Small ribosomal subunit protein bTHXc / Small ribosomal subunit protein uS17c / Small ribosomal subunit protein uS10c / Uncharacterized protein / Small ribosomal subunit protein uS11c / Small ribosomal subunit protein uS14c ...Ribosome-binding factor PSRP1, chloroplastic / Small ribosomal subunit protein cS22 / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein cS23 / Small ribosomal subunit protein bTHXc / Small ribosomal subunit protein uS17c / Small ribosomal subunit protein uS10c / Uncharacterized protein / Small ribosomal subunit protein uS11c / Small ribosomal subunit protein uS14c / Small ribosomal subunit protein uS19c / Small ribosomal subunit protein uS2c / Small ribosomal subunit protein uS3c / Small ribosomal subunit protein uS8c / Small ribosomal subunit protein uS4c / Ribosome-binding factor PSRP1, chloroplastic / Small ribosomal subunit protein bS16c / Small ribosomal subunit protein bS1c / Small ribosomal subunit protein bTHXc / Small ribosomal subunit protein uS12cz/uS12cy / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein uS7cz/uS7cy / 30S ribosomal protein S20, chloroplastic / Small ribosomal subunit protein uS17c / Small ribosomal subunit protein uS10c / Small ribosomal subunit protein uS13c / Small ribosomal subunit protein cS22 / Small ribosomal subunit protein uS9c / Small ribosomal subunit protein bS6c alpha / Small ribosomal subunit protein cS23 / Small ribosomal subunit protein uS15c / Small ribosomal subunit protein bS18c / Small ribosomal subunit protein uS5c
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsAhmed T / Shi J
Funding support Singapore, 1 items
OrganizationGrant numberCountry
MOEAcRF Tier 1, 2014-T1-001-019 (RG32/14) Singapore
CitationJournal: Nucleic Acids Res / Year: 2017
Title: Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation.
Authors: Tofayel Ahmed / Jian Shi / Shashi Bhushan /
Abstract: Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, ...Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, cS23, bTHXc, cL37 and cL38) which have been suggested to play important regulatory roles in translation. However, their exact locations on the chloroplast ribosome remain elusive due to lack of a high-resolution structure, hindering our progress to understand their possible roles. Here we present a cryo-EM structure of the 70S chloroplast ribosome from spinach resolved to 3.4 Å and focus our discussion mainly on the architecture of the 30S small subunit (SSU) which is resolved to 3.7 Å. cS22 localizes at the SSU foot where it seems to compensate for the deletions in 16S rRNA. The mRNA exit site is highly remodeled due to the presence of cS23 suggesting an alternative mode of translation initiation. bTHXc is positioned at the SSU head and appears to stabilize the intersubunit bridge B1b during thermal fluctuations. The translation factor plastid pY binds to the SSU on the intersubunit side and interacts with the conserved nucleotide bases involved in decoding. Most of the intersubunit bridges are conserved compared to the bacteria, except for a new bridge involving uL2c and bS6c.
History
DepositionMar 3, 2017-
Header (metadata) releaseJun 7, 2017-
Map releaseJun 7, 2017-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5x8r
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6710.png

Downloads & links

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Map

FileDownload / File: emd_6710.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.17213282 - 0.3157689
Average (Standard dev.)0.0006205938 (±0.008562695)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 403.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z403.200403.200403.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1720.3160.001

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Supplemental data

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Sample components

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Entire : 30S small subunit of chloroplast ribosome from spinach

EntireName: 30S small subunit of chloroplast ribosome from spinach
Components
  • Complex: 30S small subunit of chloroplast ribosome from spinach
    • Protein or peptide: 30S ribosomal protein S2, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S3, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S5, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S6 alpha, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S7, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S8, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S9, chloroplasticRibosome
    • Protein or peptide: protein S10
    • Protein or peptide: 30S ribosomal protein S11, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S12, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S13, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S15, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S16, chloroplasticRibosome
    • Protein or peptide: protein S17
    • Protein or peptide: 30S ribosomal protein S18, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S19 alpha, chloroplasticRibosome
    • Protein or peptide: protein S20
    • Protein or peptide: protein S21
    • Protein or peptide: protein plastid pY
    • RNA: 16S rRNA
    • Protein or peptide: protein cS23
    • Protein or peptide: 30S ribosomal protein S4, chloroplasticRibosome
    • Protein or peptide: protein cS22
    • Protein or peptide: 30S ribosomal protein S14, chloroplasticRibosome
    • Protein or peptide: protein bTHXc
    • Protein or peptide: 30S ribosomal protein S1, chloroplasticRibosome

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Supramolecule #1: 30S small subunit of chloroplast ribosome from spinach

SupramoleculeName: 30S small subunit of chloroplast ribosome from spinach
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#26
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 1.7 MDa

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Macromolecule #1: 30S ribosomal protein S2, chloroplastic

MacromoleculeName: 30S ribosomal protein S2, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 26.736141 KDa
SequenceString: MTRRYWNINL EEMMEAGVHF GHGTRKWNPR MSPYISAKCK GIHIINLTRT ARFLSEACDL VFDASSRGKQ FLIVGTKNKA ADSVARAAI RARCHYVNKK WLGGMLTNWS TTETRLHKFR DLRMEQTAGR LARLPKRDAA VVKRQLSHLQ TYLGGIKYMT G LPDIVIIV ...String:
MTRRYWNINL EEMMEAGVHF GHGTRKWNPR MSPYISAKCK GIHIINLTRT ARFLSEACDL VFDASSRGKQ FLIVGTKNKA ADSVARAAI RARCHYVNKK WLGGMLTNWS TTETRLHKFR DLRMEQTAGR LARLPKRDAA VVKRQLSHLQ TYLGGIKYMT G LPDIVIIV DQQEEYTALR ECITLGIPTI CLIDTNCNPD LADISIPAND DAIASIRLIL TKLVFAICEG RSSYIRNP

UniProtKB: Small ribosomal subunit protein uS2c

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Macromolecule #2: 30S ribosomal protein S3, chloroplastic

MacromoleculeName: 30S ribosomal protein S3, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 24.965156 KDa
SequenceString: MGQKINPLGF RLGTTQSHYS LWFSQPKNYA EGLQEDQKIR DCIKNYVQKN TKTSSGVEGI ARIEIQKRID LIQVIIHMGF PKLLIENRP QGVEDLKINV QKELNCVNRK LNIAITRIAK PYGDPNILAE FIAGQLKSRV SFRKAMKKAI ELTEQADTKG I QIQIAGRI ...String:
MGQKINPLGF RLGTTQSHYS LWFSQPKNYA EGLQEDQKIR DCIKNYVQKN TKTSSGVEGI ARIEIQKRID LIQVIIHMGF PKLLIENRP QGVEDLKINV QKELNCVNRK LNIAITRIAK PYGDPNILAE FIAGQLKSRV SFRKAMKKAI ELTEQADTKG I QIQIAGRI DGKEIARIEW IREGRVPLQT IRAKIDYCAY TVRTIYGVLG IKIWIFMGEE

UniProtKB: Small ribosomal subunit protein uS3c

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Macromolecule #3: 30S ribosomal protein S5, chloroplastic

MacromoleculeName: 30S ribosomal protein S5, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 27.69658 KDa
SequenceString: CIKKDDIDIT FFEQDNPDEE ITFDPPEKPE GYIPPRAVDE PPFESEEEIA LAYEELYGAA YSGESLLGND VYAMDSKIKK ATGFGSKSK KEKIRDGFEE NVVQVRRVTK VVKGGKHMRF RAIVVVGDKK GQVGVGVGKA KEVVSAVQKA AVDARRNIIT V PMTKYLTF ...String:
CIKKDDIDIT FFEQDNPDEE ITFDPPEKPE GYIPPRAVDE PPFESEEEIA LAYEELYGAA YSGESLLGND VYAMDSKIKK ATGFGSKSK KEKIRDGFEE NVVQVRRVTK VVKGGKHMRF RAIVVVGDKK GQVGVGVGKA KEVVSAVQKA AVDARRNIIT V PMTKYLTF PHRNEADYGA ARVMLRPAAP GTGVIAGGAV RTVLEMAGVE NALGKQLGSN NALNNARATI VAVQTMRQFS DV ARDRGIP MEELWK

UniProtKB: Small ribosomal subunit protein uS5c

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Macromolecule #4: 30S ribosomal protein S6 alpha, chloroplastic

MacromoleculeName: 30S ribosomal protein S6 alpha, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 16.341423 KDa
SequenceString:
DFSGSFFEGG FGGLDEDPPS TPPAGLAVEE KPEPQCPPGL RQYETMAVLR PDMTEDERLT LTQKYEELLV AGGAMYVEVF NRGVIPLAY SIKRKNKAGE TNNYLDGIYL LFTYFTKPES ISPLEAALVT DDDVIRSSSF KIRKRKY

UniProtKB: Small ribosomal subunit protein bS6c alpha

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Macromolecule #5: 30S ribosomal protein S7, chloroplastic

MacromoleculeName: 30S ribosomal protein S7, chloroplastic / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 17.378309 KDa
SequenceString:
MSRRGTVEEK TAKSDPIYRN RLVNMLVNRI LKHGKKSLAY QILYRAVKKI QQKTETNPLS VLRQAIRGVT PDIAVKARRV GGSTHQVPI EIGSTQGKAL AIRWLLGAAR KRPGRNMAFK LSSELVDAAK GSGDAVRKKE ETHRMAEANR AFAHFR

UniProtKB: Small ribosomal subunit protein uS7cz/uS7cy

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Macromolecule #6: 30S ribosomal protein S8, chloroplastic

MacromoleculeName: 30S ribosomal protein S8, chloroplastic / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 15.527256 KDa
SequenceString:
MGKDTIADII TCIRNADMNR KGTVRIVSTN ITENIVKILL REGFIENARK HQERNKYFLV LTLRHRRNKK GPYLNTFHLK RVSRPGLRI YSNYQRIPRI LGGMGIAILS TSRGIMTDRE ARLEGIGGEI LCYIW

UniProtKB: Small ribosomal subunit protein uS8c

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Macromolecule #7: 30S ribosomal protein S9, chloroplastic

MacromoleculeName: 30S ribosomal protein S9, chloroplastic / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 17.092791 KDa
SequenceString:
TSATAPVEVA ETADLEKFVK SRLPGGFAAQ TVIGTGRRKC AIARVVLQEG TGKFIINYRD AKEYLQGNPL WLQYVKTPLA TLGYETNYD VFVKAHGGGL SGQAQAISLG VARALLKVSA SHRAPLKQEG LLTRDSRIVE RKKPGLKKAR KAPQFSKR

UniProtKB: Small ribosomal subunit protein uS9c

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Macromolecule #8: protein S10

MacromoleculeName: protein S10 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 13.882167 KDa
SequenceString:
SFEDGSETSK ISIAADSDQM APKQKIRIKL RSYWVPLIED SCKQIMDAAR TTNAKIMGPV PLPTKKRIYC VLKSPHVHKD ARFHFEIRT HQRLIDILYP TAQTIDSLMQ LDLPAGVDVE VKL

UniProtKB: Small ribosomal subunit protein uS10c

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Macromolecule #9: 30S ribosomal protein S11, chloroplastic

MacromoleculeName: 30S ribosomal protein S11, chloroplastic / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 14.927551 KDa
SequenceString:
MAKPIPKIGS RRNGRISSRK SARKIPKGVI HVQASFNNTI VTVTDVRGRV VSWASAGTCG FRGTKRGTPF AAQTAAGNAI RTVVEQGMQ RAEVMIKGPG LGRDAALRAI RRSGILLSFV RDVTPMPHNG CRPPKKRRV

UniProtKB: Small ribosomal subunit protein uS11c

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Macromolecule #10: 30S ribosomal protein S12, chloroplastic

MacromoleculeName: 30S ribosomal protein S12, chloroplastic / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 13.794261 KDa
SequenceString:
MPTIKQLIRN TRQPIRNVTK SPALRGCPQR RGTCTRVYTI TPKKPNSALR KVARVRLTSG FEITAYIPGI GHNLQEHSVV LVRGGRVKD LPGVRYHIVR GTLDAVGVKD RQQGRSKYGV KKPK

UniProtKB: Small ribosomal subunit protein uS12cz/uS12cy

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Macromolecule #11: 30S ribosomal protein S13, chloroplastic

MacromoleculeName: 30S ribosomal protein S13, chloroplastic / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 14.418822 KDa
SequenceString:
ARGRSSSVSF PAPKKGGIGH GGLQIECIRI GGVEIPNHKR VEYSLQYIHG IGRSRSRQIL LDLNFDNKVT KDLSEEEVII LRKEKRFNR VAIERLKEIR CYRGIRHKLG LPVRGQRTKN NCRTLKG

UniProtKB: Small ribosomal subunit protein uS13c

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Macromolecule #12: 30S ribosomal protein S15, chloroplastic

MacromoleculeName: 30S ribosomal protein S15, chloroplastic / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 10.778763 KDa
SequenceString:
MKKNSFISVI SDEKKEENKG SVEFQVFCFT NKIRRLTLHL ELHKKDYSSQ RGLRKTLGKR QRLLAYLLKI NGVRYKELIS KLNIRELKT R

UniProtKB: Small ribosomal subunit protein uS15c

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Macromolecule #13: 30S ribosomal protein S16, chloroplastic

MacromoleculeName: 30S ribosomal protein S16, chloroplastic / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 10.454237 KDa
SequenceString:
MVKLRLKRCG RKQRAVYRIV AIDVRSRREG RDLQKVGFYD PIKSQTYLNV PAILDFLEKG AQPTETVYDI LKRAEVFKEF RLNQTKFN

UniProtKB: Small ribosomal subunit protein bS16c

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Macromolecule #14: protein S17

MacromoleculeName: protein S17 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 12.195099 KDa
SequenceString:
MRSMQGKVIC ATNDKTVNVE VVRLAPHPKY KRRVRKKKKY QAHDPDNQFK VGDWVQLDKC RPISKTKTFL AVAPEGRQSS ATRPKPIQA ASDELGIPLE SQVEGDKTV

UniProtKB: Small ribosomal subunit protein uS17c

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Macromolecule #15: 30S ribosomal protein S18, chloroplastic

MacromoleculeName: 30S ribosomal protein S18, chloroplastic / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 12.079137 KDa
SequenceString:
MDKSKRPFIK SKRSFRRRLP PIQSGDRIDY RNMSLISRFI SEQGKILSRR VNRLTLKQQR LITSAIKQAR ILSLLPFLNN EKQFERTES TTRTANFRTK NK

UniProtKB: Small ribosomal subunit protein bS18c

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Macromolecule #16: 30S ribosomal protein S19 alpha, chloroplastic

MacromoleculeName: 30S ribosomal protein S19 alpha, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 10.6325 KDa
SequenceString:
MTRSLKKNPF VANHLLRKIE KLNKKAEKEI IVTWSRASTI IPTMIGHTIA IHNGREHLPI YITDRMVGHK LGEFAPTLNF RGHAKNDNK SRR

UniProtKB: Small ribosomal subunit protein uS19c

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Macromolecule #17: protein S20

MacromoleculeName: protein S20 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 12.17809 KDa
SequenceString:
ADSAAKRTRQ AETRRLRNKA RKSEVKTRMR KVFEALDALK KKSGASTEEL VPIDNLIAEA YSAIDKAVVK GTLHRNTAAR RKSRLARNK KVVEIHHGWY TPSLAPTNV

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Macromolecule #18: protein S21

MacromoleculeName: protein S21 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 16.096171 KDa
SequenceString:
ISSKKHENAA IAKKEEYPGD LMAVVCPSLA FSNTLYFRSA YNVQVLVDDN ENEERLLNRF RREVMRAGVI QECKRRRYFE NKQEEKKRK HREAAKRNSR RRRGPFRGPF PGKEEATKVD KKEDDGDNWD MPEGGAPF

UniProtKB: Small ribosomal subunit protein bS21c

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Macromolecule #19: protein plastid pY

MacromoleculeName: protein plastid pY / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 26.85133 KDa
SequenceString: SWDGPLSSVK LILQGRNLEV SDNVRSHVED KVGKSVAKHS HLVREVDVRL SARGGDLSKG PKLRRCEVTL FTKRHGVIRA EEDAESLYS SIDLVSSIIQ RKLRKIKDKV SDHGRHMKGF NRSKVRDPEP VRITREEVLE EVESAPAPVS VEDDDFIEEV V RTKYFDMP ...String:
SWDGPLSSVK LILQGRNLEV SDNVRSHVED KVGKSVAKHS HLVREVDVRL SARGGDLSKG PKLRRCEVTL FTKRHGVIRA EEDAESLYS SIDLVSSIIQ RKLRKIKDKV SDHGRHMKGF NRSKVRDPEP VRITREEVLE EVESAPAPVS VEDDDFIEEV V RTKYFDMP PLTITEAVEQ LENVDHDFYA FRNEETGDIN ILYKRKEGGY GLIIPKDGKT EKLESLPVQT DKQPSFAE

UniProtKB: Ribosome-binding factor PSRP1, chloroplastic

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Macromolecule #21: protein cS23

MacromoleculeName: protein cS23 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 13.808066 KDa
SequenceString:
VAPETISDVA IMGNEVDIDD DLLVNKEKLK VLVKPMDKPR LVLKFIWMEK NIGLALDQTI PGHGTVPLSP YYFWPRKDAW EELKVLLEN KPWISQKQMI ILLNQATDII NLWQQSGGNL AS

UniProtKB: Small ribosomal subunit protein cS23

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Macromolecule #22: 30S ribosomal protein S4, chloroplastic

MacromoleculeName: 30S ribosomal protein S4, chloroplastic / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 23.454531 KDa
SequenceString: MSRYRGPRFK KIRRLGALPG LTNKRPRAGS DLRNQSRSGK RSQYRIRLEE KQKLRFHYGI TERQLLKYVR IARKAKGSTG QVLLQLLEM RLDNILFRLG MAPTIPGARQ LVNHRHILVN GRIVDIPSYR CKPQDTIMAR DEQKSIALIQ NSLDLSPREE L PKHLTLNP ...String:
MSRYRGPRFK KIRRLGALPG LTNKRPRAGS DLRNQSRSGK RSQYRIRLEE KQKLRFHYGI TERQLLKYVR IARKAKGSTG QVLLQLLEM RLDNILFRLG MAPTIPGARQ LVNHRHILVN GRIVDIPSYR CKPQDTIMAR DEQKSIALIQ NSLDLSPREE L PKHLTLNP FPYKGLVNQI IDSKWVGLKI NELLVVEYYS RQT

UniProtKB: Small ribosomal subunit protein uS4c

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Macromolecule #23: protein cS22

MacromoleculeName: protein cS22 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 21.691145 KDa
SequenceString: VVTEETSSSS TASSSSDGEG ARRLYVGNIP RNLNNDELRT IVEEHGAIEI AEVMYDKYSG RSRRFGFVTM KTVEDANAVI EKLNDTEIG GRKIKVNITE KPLEGMDIAT TQAEDSQFVE SPYKVYIGNL AKTVTNELLK DFFSEKGKVL GAKVQRTPGT S KSNGFGFV ...String:
VVTEETSSSS TASSSSDGEG ARRLYVGNIP RNLNNDELRT IVEEHGAIEI AEVMYDKYSG RSRRFGFVTM KTVEDANAVI EKLNDTEIG GRKIKVNITE KPLEGMDIAT TQAEDSQFVE SPYKVYIGNL AKTVTNELLK DFFSEKGKVL GAKVQRTPGT S KSNGFGFV SFSSEEEVEA AIQALNNSVL EGQKIRVNKA

UniProtKB: Small ribosomal subunit protein cS22

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Macromolecule #24: 30S ribosomal protein S14, chloroplastic

MacromoleculeName: 30S ribosomal protein S14, chloroplastic / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 11.809832 KDa
SequenceString:
MARKSLIQRE KKRRNLEQKY HLIRRSSKQE IRKVTSLSDK WEIHGKLQSP PRNSAPARLH RRCFLTGRPR ANIRDFGLSG HILREMVHT CLLPGATRSS W

UniProtKB: Small ribosomal subunit protein uS14c

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Macromolecule #25: protein bTHXc

MacromoleculeName: protein bTHXc / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 5.188887 KDa
SequenceString:
GRGDRKTAKG KRFNHSFGNA RPKNKNKGRG PPKAPIFPKG DPSQKED

UniProtKB: Small ribosomal subunit protein bTHXc

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Macromolecule #26: 30S ribosomal protein S1, chloroplastic

MacromoleculeName: 30S ribosomal protein S1, chloroplastic / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 40.472961 KDa
SequenceString: AVAVSNAQTR ERQKLKQLFE DAYERCRNAP MEGVSFTIDD FHTALDKYDF NSEMGSRVKG TVFCTDANGA LVDITAKSSA YLPLAEACI YRIKNVEEAG IIPGVREEFV IIGENEADDS LILSLRQIQY ELAWERCRQL QAEDVVVKGK IVGANKGGVV A LVEGLRGF ...String:
AVAVSNAQTR ERQKLKQLFE DAYERCRNAP MEGVSFTIDD FHTALDKYDF NSEMGSRVKG TVFCTDANGA LVDITAKSSA YLPLAEACI YRIKNVEEAG IIPGVREEFV IIGENEADDS LILSLRQIQY ELAWERCRQL QAEDVVVKGK IVGANKGGVV A LVEGLRGF VPFSQISSKS SAEELLEKEI PLKFVEVDEE QSRLVMSNRK AMADSQAQLG IGSVVTGTVQ SLKPYGAFID IG GINGLLH VSQISHDRVS DIATVLQPGD TLKVMILSHD RERGRVSLST KKLEPTPGDM IRNPKLVFEK AEEMAQTFRQ RIA QAEAMA RADMLRFQPE SGLTLSSDGI LGPLTSDLPA EGLDLSVVPP AVES

UniProtKB: Small ribosomal subunit protein bS1c

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Macromolecule #20: 16S rRNA

MacromoleculeName: 16S rRNA / type: rna / ID: 20 / Number of copies: 1
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 483.4665 KDa
SequenceString: UCUCAUGGAG AGUUCGAUCC UGGCUCAGGA UGAACGCUGG CGGCAUGCUU AACACAUGCA AGUCGGACGG GAAGUGGUGU UUCCAGUGG CGGACGGGUG AGUAACGCGU AAGAACCUGC CCUUGGGAGG GGAACAACAG CUGGAAACGG CUGCUAAUAC C CCGUAGGC ...String:
UCUCAUGGAG AGUUCGAUCC UGGCUCAGGA UGAACGCUGG CGGCAUGCUU AACACAUGCA AGUCGGACGG GAAGUGGUGU UUCCAGUGG CGGACGGGUG AGUAACGCGU AAGAACCUGC CCUUGGGAGG GGAACAACAG CUGGAAACGG CUGCUAAUAC C CCGUAGGC UGAGAAGCAA AAGGAGGAAU CCGCCCGAGG AGGGGCUCGC GUCUGAUUAG CUAGUUGGUG AGGUAAUAGC UU ACCAAGG CGAUGAUCAG UAGCUGGUCC GAGAGGAUGA UCAGCCACAC UGGGACUGAG ACACGGCCCA GACUCCUACG GGA GGCAGC AGUGGGGAAU UUUCCGCAAU GGGCGAAAGC CUGACGGAGC AAUGCCGCGU GGAGGCAGAA GGCCCACGGG UCGU GAACU UCUUUUCCCG GAGAAGAAGC AAUGACGGUA UCCGGGGAAU AAGCAUCGGC UAACUCUGUG CCAGCAGCCG CGGUA AGAC AGAGGAUGCA AGCGUUAUCC GGAAUGAUUG GGCGUAAAGC GUCUGUAGGU GGCUUUUUAA GUCCGCCGUC AAAUCC CAG GGCUCAACCC UGGACAGGCG GUGGAAACUA CCAAGCUGGA GUACGGUAGG GGCAGAGGGA AUUUCCGGUG GAGCGGU GA AAUGCGUAGA GAUCGGAAAG AACACCAACG GCGAAAGCAC UCUGCUGGGC CGACACUGAC ACUGAGAGAC GAAAGCUA G GGGAGCGAAU GGGAUUAGAU ACCCCAGUAG UCCUAGCCGU AAACGAUGGA UACUAGGCGC UGUGCGUAUC GACCCGUGC AGUGUUGUAG CUAACGCGUU AAGUAUCCCG CCUGGGGAGU ACGUUCGCAA GAAUGAAACU CAAAGGAAUU GACGGGGGCC CGCACAAGC GGUGGAGCAU GUGGUUUAAU UCGAUGCAAA GCGAAGAACC UUACCAGGGC UUGACAUGCC GCGAAUCCUC U UGAAAGAG AGGGGUGCCU UCGGGAACGC GGACACAGGU GGUGCAUGGC UGUCGUCAGC UCGUGCCGUA AGGUGUUGGG UU AAGUCCC GCAACGAGCG CAACCCUCGU GUUUAGUUGC CAACGUUGAG UUUGGAACCC UGAACAGACU GCCGGUGAUA AGC CGGAGG AAGGUGAGGA UGACGUCAAG UCAUCAUGCC CCUUAUGCCC UGGGCGACAC ACGUGCUACA AUGGCCGGGA CAAA GGGUC GCGAUCCCGC GAGGGUGAGC UAACCCCAAA AACCCGUCCU CAGUUCGGAU UGCAGGCUGC AACUCGCCUG CAUGA AGCC GGAAUCGCUA GUAAUCGCCG GUCAGCCAUA CGGCGGUGAA UUCGUUCCCG GGCCUUGUAC ACACCGCCCG UCACAC UAU GGGAGCUGGC CAUGCCCGAA GUCGUUACCU UAACCGCAAG GAGGGGGAUG CCGAAGGCAG GGCUAGUGAC UGGAGUG AA GUCGUAACAA GGUAGCCGUA CUGGAAGGUG CGGCUGGAUC ACCUCCUUU

GENBANK: GENBANK: AJ400848.1

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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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.7 µm / Calibrated defocus min: 0.4 µm / Calibrated magnification: 133333 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.7 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 75000
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 - Frames/image: 1-25 / Number grids imaged: 1 / Number real images: 3161 / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 187946
Startup modelType of model: EMDB MAP
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 81305

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