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- EMDB-3532: Cryo-EM reconstruction of the small subunit of the chloroplast ri... -

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Basic information

Entry
Database: EMDB / ID: EMD-3532
TitleCryo-EM reconstruction of the small subunit of the chloroplast ribosome
Map dataCryo-EM reconstruction of the 30S small subunit of the chloroplast ribosome
Sample
  • Complex: Chloroplast 70S ribosome
    • Protein or peptide: x 26 types
    • RNA: x 1 types
  • Ligand: x 1 types
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 / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / small ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / mitochondrion / RNA binding
Similarity search - Function
Ribosomal protein PSRP-3/Ycf65 / PSRP-3/Ycf65 superfamily / Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) / 30S ribosomal protein S31, plant / Ribosomal protein S31e / Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosome hibernation promoting factor/RaiA ...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 / 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 / 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 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. / L28p-like / 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 S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / Type-2 KH domain profile. / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S2, conserved site / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / S5 double stranded RNA-binding domain profile. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 N-terminal domain
Similarity search - Domain/homology
Small ribosomal subunit protein uS13c / Small ribosomal subunit protein bS6c alpha / Large ribosomal subunit protein bL31c / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein uS17c / Small ribosomal subunit protein uS10c / Small ribosomal subunit protein uS9c / Small ribosomal subunit protein uS11c / Small ribosomal subunit protein uS14c / Small ribosomal subunit protein uS19c ...Small ribosomal subunit protein uS13c / Small ribosomal subunit protein bS6c alpha / Large ribosomal subunit protein bL31c / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein uS17c / Small ribosomal subunit protein uS10c / Small ribosomal subunit protein uS9c / 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 bTHXc / Small ribosomal subunit protein uS12cz/uS12cy / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein uS7cz/uS7cy / Small ribosomal subunit protein uS17c / Small ribosomal subunit protein uS10c / Small ribosomal subunit protein uS13c / Large ribosomal subunit protein bL31c / 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) / Spinach (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBieri P / Leibundgut M / Saurer M / Boehringer D / Ban N
CitationJournal: EMBO J / Year: 2017
Title: The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.
Authors: Philipp Bieri / Marc Leibundgut / Martin Saurer / Daniel Boehringer / Nenad Ban /
Abstract: Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, ...Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid-specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light- and temperature-dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A-site and P-site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non-rotated state, in which the intersubunit bridges to the large subunit are stabilized.
History
DepositionDec 10, 2016-
Header (metadata) releaseJan 11, 2017-
Map releaseJan 11, 2017-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5mmj
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3532.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of the 30S small subunit of the chloroplast ribosome
Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.10384296 - 0.34530732
Average (Standard dev.)0.0009308014 (±0.010387902)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 444.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z444.800444.800444.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1040.3450.001

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Supplemental data

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Sample components

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Entire : Chloroplast 70S ribosome

EntireName: Chloroplast 70S ribosome
Components
  • Complex: Chloroplast 70S ribosome
    • Protein or peptide: 50S ribosomal protein L31
    • Protein or peptide: plastid ribosomal protein bS1c
    • RNA: 16S ribosomal RNA
    • Protein or peptide: 30S ribosomal protein S2, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S3, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S4, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S5, chloroplasticRibosome
    • Protein or peptide: plastid ribosomal protein bS6c
    • Protein or peptide: 30S ribosomal protein S7, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S8, chloroplasticRibosome
    • Protein or peptide: plastid ribosomal protein uS9c
    • Protein or peptide: plastid ribosomal protein uS10c
    • Protein or peptide: 30S ribosomal protein S11, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S12, chloroplasticRibosome
    • Protein or peptide: plastid ribosomal protein uS13c
    • Protein or peptide: 30S ribosomal protein S14, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S15, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S16, chloroplasticRibosome
    • Protein or peptide: plastid ribosomal protein uS17c
    • Protein or peptide: 30S ribosomal protein S18, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S19 alpha, chloroplasticRibosome
    • Protein or peptide: plastid ribosomal protein bS20c
    • Protein or peptide: plastid ribosomal protein bS21c
    • Protein or peptide: 30S ribosomal protein 2, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein 3, chloroplasticRibosome
    • Protein or peptide: 30S ribosomal protein S31, chloroplasticRibosome
    • Protein or peptide: Ribosome-binding factor PSRP1, chloroplastic
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Chloroplast 70S ribosome

SupramoleculeName: Chloroplast 70S ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#27
Source (natural)Organism: Spinacia oleracea (spinach) / Tissue: leaf / Organelle: chloroplast
Molecular weightTheoretical: 2.4 MDa

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Macromolecule #1: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 14.748201 KDa
SequenceString:
MVLTLSNQFL AKIPATPKTL TLPKTSSSTL RPQWSCRKSD IHPEFREDAK VYCNGELVMT TGGTQKDYTV EVWSGNHPFY LGNRSALLL DADQVEKFRK KYGELTQIME IPVLKGEIIL PPKKKSKAKK K

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Macromolecule #2: plastid ribosomal protein bS1c

MacromoleculeName: plastid ribosomal protein bS1c / type: protein_or_peptide / ID: 2
Details: Residues were built as poly-alanine and deposited as UNK.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 14.826253 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

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Macromolecule #4: 30S ribosomal protein S2, chloroplastic

MacromoleculeName: 30S ribosomal protein S2, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (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

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Macromolecule #5: 30S ribosomal protein S3, chloroplastic

MacromoleculeName: 30S ribosomal protein S3, chloroplastic / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (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

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Macromolecule #6: 30S ribosomal protein S4, chloroplastic

MacromoleculeName: 30S ribosomal protein S4, chloroplastic / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (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

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Macromolecule #7: 30S ribosomal protein S5, chloroplastic

MacromoleculeName: 30S ribosomal protein S5, chloroplastic / type: protein_or_peptide / ID: 7
Details: Residues 122-150 were built as poly-alanine and deposited as UNK.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 33.626363 KDa
SequenceString: MATTATTTPS ATSLTTLHRR IPLFPTTTTL LSLSSSSKPL FLSLSSTRSF PTHLYCIKKD DIDITFFEQD NPDEEITFDP PEKPEGYIP PRAVDEPPFE SEEEIALAYE ELYGAAYSGE SLLGNDVYAM DSKIKKATGF GSKSKKEKIR DGFEENVVQV R RVTKVVKG ...String:
MATTATTTPS ATSLTTLHRR IPLFPTTTTL LSLSSSSKPL FLSLSSTRSF PTHLYCIKKD DIDITFFEQD NPDEEITFDP PEKPEGYIP PRAVDEPPFE SEEEIALAYE ELYGAAYSGE SLLGNDVYAM DSKIKKATGF GSKSKKEKIR DGFEENVVQV R RVTKVVKG GKHMRFRAIV VVGDKKGQVG VGVGKAKEVV SAVQKAAVDA RRNIITVPMT KYLTFPHRNE ADYGAARVML RP AAPGTGV IAGGAVRTVL EMAGVENALG KQLGSNNALN NARATIVAVQ TMRQFSDVAR DRGIPMEELW K

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Macromolecule #8: plastid ribosomal protein bS6c

MacromoleculeName: plastid ribosomal protein bS6c / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 23.510664 KDa
SequenceString: MATFSLTSTL PSSSPTTSLH SIPKPKLKPS TINFTHNLNP FNPNLKPSRH HYLSNYGPYV KAIALDFSGS FFEGGFGGLD EDPPSTPPA GLAVEEKPEP QCPPGLRQYE TMAVLRPDMT EDERLTLTQK YEELLVAGGA MYVEVFNRGV IPLAYSIKRK N KAGETNNY ...String:
MATFSLTSTL PSSSPTTSLH SIPKPKLKPS TINFTHNLNP FNPNLKPSRH HYLSNYGPYV KAIALDFSGS FFEGGFGGLD EDPPSTPPA GLAVEEKPEP QCPPGLRQYE TMAVLRPDMT EDERLTLTQK YEELLVAGGA MYVEVFNRGV IPLAYSIKRK N KAGETNNY LDGIYLLFTY FTKPESISPL EAALVTDDDV IRSSSFKIRK RKY

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Macromolecule #9: 30S ribosomal protein S7, chloroplastic

MacromoleculeName: 30S ribosomal protein S7, chloroplastic / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 17.378309 KDa
SequenceString:
MSRRGTVEEK TAKSDPIYRN RLVNMLVNRI LKHGKKSLAY QILYRAVKKI QQKTETNPLS VLRQAIRGVT PDIAVKARRV GGSTHQVPI EIGSTQGKAL AIRWLLGAAR KRPGRNMAFK LSSELVDAAK GSGDAVRKKE ETHRMAEANR AFAHFR

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Macromolecule #10: 30S ribosomal protein S8, chloroplastic

MacromoleculeName: 30S ribosomal protein S8, chloroplastic / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 15.527256 KDa
SequenceString:
MGKDTIADII TCIRNADMNR KGTVRIVSTN ITENIVKILL REGFIENARK HQERNKYFLV LTLRHRRNKK GPYLNTFHLK RVSRPGLRI YSNYQRIPRI LGGMGIAILS TSRGIMTDRE ARLEGIGGEI LCYIW

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Macromolecule #11: plastid ribosomal protein uS9c

MacromoleculeName: plastid ribosomal protein uS9c / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 22.415057 KDa
SequenceString: MAVSISSLTS SFASLSFTSN LTPKPQTLPM ARTKPFSLSN PAVVKPLVIT ATSATAPVEV AETADLEKFV KSRLPGGFAA QTVIGTGRR KCAIARVVLQ EGTGKFIINY RDAKEYLQGN PLWLQYVKTP LATLGYETNY DVFVKAHGGG LSGQAQAISL G VARALLKV ...String:
MAVSISSLTS SFASLSFTSN LTPKPQTLPM ARTKPFSLSN PAVVKPLVIT ATSATAPVEV AETADLEKFV KSRLPGGFAA QTVIGTGRR KCAIARVVLQ EGTGKFIINY RDAKEYLQGN PLWLQYVKTP LATLGYETNY DVFVKAHGGG LSGQAQAISL G VARALLKV SASHRAPLKQ EGLLTRDSRI VERKKPGLKK ARKAPQFSKR

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Macromolecule #12: plastid ribosomal protein uS10c

MacromoleculeName: plastid ribosomal protein uS10c / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 21.440539 KDa
SequenceString: MATSSISAAL LSPLTLRNAS SSSTKQDFST LSSLNLRRTL TPTLQSGHTL SNSSNFATFA APGALEVLET SPDSFEDGSE TSKISIAAD SDQMAPKQKI RIKLRSYWVP LIEDSCKQIM DAARTTNAKI MGPVPLPTKK RIYCVLKSPH VHKDARFHFE I RTHQRLID ...String:
MATSSISAAL LSPLTLRNAS SSSTKQDFST LSSLNLRRTL TPTLQSGHTL SNSSNFATFA APGALEVLET SPDSFEDGSE TSKISIAAD SDQMAPKQKI RIKLRSYWVP LIEDSCKQIM DAARTTNAKI MGPVPLPTKK RIYCVLKSPH VHKDARFHFE I RTHQRLID ILYPTAQTID SLMQLDLPAG VDVEVKL

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Macromolecule #13: 30S ribosomal protein S11, chloroplastic

MacromoleculeName: 30S ribosomal protein S11, chloroplastic / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 14.927551 KDa
SequenceString:
MAKPIPKIGS RRNGRISSRK SARKIPKGVI HVQASFNNTI VTVTDVRGRV VSWASAGTCG FRGTKRGTPF AAQTAAGNAI RTVVEQGMQ RAEVMIKGPG LGRDAALRAI RRSGILLSFV RDVTPMPHNG CRPPKKRRV

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Macromolecule #14: 30S ribosomal protein S12, chloroplastic

MacromoleculeName: 30S ribosomal protein S12, chloroplastic / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 13.794261 KDa
SequenceString:
MPTIKQLIRN TRQPIRNVTK SPALRGCPQR RGTCTRVYTI TPKKPNSALR KVARVRLTSG FEITAYIPGI GHNLQEHSVV LVRGGRVKD LPGVRYHIVR GTLDAVGVKD RQQGRSKYGV KKPK

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Macromolecule #15: plastid ribosomal protein uS13c

MacromoleculeName: plastid ribosomal protein uS13c / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 19.310641 KDa
SequenceString:
MAHTLATPVA PSVSLICNTK LSVSLSSSSL AFRPVNPKNG GGLSIKCVRV GNVEIPNNKR VEYSLQYIHG IGRSRARQIL CDLTLENKL TKELSEDELL QVRDEVTKYM IEGDLRRFNA IAIRRLKEIQ CYRGVRHIQG LPCRGQRTKN NCRTLKRGKR V QIAGKKKP PGPK

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Macromolecule #16: 30S ribosomal protein S14, chloroplastic

MacromoleculeName: 30S ribosomal protein S14, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 11.809832 KDa
SequenceString:
MARKSLIQRE KKRRNLEQKY HLIRRSSKQE IRKVTSLSDK WEIHGKLQSP PRNSAPARLH RRCFLTGRPR ANIRDFGLSG HILREMVHT CLLPGATRSS W

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Macromolecule #17: 30S ribosomal protein S15, chloroplastic

MacromoleculeName: 30S ribosomal protein S15, chloroplastic / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 10.778763 KDa
SequenceString:
MKKNSFISVI SDEKKEENKG SVEFQVFCFT NKIRRLTLHL ELHKKDYSSQ RGLRKTLGKR QRLLAYLLKI NGVRYKELIS KLNIRELKT R

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Macromolecule #18: 30S ribosomal protein S16, chloroplastic

MacromoleculeName: 30S ribosomal protein S16, chloroplastic / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 10.454237 KDa
SequenceString:
MVKLRLKRCG RKQRAVYRIV AIDVRSRREG RDLQKVGFYD PIKSQTYLNV PAILDFLEKG AQPTETVYDI LKRAEVFKEF RLNQTKFN

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Macromolecule #19: plastid ribosomal protein uS17c

MacromoleculeName: plastid ribosomal protein uS17c / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 18.151936 KDa
SequenceString:
MSLSFSLLKP PLSSSNPNPF LHGTTTKLSL LPSFSALSLS SSPPSSSTTY TFPVIKAMRS MQGKVICATN DKTVNVEVVR LAPHPKYKR RVRKKKKYQA HDPDNQFKVG DWVQLDKCRP ISKTKTFLAV APEGRQSSAT RPKPIQAASD ELGIPLESQV E GDKTV

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Macromolecule #20: 30S ribosomal protein S18, chloroplastic

MacromoleculeName: 30S ribosomal protein S18, chloroplastic / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 12.079137 KDa
SequenceString:
MDKSKRPFIK SKRSFRRRLP PIQSGDRIDY RNMSLISRFI SEQGKILSRR VNRLTLKQQR LITSAIKQAR ILSLLPFLNN EKQFERTES TTRTANFRTK NK

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Macromolecule #21: 30S ribosomal protein S19 alpha, chloroplastic

MacromoleculeName: 30S ribosomal protein S19 alpha, chloroplastic / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 10.6325 KDa
SequenceString:
MTRSLKKNPF VANHLLRKIE KLNKKAEKEI IVTWSRASTI IPTMIGHTIA IHNGREHLPI YITDRMVGHK LGEFAPTLNF RGHAKNDNK SRR

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Macromolecule #22: plastid ribosomal protein bS20c

MacromoleculeName: plastid ribosomal protein bS20c / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 20.147291 KDa
SequenceString:
MAAISMACVS SQCLSISSKL HNLSFSSTQF PNSSLKPLTF SANLSQPLFS QGCSSLGSFQ RRGFSVVCEV ATLKKADSAA KRTRQAETR RLRNKARKSE VKTRMRKVFE ALDALKKKSG ASTEELVPID NLIAEAYSAI DKAVVKGTLH RNTAARRKSR L ARNKKVVE IHHGWYTPSL APTNV

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Macromolecule #23: plastid ribosomal protein bS21c

MacromoleculeName: plastid ribosomal protein bS21c / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 20.61615 KDa
SequenceString:
MASTSSLLNF LSPLFPSNTS LPPSSNPKFP NPNSLSSQQN SISISSKKHE NAAIAKKEEY PGDLMAVVCP SLAFSNTLYF RSAYNVQVL VDDNENEERL LNRFRREVMR AGVIQECKRR RYFENKQEEK KRKHREAAKR NSRRRRGPFR GPFPGKEEAT K VDKKEDDG DNWDMPEGGA PF

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Macromolecule #24: 30S ribosomal protein 2, chloroplastic

MacromoleculeName: 30S ribosomal protein 2, chloroplastic / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 28.327863 KDa
SequenceString: MATISSILPC HGLLQHCSSS SSSSKPKFSS QNLVQLQSFS NGFGLKLKTR VSTNPPLLKV RAVVTEETSS SSTASSSSDG EGARRLYVG NIPRNLNNDE LRTIVEEHGA IEIAEVMYDK YSGRSRRFGF VTMKTVEDAN AVIEKLNDTE IGGRKIKVNI T EKPLEGMD ...String:
MATISSILPC HGLLQHCSSS SSSSKPKFSS QNLVQLQSFS NGFGLKLKTR VSTNPPLLKV RAVVTEETSS SSTASSSSDG EGARRLYVG NIPRNLNNDE LRTIVEEHGA IEIAEVMYDK YSGRSRRFGF VTMKTVEDAN AVIEKLNDTE IGGRKIKVNI T EKPLEGMD IATTQAEDSQ FVESPYKVYI GNLAKTVTNE LLKDFFSEKG KVLGAKVQRT PGTSKSNGFG FVSFSSEEEV EA AIQALNN SVLEGQKIRV NKA

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Macromolecule #25: 30S ribosomal protein 3, chloroplastic

MacromoleculeName: 30S ribosomal protein 3, chloroplastic / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 20.31275 KDa
SequenceString:
MLSMAVQPNI NAIAKPSIYQ SPKLSLKPFK TPAFANPKPF FSSPSFSQLK KKNNWSLFVA PETISDVAIM GNEVDIDDDL LVNKEKLKV LVKPMDKPRL VLKFIWMEKN IGLALDQTIP GHGTVPLSPY YFWPRKDAWE ELKVLLENKP WISQKQMIIL L NQATDIIN LWQQSGGNLA S

+
Macromolecule #26: 30S ribosomal protein S31, chloroplastic

MacromoleculeName: 30S ribosomal protein S31, chloroplastic / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 10.602076 KDa
SequenceString:
MASLLLGTPS MACHSVSFSF SHSQSVAGVS LSSPPTLSLS SSVSTSPALP LIYCGRGDRK TAKGKRFNHS FGNARPKNKN KGRGPPKAP IFPKGDPSQK ED

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Macromolecule #27: Ribosome-binding factor PSRP1, chloroplastic

MacromoleculeName: Ribosome-binding factor PSRP1, chloroplastic / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 33.799266 KDa
SequenceString: MATLCTSAIN MNPNLTNSLS NSINLSSTPT NLSSLRSTFT NSCSLGLNVA VKSVQISRNK PNVVCMSWDG PLSSVKLILQ GRNLEVSDN VRSHVEDKVG KSVAKHSHLV REVDVRLSAR GGDLSKGPKL RRCEVTLFTK RHGVIRAEED AESLYSSIDL V SSIIQRKL ...String:
MATLCTSAIN MNPNLTNSLS NSINLSSTPT NLSSLRSTFT NSCSLGLNVA VKSVQISRNK PNVVCMSWDG PLSSVKLILQ GRNLEVSDN VRSHVEDKVG KSVAKHSHLV REVDVRLSAR GGDLSKGPKL RRCEVTLFTK RHGVIRAEED AESLYSSIDL V SSIIQRKL RKIKDKVSDH GRHMKGFNRS KVRDPEPVRI TREEVLEEVE SAPAPVSVED DDFIEEVVRT KYFDMPPLTI TE AVEQLEN VDHDFYAFRN EETGDINILY KRKEGGYGLI IPKDGKTEKL ESLPVQTDKQ PSFAE

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Macromolecule #3: 16S ribosomal RNA

MacromoleculeName: 16S ribosomal RNA / type: rna / ID: 3 / 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

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Macromolecule #28: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 28 / Number of copies: 185 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.12 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
25.0 mMTris-HClTrisTris hydrochloride
25.0 mMKClPotassium chloride
25.0 mMMg(CH3COO)2Magnesium acetate
2.0 mMDTTDithiothreitol
0.05 mMSpermine
2.0 mMSpermidine
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 2-8 / Number real images: 2796 / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 326094
CTF correctionSoftware:
Namedetails
CTFFIND (ver. 3)CTF estimation
RELION (ver. 1.4)Amplitude correction
Startup modelType of model: EMDB MAP
EMDB ID:
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationSoftware - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 127031
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 111.6
Output model

PDB-5mmj:
Structure of the small subunit of the chloroplast ribosome

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