› 5x8r

Electron Microscopy
3.7Å resolution

Structure of the 30S small subunit of chloroplast ribosome from spinach

Released:
DOI: 10.2210/pdb5x8r/pdb
PDB entry 5x8r coloured by chain, front view.
PDB entry 5x8r coloured by chain, side view.
PDB entry 5x8r 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
Nucleic Acids Res 45 8581-8595 (2017)
PMID: 28582576
Related structures: EMD-6710

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 26-mer (preferred)
PDBe Complex ID:
PDB-CPX-110670 (preferred)
Entry contents:
25 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (26 distinct):
Small ribosomal subunit protein uS2c Chain: b
Molecule details ›
Chain: b
Length: 236 amino acids
Theoretical weight: 26.74 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P08242 (Residues: 1-236; Coverage: 100%)
Gene name: rps2
Sequence domains: Ribosomal protein S2
Structure domains:
Small ribosomal subunit protein uS3c Chain: c
Molecule details ›
Chain: c
Length: 218 amino acids
Theoretical weight: 24.97 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P09595 (Residues: 1-218; Coverage: 100%)
Gene name: rps3
Sequence domains: Ribosomal protein S3, C-terminal domain
Structure domains: Ribosomal protein S3, C-terminal domain
Small ribosomal subunit protein uS5c Chain: e
Molecule details ›
Chain: e
Length: 253 amino acids
Theoretical weight: 27.7 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9ST69 (Residues: 56-308; Coverage: 82%)
Gene names: SOVF_195380, rps5
Sequence domains:
Small ribosomal subunit protein bS6c alpha Chain: f
Molecule details ›
Chain: f
Length: 146 amino acids
Theoretical weight: 16.34 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82403 (Residues: 66-211; Coverage: 69%)
Gene names: RPS6, SOVF_120630
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7cz/uS7cy Chain: g
Molecule details ›
Chain: g
Length: 155 amino acids
Theoretical weight: 17.38 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82129 (Residues: 1-155; Coverage: 100%)
Gene names: rps7-A, rps7-B
Sequence domains: Ribosomal protein S7p/S5e
Structure domains: Ribosomal protein S7 domain
Small ribosomal subunit protein uS8c Chain: h
Molecule details ›
Chain: h
Length: 134 amino acids
Theoretical weight: 15.53 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P09597 (Residues: 1-134; Coverage: 100%)
Gene name: rps8
Sequence domains: Ribosomal protein S8
Structure domains:
Small ribosomal subunit protein uS9c Chain: i
Molecule details ›
Chain: i
Length: 157 amino acids
Theoretical weight: 17.09 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82278 (Residues: 52-208; Coverage: 76%)
Gene names: PRPS9, SOVF_016530
Sequence domains: Ribosomal protein S9/S16
Structure domains: Ribosomal Protein S5; domain 2
30S ribosomal protein S10 beta, chloroplastic Chain: j
Molecule details ›
Chain: j
Length: 122 amino acids
Theoretical weight: 13.88 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82162 (Residues: 74-195; Coverage: 63%)
Gene names: RPS10, SOVF_026730
Sequence domains: Ribosomal protein S10p/S20e
Structure domains: Ribosomal protein S10 domain
Small ribosomal subunit protein uS11c Chain: k
Molecule details ›
Chain: k
Length: 138 amino acids
Theoretical weight: 14.93 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06506 (Residues: 1-138; Coverage: 100%)
Gene name: rps11
Sequence domains: Ribosomal protein S11
Structure domains: Ribosomal protein S11
Small ribosomal subunit protein uS12cz/uS12cy Chain: l
Molecule details ›
Chain: l
Length: 123 amino acids
Theoretical weight: 13.79 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P62128 (Residues: 1-123; Coverage: 100%)
Gene names: rps12-A, rps12-B
Sequence domains: Ribosomal protein S12/S23
Structure domains: Nucleic acid-binding proteins
30S ribosomal protein S13, chloroplastic Chain: m
Molecule details ›
Chain: m
Length: 126 amino acids
Theoretical weight: 14.42 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: B8AQA7 (Residues: 20-155; Coverage: 74%)
Gene name: OsI_13197
Sequence domains: Ribosomal protein S13/S18
Structure domains: 30s ribosomal protein s13, domain 2
Small ribosomal subunit protein uS15c Chain: o
Molecule details ›
Chain: o
Length: 90 amino acids
Theoretical weight: 10.78 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9M3I4 (Residues: 1-90; Coverage: 100%)
Gene name: rps15
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16c Chain: p
Molecule details ›
Chain: p
Length: 88 amino acids
Theoretical weight: 10.45 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P28807 (Residues: 1-88; Coverage: 100%)
Gene name: rps16
Sequence domains: Ribosomal protein S16
Structure domains: S16 Ribosomal Protein; Chain: A;
Small ribosomal subunit protein uS17c Chain: q
Molecule details ›
Chain: q
Length: 108 amino acids
Theoretical weight: 12.2 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82137 (Residues: 58-165; Coverage: 66%)
Gene names: RPS17, SOVF_042540
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18c Chain: r
Molecule details ›
Chain: r
Length: 101 amino acids
Theoretical weight: 12.08 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9M3K7 (Residues: 1-101; Coverage: 100%)
Gene name: RPS18
Sequence domains: Ribosomal protein S18
Structure domains: Ribosomal protein S18
Small ribosomal subunit protein uS19c Chain: s
Molecule details ›
Chain: s
Length: 92 amino acids
Theoretical weight: 10.63 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06508 (Residues: 1-92; Coverage: 100%)
Gene name: rps19
Sequence domains: Ribosomal protein S19
Structure domains: 30s Ribosomal Protein S19; Chain A
Small ribosomal subunit protein bS20c Chain: t
Molecule details ›
Chain: t
Length: 108 amino acids
Theoretical weight: 12.18 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82130 (Residues: 76-183; Coverage: 59%)
Gene name: RPS20
Sequence domains: Ribosomal protein S20
Structure domains: Ribosomal protein S20
Small ribosomal subunit protein bS21c Chain: u
Molecule details ›
Chain: u
Length: 137 amino acids
Theoretical weight: 16.1 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82024 (Residues: 44-180; Coverage: 76%)
Gene names: SOVF_070750, rps21
Sequence domains: Ribosomal protein S21
Ribosome-binding factor PSRP1, chloroplastic Chain: y
Molecule details ›
Chain: y
Length: 236 amino acids
Theoretical weight: 26.85 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P19954 (Residues: 67-302; Coverage: 78%)
Gene names: PSRP1, RPS22, RPS30, SOVF_177810
Sequence domains:
Small ribosomal subunit protein cS23 Chain: w
Molecule details ›
Chain: w
Length: 121 amino acids
Theoretical weight: 13.81 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82412 (Residues: 59-179; Coverage: 68%)
Gene names: PSRP3, SOVF_058240
Sequence domains: Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65)
Small ribosomal subunit protein uS4c Chain: d
Molecule details ›
Chain: d
Length: 201 amino acids
Theoretical weight: 23.45 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P13788 (Residues: 1-201; Coverage: 100%)
Gene name: rps4
Sequence domains:
Structure domains:
Small ribosomal subunit protein cS22 Chain: v
Molecule details ›
Chain: v
Length: 198 amino acids
Theoretical weight: 21.69 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82277 (Residues: 63-260; Coverage: 76%)
Gene names: PSRP2, SOVF_116380
Sequence domains: RNA recognition motif
Small ribosomal subunit protein uS14c Chain: n
Molecule details ›
Chain: n
Length: 100 amino acids
Theoretical weight: 11.81 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06507 (Residues: 1-100; Coverage: 100%)
Gene name: rps14
Sequence domains: Ribosomal protein S14p/S29e
Structure domains: Helix Hairpins
Small ribosomal subunit protein bTHXc Chain: x
Molecule details ›
Chain: x
Length: 47 amino acids
Theoretical weight: 5.19 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P47910 (Residues: 55-101; Coverage: 47%)
Gene names: PSRP4, RPS31, SOVF_048530
Sequence domains: Ribosomal protein S31e
Small ribosomal subunit protein bS1c Chain: 8
Molecule details ›
Chain: 8
Length: 370 amino acids
Theoretical weight: 40.47 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P29344 (Residues: 42-411; Coverage: 90%)
Gene names: RPS1, SOVF_099990
Sequence domains: S1 RNA binding domain
16S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1491 nucleotides
Theoretical weight: 483.47 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-6710

Quick links

Citations

1 review citation

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

1 mention without citation

Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation.
Ahmed et al. (2017)