› 5x8t

Electron Microscopy
3.3Å resolution

Structure of the 50S large subunit of chloroplast ribosome from spinach

Released:
DOI: 10.2210/pdb5x8t/pdb
PDB entry 5x8t coloured by chain, front view.
PDB entry 5x8t coloured by chain, side view.
PDB entry 5x8t coloured by chain, top view.
Source organism: Spinacia oleracea
Primary publication:
Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation.
Ahmed T, Shi J, Bhushan S
OpenAccess logo Nucleic Acids Res 45 8581-8595 (2017)
PMID: 28582576
Related structures: EMD-6711

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 32-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-520368 (preferred)
Entry contents:
29 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (32 distinct):
Large ribosomal subunit protein bL32c Chain: 1
Molecule details ›
Chain: 1
Length: 56 amino acids
Theoretical weight: 6.52 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P28804 (Residues: 2-57; Coverage: 98%)
Gene name: rpl32
Large ribosomal subunit protein bL33c Chain: 2
Molecule details ›
Chain: 2
Length: 65 amino acids
Theoretical weight: 7.54 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P28805 (Residues: 2-66; Coverage: 99%)
Gene name: rpl33
Sequence domains: Ribosomal protein L33
Structure domains: Ribosomal protein L33
Large ribosomal subunit protein bL34c Chain: 3
Molecule details ›
Chain: 3
Length: 61 amino acids
Theoretical weight: 6.79 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82244 (Residues: 92-152; Coverage: 40%)
Gene names: RPL34, SOVF_073030
Sequence domains: Ribosomal protein L34
Structure domains: Helix Hairpins
Large ribosomal subunit protein bL35c Chain: 4
Molecule details ›
Chain: 4
Length: 73 amino acids
Theoretical weight: 8.46 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P23326 (Residues: 87-159; Coverage: 46%)
Gene names: RPL35, SOVF_080710
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36c Chain: 5
Molecule details ›
Chain: 5
Length: 37 amino acids
Theoretical weight: 4.41 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P12230 (Residues: 1-37; Coverage: 100%)
Gene name: rpl36
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein cL37 alpha Chain: 6
Molecule details ›
Chain: 6
Length: 142 amino acids
Theoretical weight: 15.69 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P27684 (Residues: 1-142; Coverage: 100%)
Gene names: PSRP5, RPL40, SOVF_000530
Large ribosomal subunit protein cL38 Chain: 7
Molecule details ›
Chain: 7
Length: 116 amino acids
Theoretical weight: 12.08 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82411 (Residues: 1-116; Coverage: 100%)
Gene names: PSRP6, SOVF_082300
Sequence domains: Family of unknown function (DUF5323)
Large ribosomal subunit protein uL2cz/uL2cy Chain: C
Molecule details ›
Chain: C
Length: 271 amino acids
Theoretical weight: 29.72 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06509 (Residues: 2-272; Coverage: 100%)
Gene names: rpl2-A, rpl2-B
Sequence domains:
Structure domains: Nucleic acid-binding proteins
Large ribosomal subunit protein uL3c Chain: D
Molecule details ›
Chain: D
Length: 221 amino acids
Theoretical weight: 24.12 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82191 (Residues: 85-305; Coverage: 73%)
Gene names: RPL3, SOVF_195350
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4c Chain: E
Molecule details ›
Chain: E
Length: 243 amino acids
Theoretical weight: 27.2 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: O49937 (Residues: 51-293; Coverage: 83%)
Gene names: RPL4, SOVF_029280
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5c Chain: F
Molecule details ›
Chain: F
Length: 220 amino acids
Theoretical weight: 24.25 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82192 (Residues: 39-258; Coverage: 85%)
Gene names: PrpL5, RPL5, SOVF_057730
Sequence domains:
Structure domains: 50s Ribosomal Protein L5; Chain: A,
Large ribosomal subunit protein uL6c Chain: G
Molecule details ›
Chain: G
Length: 182 amino acids
Theoretical weight: 20.26 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82193 (Residues: 39-220; Coverage: 83%)
Gene names: RPL6, SOVF_107200
Sequence domains: Ribosomal protein L6
Structure domains: Ribosomal protein L6, alpha-beta domain
Large ribosomal subunit protein bL9c Chain: H
Molecule details ›
Chain: H
Length: 155 amino acids
Theoretical weight: 17.67 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82180 (Residues: 42-196; Coverage: 79%)
Gene names: RPL9, SOVF_040960
Sequence domains:
Large ribosomal subunit protein uL13c Chain: K
Molecule details ›
Chain: K
Length: 197 amino acids
Theoretical weight: 22.77 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P12629 (Residues: 54-250; Coverage: 79%)
Gene names: RPL13, SOVF_093170
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14c Chain: L
Molecule details ›
Chain: L
Length: 121 amino acids
Theoretical weight: 13.48 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P09596 (Residues: 1-121; Coverage: 100%)
Gene name: rpl14
Sequence domains: Ribosomal protein L14p/L23e
Structure domains: Ribosomal protein L14
Large ribosomal subunit protein uL15c Chain: M
Molecule details ›
Chain: M
Length: 192 amino acids
Theoretical weight: 20.68 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P22798 (Residues: 80-271; Coverage: 71%)
Gene names: RPL15, SOVF_177460
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16c Chain: N
Molecule details ›
Chain: N
Length: 135 amino acids
Theoretical weight: 15.33 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P17353 (Residues: 1-135; Coverage: 100%)
Gene name: rpl16
Sequence domains: Ribosomal protein L16p/L10e
Structure domains: Ribosomal protein L10e/L16
Large ribosomal subunit protein bL17c Chain: O
Molecule details ›
Chain: O
Length: 116 amino acids
Theoretical weight: 13.47 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82194 (Residues: 11-126; Coverage: 92%)
Gene names: RPL17, SOVF_059230
Sequence domains: Ribosomal protein L17
Structure domains: Ribosomal protein L17
Large ribosomal subunit protein uL18c Chain: P
Molecule details ›
Chain: P
Length: 123 amino acids
Theoretical weight: 13.8 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82195 (Residues: 44-166; Coverage: 74%)
Gene names: PRPL18, RPL18, SOVF_159210
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Structure domains: Nucleotidyltransferase; domain 5
Large ribosomal subunit protein bL19c Chain: Q
Molecule details ›
Chain: Q
Length: 156 amino acids
Theoretical weight: 17.6 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82413 (Residues: 78-233; Coverage: 67%)
Gene names: PRPL19, RPL19, SOVF_150800
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20c Chain: R
Molecule details ›
Chain: R
Length: 127 amino acids
Theoretical weight: 15.59 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P28803 (Residues: 2-128; Coverage: 99%)
Gene name: rpl20
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21c Chain: S
Molecule details ›
Chain: S
Length: 201 amino acids
Theoretical weight: 22.79 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P24613 (Residues: 56-256; Coverage: 79%)
Gene names: RPL21, SOVF_056040
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22c Chain: T
Molecule details ›
Chain: T
Length: 199 amino acids
Theoretical weight: 23.29 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P09594 (Residues: 1-199; Coverage: 100%)
Gene name: rpl22
Sequence domains: Ribosomal protein L22p/L17e
Structure domains: Ribosomal protein L22/L17
Large ribosomal subunit protein uL23c Chain: U
Molecule details ›
Chain: U
Length: 122 amino acids
Theoretical weight: 13.58 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9LWB5 (Residues: 77-198; Coverage: 62%)
Gene names: RPL23, SOVF_109700
Sequence domains: Ribosomal protein L23
Structure domains: Alpha-Beta Plaits
Large ribosomal subunit protein uL24c Chain: V
Molecule details ›
Chain: V
Length: 145 amino acids
Theoretical weight: 16.55 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P27683 (Residues: 48-192; Coverage: 76%)
Gene names: RPL24, SOVF_183870
Sequence domains:
Large ribosomal subunit protein bL27c Chain: X
Molecule details ›
Chain: X
Length: 137 amino acids
Theoretical weight: 15.33 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82190 (Residues: 58-194; Coverage: 71%)
Gene names: RPL27, SOVF_107450
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28c Chain: Y
Molecule details ›
Chain: Y
Length: 77 amino acids
Theoretical weight: 9.02 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82245 (Residues: 72-148; Coverage: 52%)
Gene names: RPL28, SOVF_085320
Sequence domains: Ribosomal L28 family
Structure domains: Ribosomal protein L28/L24
Large ribosomal subunit protein uL29c Chain: Z
Molecule details ›
Chain: Z
Length: 109 amino acids
Theoretical weight: 12.9 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82248 (Residues: 60-168; Coverage: 65%)
Gene names: RPL29, SOVF_096810
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein bL31c Chain: 0
Molecule details ›
Chain: 0
Length: 94 amino acids
Theoretical weight: 10.8 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82249 (Residues: 37-130; Coverage: 72%)
Gene names: RPL31, SOVF_125040
Sequence domains: Ribosomal protein L31
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 121 nucleotides
Theoretical weight: 39.01 KDa
Sequence domains: 5S ribosomal RNA
4.8S rRNA Chain: W
Molecule details ›
Chain: W
Length: 106 nucleotides
Theoretical weight: 34.33 KDa
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2810 nucleotides
Theoretical weight: 911.34 KDa
Sequence domains: Bacterial large subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-6711

Quick links

Citations

1 review citation

Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM.
Poitevin et al. (2020)
14 other articles

2 mentions without citation

Differences in the path to exit the ribosome across the three domains of life.
Dao Duc et al. (2019)
1 more