› 5mmj

Electron Microscopy
3.65Å resolution

Structure of the small subunit of the chloroplast ribosome

Released:
DOI: 10.2210/pdb5mmj/pdb
PDB entry 5mmj coloured by chain, front view.
PDB entry 5mmj coloured by chain, side view.
PDB entry 5mmj coloured by chain, top view.
Source organism: Spinacia oleracea
Primary publication:
The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.
Bieri P, Leibundgut M, Saurer M, Boehringer D, Ban N
EMBO J 36 475-486 (2017)
PMID: 28007896
Related structures: EMD-3532

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 27-mer (preferred)
PDBe Complex ID:
PDB-CPX-139069 (preferred)
Entry contents:
26 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (27 distinct):
Large ribosomal subunit protein bL31c Chain: 0
Molecule details ›
Chain: 0
Length: 130 amino acids
Theoretical weight: 14.75 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82249 (Residues: 1-130; Coverage: 100%)
Gene names: RPL31, SOVF_125040
Sequence domains: Ribosomal protein L31
plastid ribosomal protein bS1c Chain: 8
Molecule details ›
Chain: 8
Length: 174 amino acids
Theoretical weight: 14.83 KDa
Source organism: Spinacia oleracea
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 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 uS5c Chain: e
Molecule details ›
Chain: e
Length: 308 amino acids
Theoretical weight: 33.63 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9ST69 (Residues: 1-308; Coverage: 100%)
Gene names: SOVF_195380, rps5
Sequence domains:
Small ribosomal subunit protein bS6c alpha Chain: f
Molecule details ›
Chain: f
Length: 211 amino acids
Theoretical weight: 23.51 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82403 (Residues: 1-211; Coverage: 100%)
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: 208 amino acids
Theoretical weight: 22.42 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82278 (Residues: 1-208; Coverage: 100%)
Gene names: PRPS9, SOVF_016530
Sequence domains: Ribosomal protein S9/S16
Structure domains: Ribosomal Protein S5; domain 2
Small ribosomal subunit protein uS10c Chain: j
Molecule details ›
Chain: j
Length: 195 amino acids
Theoretical weight: 21.44 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82162 (Residues: 1-195; Coverage: 100%)
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
Small ribosomal subunit protein uS13c Chain: m
Molecule details ›
Chain: m
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82163 (Residues: 1-172; Coverage: 100%)
Gene names: RPS13, SOVF_121110
Sequence domains: Ribosomal protein S13/S18
Structure domains:
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 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
Structure domains: S15/NS1, RNA-binding
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: 165 amino acids
Theoretical weight: 18.15 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82137 (Residues: 1-165; Coverage: 100%)
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
plastid ribosomal protein bS20c Chain: t
Molecule details ›
Chain: t
Length: 183 amino acids
Theoretical weight: 20.15 KDa
Source organism: Spinacia oleracea
Structure domains: Ribosomal protein S20
Small ribosomal subunit protein bS21c Chain: u
Molecule details ›
Chain: u
Length: 180 amino acids
Theoretical weight: 20.62 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82024 (Residues: 1-180; Coverage: 100%)
Gene names: SOVF_070750, rps21
Sequence domains: Ribosomal protein S21
Small ribosomal subunit protein cS22 Chain: v
Molecule details ›
Chain: v
Length: 260 amino acids
Theoretical weight: 28.33 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82277 (Residues: 1-260; Coverage: 100%)
Gene names: PSRP2, SOVF_116380
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
Small ribosomal subunit protein cS23 Chain: w
Molecule details ›
Chain: w
Length: 179 amino acids
Theoretical weight: 20.31 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82412 (Residues: 1-179; Coverage: 100%)
Gene names: PSRP3, SOVF_058240
Sequence domains: Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65)
Small ribosomal subunit protein bTHXc Chain: x
Molecule details ›
Chain: x
Length: 101 amino acids
Theoretical weight: 10.6 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P47910 (Residues: 1-101; Coverage: 100%)
Gene names: PSRP4, RPS31, SOVF_048530
Sequence domains: Ribosomal protein S31e
Ribosome-binding factor PSRP1, chloroplastic Chain: y
Molecule details ›
Chain: y
Length: 302 amino acids
Theoretical weight: 33.8 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P19954 (Residues: 1-302; Coverage: 100%)
Gene names: PSRP1, RPS22, RPS30, SOVF_177810
Sequence domains:
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

1 bound ligand:
Ligand MG 185 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.646Å
Relevant EMDB volumes: EMD-3532

Quick links

Citations

13 review citations

Does functional specialization of ribosomes really exist?
Ferretti et al. (2019)
12 more

4 mentions without citation

Molecular landscape of etioplast inner membranes in higher plants.
Floris et al. (2021)
3 more