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- EMDB-3531: Cryo-EM reconstruction of the large subunit of the chloroplast ri... -

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Basic information

Entry
Database: EMDB / ID: EMD-3531
TitleCryo-EM reconstruction of the large subunit of the chloroplast ribosome
Map dataCryo-EM reconstruction of the 50S large subunit of the chloroplast ribosome
Sample
  • Complex: Chloroplast 70S ribosome
    • Protein or peptide: x 31 types
    • RNA: x 4 types
  • Ligand: x 2 types
Keywordschloroplast / translation / ribosome / cryo-EM
Function / homology
Function and homology information


plastid translation / chloroplast envelope / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast thylakoid membrane / chloroplast / DNA-templated transcription termination / large ribosomal subunit / transferase activity / 5S rRNA binding ...plastid translation / chloroplast envelope / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast thylakoid membrane / chloroplast / DNA-templated transcription termination / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / structural constituent of ribosome / 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 L10 / : / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 ...Ribosomal protein L6, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / Ribosomal protein L10 / : / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / 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 L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / : / L28p-like / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L5, conserved site
Similarity search - Domain/homology
Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL24c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL31c / Large ribosomal subunit protein uL10c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein bL28c ...Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL24c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL31c / Large ribosomal subunit protein uL10c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein bL28c / Large ribosomal subunit protein uL5c / Large ribosomal subunit protein bL17c / Large ribosomal subunit protein bL9c / Large ribosomal subunit protein uL4c / Large ribosomal subunit protein cL37 alpha / 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 uL11c / Large ribosomal subunit protein uL10c / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBieri P / Leibundgut M
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-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5mmi
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3531.png

Downloads & links

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Map

FileDownload / File: emd_3531.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of the 50S large subunit of the chloroplast ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 320 pix.
= 444.8 Å		1.39 Å/pix.
x 320 pix.
= 444.8 Å		1.39 Å/pix.
x 320 pix.
= 444.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.2699295 - 0.6163046
Average (Standard dev.)0.0016259291 (±0.0172451)
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-0.2700.6160.002

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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: 50S ribosomal protein L32, chloroplastic
    • Protein or peptide: 50S ribosomal protein L33, chloroplastic
    • Protein or peptide: 50S ribosomal protein L34, chloroplastic
    • Protein or peptide: 50S ribosomal protein L35, chloroplastic
    • Protein or peptide: 50S ribosomal protein L36, chloroplastic
    • Protein or peptide: plastid ribosomal protein cL37, PSRP5
    • Protein or peptide: 50S ribosomal protein 6, chloroplastic
    • RNA: 23S ribosomal RNA
    • RNA: 5S ribosomal RNA
    • Protein or peptide: 50S ribosomal protein L2, chloroplastic
    • Protein or peptide: plastid ribosomal protein uL3c
    • Protein or peptide: plastid ribosomal protein uL4c
    • Protein or peptide: plastid ribosomal protein uL5c
    • Protein or peptide: plastid ribosomal protein uL6c
    • Protein or peptide: plastid ribosomal protein bL9c
    • Protein or peptide: plastid ribosomal protein uL10c
    • Protein or peptide: 50S ribosomal protein L11, chloroplastic
    • Protein or peptide: 50S ribosomal protein L13, chloroplastic
    • Protein or peptide: 50S ribosomal protein L14, chloroplastic
    • Protein or peptide: plastid ribosomal protein uL15c
    • Protein or peptide: 50S ribosomal protein L16, chloroplastic
    • Protein or peptide: plastid ribosomal protein bL17c
    • Protein or peptide: plastid ribosomal protein uL18c
    • Protein or peptide: 50S ribosomal protein L19, chloroplastic
    • Protein or peptide: 50S ribosomal protein L20, chloroplastic
    • Protein or peptide: 50S ribosomal protein L21, chloroplastic
    • Protein or peptide: 50S ribosomal protein L22, chloroplastic
    • Protein or peptide: 50S ribosomal protein L23, chloroplastic
    • Protein or peptide: plastid ribosomal protein uL24c
    • RNA: 4.5S ribosomal RNA
    • Protein or peptide: plastid ribosomal protein bL27c
    • Protein or peptide: plastid ribosomal protein bL28c
    • Protein or peptide: plastid ribosomal protein uL29c
    • RNA: E-site tRNA
  • Ligand: ZINC ION
  • 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-#35
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: Spinacia oleracea (spinach)
Molecular weightTheoretical: 14.748201 KDa
SequenceString:
MVLTLSNQFL AKIPATPKTL TLPKTSSSTL RPQWSCRKSD IHPEFREDAK VYCNGELVMT TGGTQKDYTV EVWSGNHPFY LGNRSALLL DADQVEKFRK KYGELTQIME IPVLKGEIIL PPKKKSKAKK K

UniProtKB: Large ribosomal subunit protein bL31c

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Macromolecule #2: 50S ribosomal protein L32, chloroplastic

MacromoleculeName: 50S ribosomal protein L32, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 6.650969 KDa
SequenceString:
MAVPKKRTSI YKKRIRKNIW KKKGYWAALK AFSLAKSLST GNSKSFFVRK ISNQTLE

UniProtKB: Large ribosomal subunit protein bL32c

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Macromolecule #3: 50S ribosomal protein L33, chloroplastic

MacromoleculeName: 50S ribosomal protein L33, chloroplastic / type: protein_or_peptide / ID: 3 / Details: Zn-binding protein / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 7.668121 KDa
SequenceString:
MAKGKDVRVK VILECTGCVR KSVNKGSRGV SRYITQKNRH NTPSRLELRK FCPYCYKHTI HGEIKK

UniProtKB: Large ribosomal subunit protein bL33c

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Macromolecule #4: 50S ribosomal protein L34, chloroplastic

MacromoleculeName: 50S ribosomal protein L34, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 16.126633 KDa
SequenceString:
MATLSLLSTG VGAAITNRTP SASLTFITGS RTTNKRVSFN GGSARSGSLH CSFLAPSSSL SSNFSGLSLG LDLTSNTGVS TDRCRRFVV RAGKAALCLT KRSRSRKSLA RTHGFRLRMS TTSGRALLKR RRAKGRKILC TKTNPSSGKR ASP

UniProtKB: Large ribosomal subunit protein bL34c

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Macromolecule #5: 50S ribosomal protein L35, chloroplastic

MacromoleculeName: 50S ribosomal protein L35, chloroplastic / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 17.376322 KDa
SequenceString:
MAMASATATL SFKTPSLSLS PPSTRCSAAQ GISLTHFNKQ LKSTLNLSSS SSISSSKVQP IVLKNKRIST VDSSVSTSSP SFTVFAAKG YKMKTHKASA KRFRVTGKGK IVRRRAGKQH LLAKKNTKRK NRLSKLIQVD RSDYDNVIGA LPYLKVNRKV

UniProtKB: Large ribosomal subunit protein bL35c

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Macromolecule #6: 50S ribosomal protein L36, chloroplastic

MacromoleculeName: 50S ribosomal protein L36, chloroplastic / type: protein_or_peptide / ID: 6 / Details: Zn-binding protein / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 4.414462 KDa
SequenceString:
MKIRASVRPI CEKCRLIRRR GRIIVICSNP KHKQRQG

UniProtKB: Large ribosomal subunit protein bL36c

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Macromolecule #7: plastid ribosomal protein cL37, PSRP5

MacromoleculeName: plastid ribosomal protein cL37, PSRP5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 15.694817 KDa
SequenceString:
MALLSPLLSL SSVPPITSIA VSSSSFPIKL QNVSVALLPT LGQRLMTHGP VIAQKRGTVV AMVSAAADET AGEDGDQSKV EEANISVQN LPLESKLQLK LEQKMKMKMA KKIRLRRNRL MRKRKLRKRG AWPPSKMKKL KNV

UniProtKB: Large ribosomal subunit protein cL37 alpha

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Macromolecule #8: 50S ribosomal protein 6, chloroplastic

MacromoleculeName: 50S ribosomal protein 6, chloroplastic / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 12.080688 KDa
SequenceString:
MSVSAIFGAR VVTIPSVLRT SSVDGRTVKL QPSTGGSCGG GVITIECSSR PQKKGTAHHM KTRPKKTARW DIKRGPAVYP PLPPLPAEW TIVSSAVDEA DSSSSTTSSS AEIAQSA

UniProtKB: Large ribosomal subunit protein cL38

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Macromolecule #11: 50S ribosomal protein L2, chloroplastic

MacromoleculeName: 50S ribosomal protein L2, chloroplastic / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 29.853623 KDa
SequenceString: MAIHLYKTST SSTRNGAVQV KSNPRNNLIS GQRRCGKGRN ARGIITARHR GGGHKRLYRK IDFRRNEKDI YGKIVTIEYD PNRNAYICL IHYGDGEKRY ILHPRGAIIG DTIVSGTEVP IKMGNALPLT DMPLGTAIHN IEITLGRGGQ LARAAGAVAK L IAKEGKSA ...String:
MAIHLYKTST SSTRNGAVQV KSNPRNNLIS GQRRCGKGRN ARGIITARHR GGGHKRLYRK IDFRRNEKDI YGKIVTIEYD PNRNAYICL IHYGDGEKRY ILHPRGAIIG DTIVSGTEVP IKMGNALPLT DMPLGTAIHN IEITLGRGGQ LARAAGAVAK L IAKEGKSA TLKLPSGEVR LISKNCSATV GQVGNVGVNQ KRLGRAGSKR WLGKRPVVRG VVMNPVDHPH GGGEGRAPIG RK SPTTPWG YPALGRRSRK RNKYSDNFII RRRSK

UniProtKB: Large ribosomal subunit protein uL2cz/uL2cy

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Macromolecule #12: plastid ribosomal protein uL3c

MacromoleculeName: plastid ribosomal protein uL3c / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 33.03475 KDa
SequenceString: MAAILPTFSI KSSSCTYSSS KRSLSSPKAV SLSSSVNGTP KVQSLRLSTS FVCSPNQIIK LKSVSPSRST QLRRAVGGLE IKMMSVDAG IGVMGTKLGM MSFFEEDGTV VPVTVIGFKE GNIVTQVKTE STDGYNAVQV GYERLRDRKL TMPERGHLNK A GVIPMRHL ...String:
MAAILPTFSI KSSSCTYSSS KRSLSSPKAV SLSSSVNGTP KVQSLRLSTS FVCSPNQIIK LKSVSPSRST QLRRAVGGLE IKMMSVDAG IGVMGTKLGM MSFFEEDGTV VPVTVIGFKE GNIVTQVKTE STDGYNAVQV GYERLRDRKL TMPERGHLNK A GVIPMRHL QEFRLVSVDD FTPSQKLLFE ELFKEGDMVD ISGTTIGKGF QGGIKRHNFK RGLMTHGSKS HRALGSIGAG TT PGHVYKG KKMPGRMGGT KTKIRKLKIM KIDTDLRVVM IKGAVPGKPG NLLRLAPAKI VGKNIPKN

UniProtKB: Large ribosomal subunit protein uL3c

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Macromolecule #13: plastid ribosomal protein uL4c

MacromoleculeName: plastid ribosomal protein uL4c / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 32.541645 KDa
SequenceString: MATSTSSSLS LSFFSSSLFS SKSRNFSSKP ILKLPSSSHS QTSLSLSIKS ELIPLPILNF SGEKVGETFL NLKTAPSETA RAVVHRGLI THLQNKRRGT ASTLTRAEVR GGGRKPYPQK KTGRARRGSQ RSPLRPGGGV IFGPKPRDWT IKMNKKERRL A LSTAIASA ...String:
MATSTSSSLS LSFFSSSLFS SKSRNFSSKP ILKLPSSSHS QTSLSLSIKS ELIPLPILNF SGEKVGETFL NLKTAPSETA RAVVHRGLI THLQNKRRGT ASTLTRAEVR GGGRKPYPQK KTGRARRGSQ RSPLRPGGGV IFGPKPRDWT IKMNKKERRL A LSTAIASA VGNSFVVEEF AENFEKPKTK DFIAAMQRWG LDPAEKSLFF LMDLVENVEK SGRNIRTLKL LTPRSLNLFD VL NAEKLVF TEGTIQYLNQ RYGVDTLEDE DEEEEEEEEG EEVDDGVEDG TPEPAE

UniProtKB: Large ribosomal subunit protein uL4c

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Macromolecule #14: plastid ribosomal protein uL5c

MacromoleculeName: plastid ribosomal protein uL5c / type: protein_or_peptide / ID: 14
Details: Residues 39-52 were built as poly-alanine and deposited as UNK.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 28.182688 KDa
SequenceString: MASTSLLQST SSSFAGVRFH CRTSAAPRVG LSSFTVKAAA GTAVFVDKAE AETINRLKTN YIEKMVPLLK EEFSYSNILE VPKVVKIVV NCGIGDASQN AKGLDAAINE LALITGQRPV KTKAKTSIAG FKVREGMTLG IAVTLRGNLM YSFLDRLINL A LPRTRDFQ ...String:
MASTSLLQST SSSFAGVRFH CRTSAAPRVG LSSFTVKAAA GTAVFVDKAE AETINRLKTN YIEKMVPLLK EEFSYSNILE VPKVVKIVV NCGIGDASQN AKGLDAAINE LALITGQRPV KTKAKTSIAG FKVREGMTLG IAVTLRGNLM YSFLDRLINL A LPRTRDFQ GVNPNSFDGH GNYSVGFREQ SVFPEIKPEI VGKARGMDVC ITTTAKTDKE AYKLLSLMGM PFREGSGPST LV RKKKLKS HHFDAKKGRR Y

UniProtKB: Large ribosomal subunit protein uL5c

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Macromolecule #15: plastid ribosomal protein uL6c

MacromoleculeName: plastid ribosomal protein uL6c / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 24.516748 KDa
SequenceString: MSLPLPSHMK SVFLGMKVEI STSVPVTRIG FWRKSVDCKE SRIGKQPITV PANVAIAMEG QDLKVKGPLG ELSITYPREV LVEKQESGF LRVRKAVETR RANQMHGLFR TLTDNMVVGV SKGFEKKLQL VGVGYRATVE GKDLILSLGF SHPVRMAIPD E LQVKVEEN ...String:
MSLPLPSHMK SVFLGMKVEI STSVPVTRIG FWRKSVDCKE SRIGKQPITV PANVAIAMEG QDLKVKGPLG ELSITYPREV LVEKQESGF LRVRKAVETR RANQMHGLFR TLTDNMVVGV SKGFEKKLQL VGVGYRATVE GKDLILSLGF SHPVRMAIPD E LQVKVEEN TKVTVSGRDK SVVGQFAATI RSWRPPEPYK GKGVRYVDEV VRRKEGKAGK KK

UniProtKB: Large ribosomal subunit protein uL6c

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Macromolecule #16: plastid ribosomal protein bL9c

MacromoleculeName: plastid ribosomal protein bL9c / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 22.038904 KDa
SequenceString: MASTTSTLSL SWSNSFHSFA GAISEPQKSP ENCRVMLPIV AQKKVKKIRK IILKEDIPDL GKKGQLLDVR AGFLRNFLLP LGKAEVVTP LLLKEMKMED ERIEAEKKRV KEEAQQLARM FETVGAFKVK RKGGKGKQIF GSVTAQDLVD IIKAQLQRDV D KKVVFLPD ...String:
MASTTSTLSL SWSNSFHSFA GAISEPQKSP ENCRVMLPIV AQKKVKKIRK IILKEDIPDL GKKGQLLDVR AGFLRNFLLP LGKAEVVTP LLLKEMKMED ERIEAEKKRV KEEAQQLARM FETVGAFKVK RKGGKGKQIF GSVTAQDLVD IIKAQLQRDV D KKVVFLPD IRETGEYIAE LKLHPDVTAQ VRVTVFAN

UniProtKB: Large ribosomal subunit protein bL9c

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Macromolecule #17: plastid ribosomal protein uL10c

MacromoleculeName: plastid ribosomal protein uL10c / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 26.12823 KDa
SequenceString: MESTLFLSKP LPTTIKTTTH SLSSVYPNPF KPNNLTFPRT THKHPTTTTI TAAISRTKKE ETVETVQKHL ENCYLLAAIN YKGFTVKQF QDLRKALPEN TTLIVAKNTL VEKAVQDTQW AAIKPCMKGM NAWLFVHSEE IPIAIKPYRT FQKERKLEDN D FTGACFEG ...String:
MESTLFLSKP LPTTIKTTTH SLSSVYPNPF KPNNLTFPRT THKHPTTTTI TAAISRTKKE ETVETVQKHL ENCYLLAAIN YKGFTVKQF QDLRKALPEN TTLIVAKNTL VEKAVQDTQW AAIKPCMKGM NAWLFVHSEE IPIAIKPYRT FQKERKLEDN D FTGACFEG KFYGPGEVKR LETMPSKAEI FAKLLGSLKS PGSALVGTLQ APARDLVFLL KAYIKKLEDE QQQG

UniProtKB: Large ribosomal subunit protein uL10c

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Macromolecule #18: 50S ribosomal protein L11, chloroplastic

MacromoleculeName: 50S ribosomal protein L11, chloroplastic / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 23.68998 KDa
SequenceString: MAQPLVAAPS SSSITSPIPR KLCSSLLTPS SLSLSSNPRN SLQFLNSKLF LSPPSTSHRR LSIVAMAPKP GKAKKVIGVI KLALEAGKA TPAPPVGPAL GSKGVNIMAF CKDYNARTAD KPGFVIPVEI TVFDDKSFTF ILKTPPASVL LLKASGAEKG S KDPQMEKV ...String:
MAQPLVAAPS SSSITSPIPR KLCSSLLTPS SLSLSSNPRN SLQFLNSKLF LSPPSTSHRR LSIVAMAPKP GKAKKVIGVI KLALEAGKA TPAPPVGPAL GSKGVNIMAF CKDYNARTAD KPGFVIPVEI TVFDDKSFTF ILKTPPASVL LLKASGAEKG S KDPQMEKV GKITIDQLRG IATEKLPDLN CTTIESAMRI IAGTAANMGI DIDPPILVKK KKEVIF

UniProtKB: Large ribosomal subunit protein uL11c

+
Macromolecule #19: 50S ribosomal protein L13, chloroplastic

MacromoleculeName: 50S ribosomal protein L13, chloroplastic / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 28.211629 KDa
SequenceString: MATMACASSL TFPSAQTQKS FFGTNVKQTP VLSFPRPTVA AAVAVSARKS TSASTKCTEE WRQLKEAVKK EFAIPHVPLD QRWMFTLEE ATGPDIWNTT WYPKSADHVP TDKKWYVVDA TDLILGRMAS TIAIHIRGKN LASYTPSVDM GAFVIVVNAD K VAVSGKKR ...String:
MATMACASSL TFPSAQTQKS FFGTNVKQTP VLSFPRPTVA AAVAVSARKS TSASTKCTEE WRQLKEAVKK EFAIPHVPLD QRWMFTLEE ATGPDIWNTT WYPKSADHVP TDKKWYVVDA TDLILGRMAS TIAIHIRGKN LASYTPSVDM GAFVIVVNAD K VAVSGKKR TQKLYRRHSG RPGGLKEETF DQLQKRIPER IIEHAVRGML PKGRLGRYLF NHLKVYKGAE HPHQAQQPID LP LRDKRIR VEK

UniProtKB: Large ribosomal subunit protein uL13c

+
Macromolecule #20: 50S ribosomal protein L14, chloroplastic

MacromoleculeName: 50S ribosomal protein L14, chloroplastic / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 13.484741 KDa
SequenceString:
MIQPQTHLNV ADNSGARELM CIRIIGASNR RYARIGDVIV AVIKEAIPNT PLERSEVIRA VVVRTCKELK RDNGMIIRYD DNAAVIIDQ EGNPKGTRIF GAIARELRQK FAKIVSLAPE VL

UniProtKB: Large ribosomal subunit protein uL14c

+
Macromolecule #21: plastid ribosomal protein uL15c

MacromoleculeName: plastid ribosomal protein uL15c / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 29.081514 KDa
SequenceString: MASLLSLSST PPSTANSNNY PSSTFKGNIN NFRINPFNFA PLKLHLRNIV KKESTRLVVV ASASSSNVSP SIGSGSETRF RLDNLGPQP GSRKKGKRKG RGHAAGQGGS CGFGMRGQKS RSGPGIMRGF EGGQMPLYRR IPKLRGIAGG MRAGLPKYVP I NLRDIEVA ...String:
MASLLSLSST PPSTANSNNY PSSTFKGNIN NFRINPFNFA PLKLHLRNIV KKESTRLVVV ASASSSNVSP SIGSGSETRF RLDNLGPQP GSRKKGKRKG RGHAAGQGGS CGFGMRGQKS RSGPGIMRGF EGGQMPLYRR IPKLRGIAGG MRAGLPKYVP I NLRDIEVA GFKEGEEVSL ESLKAKGIIN PSGRERRLPL KILGEGELST KLQIKARAFS GSAKEKLEAA GCSVTVLPGR KK YIKESVR KNLARADEYF AKKRAASASE AESA

UniProtKB: Large ribosomal subunit protein uL15c

+
Macromolecule #22: 50S ribosomal protein L16, chloroplastic

MacromoleculeName: 50S ribosomal protein L16, chloroplastic / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 15.328068 KDa
SequenceString:
MLSPKRTRFR KQHRGRMKGI SYRGNRICFG RYALQALEPA WITSRQIEAG RRAMTRNARR GGKIWVRIFP DKPVTVRPAE TRMGSGKGS PEYWVAVVKP GRILYEISGV AENIARRAVA IAASKMPIRT QFIISG

UniProtKB: Large ribosomal subunit protein uL16c

+
Macromolecule #23: plastid ribosomal protein bL17c

MacromoleculeName: plastid ribosomal protein bL17c / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 14.577172 KDa
SequenceString:
MIDNGGRFFA MKHGRKIHRL SRPADQRRAL LRGLTTQLLK HGRIKTTRAK ASAMRKYVDK MITLAKEGSL HKRRQALGFI YEKQIVHAL FAEVPERYGD RNGGYTRIIR TLPRRGDNAP MAYIELV

UniProtKB: Large ribosomal subunit protein bL17c

+
Macromolecule #24: plastid ribosomal protein uL18c

MacromoleculeName: plastid ribosomal protein uL18c / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 18.410205 KDa
SequenceString:
MAAATSLSFF HSTLASSSSS SVQQLSLPPK FVNFRPQTLP LIQAKAHTRR EDRTARHVRI RKKVEGTPER PRLCVFRSNK HLYVQVIDD TKMHTLAAAS TMQKAISENI DYSAGPTVEV AQKIGEMIAK SCLEKGITKV AFDRGGYPYH GRVKALADAA R EHGLVF

UniProtKB: Large ribosomal subunit protein uL18c

+
Macromolecule #25: 50S ribosomal protein L19, chloroplastic

MacromoleculeName: 50S ribosomal protein L19, chloroplastic / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 26.121254 KDa
SequenceString: MASKVLPQAL LVIPSNHSLQ CPPLKKQLGF PIDSNRRFSL SSNCRSNLMV SRASSNLFSS NFSSIFSFPA RNSFVVRSEA EDSSDAPAE SVAVVAEEEL PVESEAEAEE RPPRQQRVKL GDIMGILNKK AVHAAEELRP VPGIRTGDIV QIRLEVPENK R RLSVYKGI ...String:
MASKVLPQAL LVIPSNHSLQ CPPLKKQLGF PIDSNRRFSL SSNCRSNLMV SRASSNLFSS NFSSIFSFPA RNSFVVRSEA EDSSDAPAE SVAVVAEEEL PVESEAEAEE RPPRQQRVKL GDIMGILNKK AVHAAEELRP VPGIRTGDIV QIRLEVPENK R RLSVYKGI VISRQNAGIH TTIRIRRIIA GVGVEIVFPL YSPNIKEIKV VSHRKVRKAR LYYLRDKLPR LSTFK

UniProtKB: Large ribosomal subunit protein bL19c

+
Macromolecule #26: 50S ribosomal protein L20, chloroplastic

MacromoleculeName: 50S ribosomal protein L20, chloroplastic / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 15.725687 KDa
SequenceString:
MTRVKRGYIA RRRRKKIRFF ASSFRGAHSR LTRTIAQQKI RALVSAHRDR DRQKRDFRRL WITRINAAIR ERGVYYNYSK FIHDLYKRQ LLLNRKILAQ IAILNPNCIY MIYNEIIKKE DCKKYLEII

UniProtKB: Large ribosomal subunit protein bL20c

+
Macromolecule #27: 50S ribosomal protein L21, chloroplastic

MacromoleculeName: 50S ribosomal protein L21, chloroplastic / type: protein_or_peptide / ID: 27
Details: Residues 68-81 were built as poly-alanine and deposited as UNK.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 28.44173 KDa
SequenceString: MASATLAFSC SSLCATLKLP QNLNPLLLNV PPLSKPFSGV VSPPSLSRLS LLPVAAKRRR FQEIPEELKA EFEEFQRPPN QKPQLSDVL PDDFQAPEPG TPEYNDIINQ FLPKKGPPPP REEIFAVVVI GSRQYIVIPG RWIYTQRLKG ATVNDKIVLN K VLLVGTKA ...String:
MASATLAFSC SSLCATLKLP QNLNPLLLNV PPLSKPFSGV VSPPSLSRLS LLPVAAKRRR FQEIPEELKA EFEEFQRPPN QKPQLSDVL PDDFQAPEPG TPEYNDIINQ FLPKKGPPPP REEIFAVVVI GSRQYIVIPG RWIYTQRLKG ATVNDKIVLN K VLLVGTKA STYIGTPIVT NAAVHAVVEE QLLDDKVIVF KYKKKKNYRR NIGHRQPITR IKITGITGYE DYPASTLEAE VE AKEEAEA EAEAEAVPV

UniProtKB: Large ribosomal subunit protein bL21c

+
Macromolecule #28: 50S ribosomal protein L22, chloroplastic

MacromoleculeName: 50S ribosomal protein L22, chloroplastic / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (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

UniProtKB: Large ribosomal subunit protein uL22c

+
Macromolecule #29: 50S ribosomal protein L23, chloroplastic

MacromoleculeName: 50S ribosomal protein L23, chloroplastic / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 21.832164 KDa
SequenceString: MATTAPNLHS LSSSFAFSNP SSNVSATSFT FQIPNKKAQI SCISSKKLHT QKSFNFHDAV TPMNKPSFGR DLMVAQATEA VAPTTEEAA TSQPKTSKKA KKLKYPRRIL DVYQILQSPI ITEAAIKNIA DENSLLFTVD VRADKKMIRE AISNFFGVKV R KVNTLIRP ...String:
MATTAPNLHS LSSSFAFSNP SSNVSATSFT FQIPNKKAQI SCISSKKLHT QKSFNFHDAV TPMNKPSFGR DLMVAQATEA VAPTTEEAA TSQPKTSKKA KKLKYPRRIL DVYQILQSPI ITEAAIKNIA DENSLLFTVD VRADKKMIRE AISNFFGVKV R KVNTLIRP DGTKKAYIML NKEYNASELA KKIGIFPGGN

UniProtKB: Large ribosomal subunit protein uL23c

+
Macromolecule #30: plastid ribosomal protein uL24c

MacromoleculeName: plastid ribosomal protein uL24c / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 21.417945 KDa
SequenceString: MAAMAALQSS FTSLSLSSNS FLGQRLFPSP TTLQVKTEGH SPCLIVMRIK RWERKDCKPN SLPKLHKMHV KVGDTVKVIS GGEKGKIGE ISKIHKHNST VIIKDLNLKT KHVKSKEEGE QGQIIKIEAA IHSSNVMLYS KEQEVASRVG HKILEDGRKV R YLIKTGEI ...String:
MAAMAALQSS FTSLSLSSNS FLGQRLFPSP TTLQVKTEGH SPCLIVMRIK RWERKDCKPN SLPKLHKMHV KVGDTVKVIS GGEKGKIGE ISKIHKHNST VIIKDLNLKT KHVKSKEEGE QGQIIKIEAA IHSSNVMLYS KEQEVASRVG HKILEDGRKV R YLIKTGEI VDTPDRWKEI QNKKESETAV AVAA

UniProtKB: Large ribosomal subunit protein uL24c

+
Macromolecule #32: plastid ribosomal protein bL27c

MacromoleculeName: plastid ribosomal protein bL27c / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 21.366447 KDa
SequenceString: MAVTTSMSFN LMASFRGMSL SSSSSSSFFK GEFGPSSLRL PNKSPLSVSP FPLTIESAHK KGAGSTKNGR DSKGQRLGVK IYGDQVAKP GAIIIRQRGT KFHPGKNVGI GKDHTIFALI DGLVKFEKYG PDKKKVSVYP REIQPENPNS YRARKRENFR L QREKKKAR ...String:
MAVTTSMSFN LMASFRGMSL SSSSSSSFFK GEFGPSSLRL PNKSPLSVSP FPLTIESAHK KGAGSTKNGR DSKGQRLGVK IYGDQVAKP GAIIIRQRGT KFHPGKNVGI GKDHTIFALI DGLVKFEKYG PDKKKVSVYP REIQPENPNS YRARKRENFR L QREKKKAR REGYSFQPQL ILASAATDNA DESAVC

UniProtKB: Large ribosomal subunit protein bL27c

+
Macromolecule #33: plastid ribosomal protein bL28c

MacromoleculeName: plastid ribosomal protein bL28c / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 16.460488 KDa
SequenceString:
MAASGMLISN PSNVCFRKPQ FSCSLKPKAT VSELGFLTSQ LSGIQISPSP LFPIISKPIS APLKPSLQPV ARRICPFTGK KSNKANRVS HSNHKTKRLQ FVNLQYKRVW WEAGKRFVKL RLSTKALKTI EKNGLDAVAK KAGIDLRKE

UniProtKB: Large ribosomal subunit protein bL28c

+
Macromolecule #34: plastid ribosomal protein uL29c

MacromoleculeName: plastid ribosomal protein uL29c / type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 19.083385 KDa
SequenceString:
MLAIHSLSST PCSSGLTSPP KSTLLTKSSF HGLRLPSVNL SSSLRLRVQT PPSSVVVMVK KEDELKELRT KTNEQLNEEI LQLKGELFM LRLQRSAREN FKPSDFGRMR KRVARMLTVK REREIEQGVG KRLSRKLDKA WKRSIVVRPP PSLKKLQEKA T AEAEAEKA

UniProtKB: Large ribosomal subunit protein uL29c

+
Macromolecule #9: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 9 / Number of copies: 1
Source (natural)Organism: Spinacia oleracea (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

GENBANK: GENBANK: AJ400848.1

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Macromolecule #10: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 10 / Number of copies: 1
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 39.014184 KDa
SequenceString:
UAUUCUGGUG UCCUAGGCGU AGAGGAACCA CACCAAUCCA UCCCGAACUU GGUGGUUAAA CUCUACUGCG GUGACGAUAC UGUAGGGGA GGUCCUGCGG AAAAAUAGCU CGACGCCAGG AU

+
Macromolecule #31: 4.5S ribosomal RNA

MacromoleculeName: 4.5S ribosomal RNA / type: rna / ID: 31 / Number of copies: 1
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 34.334488 KDa
SequenceString:
AGAGAAGGUC ACGGCGAGAC GAGCCGUUUA UCAUUACGAU AGGUGUCAAG UGGAAGUGCA GUGAUGUAUG CAGCUGAGGC AUCCUAACA GACCCACAGA CUUGAAC

GENBANK: GENBANK: X04977.1

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Macromolecule #35: E-site tRNA

MacromoleculeName: E-site tRNA / type: rna / ID: 35 / Details: CA-3' end of E-site tRNA / Number of copies: 1
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 589.43 Da
SequenceString:
CA

+
Macromolecule #36: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 36 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #37: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 37 / Number of copies: 501 / 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-HClTris 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
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 326094
Startup modelType of model: EMDB MAP
EMDB ID:

2847

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 154332
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationSoftware - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 56.9
Output model

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

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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