› 5mlc

Electron Microscopy
3.9Å resolution

Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions

Released:
DOI: 10.2210/pdb5mlc/pdb
PDB entry 5mlc coloured by chain, front view.
PDB entry 5mlc coloured by chain, side view.
PDB entry 5mlc coloured by chain, top view.
Source organism: Spinacia oleracea
Primary publication:
Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions.
Graf M, Arenz S, Huter P, Dönhöfer A, Novácek J, Wilson DN
Nucleic Acids Res 45 2887-2896 (2017)
PMID: 27986857
Related structures: EMD-3525

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 32-mer (preferred)
PDBe Complex ID:
PDB-CPX-129288 (preferred)
Entry contents:
29 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (32 distinct):
Large ribosomal subunit protein uL2cz/uL2cy Chain: D
Molecule details ›
Chain: D
Length: 272 amino acids
Theoretical weight: 29.85 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06509 (Residues: 1-272; Coverage: 100%)
Gene names: rpl2-A, rpl2-B
Sequence domains:
Structure domains: Nucleic acid-binding proteins
Large ribosomal subunit protein uL3c Chain: E
Molecule details ›
Chain: E
Length: 305 amino acids
Theoretical weight: 33.03 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82191 (Residues: 1-305; Coverage: 100%)
Gene names: RPL3, SOVF_195350
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4c Chain: F
Molecule details ›
Chain: F
Length: 293 amino acids
Theoretical weight: 32.48 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: O49937 (Residues: 1-293; Coverage: 100%)
Gene names: RPL4, SOVF_029280
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5c Chain: G
Molecule details ›
Chain: G
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: H
Molecule details ›
Chain: H
Length: 220 amino acids
Theoretical weight: 24.52 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82193 (Residues: 1-220; Coverage: 100%)
Gene names: RPL6, SOVF_107200
Sequence domains: Ribosomal protein L6
Structure domains: Ribosomal protein L6, alpha-beta domain
Large ribosomal subunit protein bL9c Chain: I
Molecule details ›
Chain: I
Length: 196 amino acids
Theoretical weight: 22.04 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82180 (Residues: 1-196; Coverage: 100%)
Gene names: RPL9, SOVF_040960
Sequence domains:
Large ribosomal subunit protein uL13c Chain: L
Molecule details ›
Chain: L
Length: 250 amino acids
Theoretical weight: 28.21 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P12629 (Residues: 1-250; Coverage: 100%)
Gene names: RPL13, SOVF_093170
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14c Chain: M
Molecule details ›
Chain: M
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: N
Molecule details ›
Chain: N
Length: 271 amino acids
Theoretical weight: 29.08 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P22798 (Residues: 1-271; Coverage: 100%)
Gene names: RPL15, SOVF_177460
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16c Chain: O
Molecule details ›
Chain: O
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: P
Molecule details ›
Chain: P
Length: 126 amino acids
Theoretical weight: 14.58 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82194 (Residues: 1-126; Coverage: 100%)
Gene names: RPL17, SOVF_059230
Sequence domains: Ribosomal protein L17
Structure domains: Ribosomal protein L17
Large ribosomal subunit protein uL18c Chain: Q
Molecule details ›
Chain: Q
Length: 166 amino acids
Theoretical weight: 18.41 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82195 (Residues: 1-166; Coverage: 100%)
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: R
Molecule details ›
Chain: R
Length: 233 amino acids
Theoretical weight: 26.12 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82413 (Residues: 1-233; Coverage: 100%)
Gene names: PRPL19, RPL19, SOVF_150800
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20c Chain: S
Molecule details ›
Chain: S
Length: 128 amino acids
Theoretical weight: 15.73 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P28803 (Residues: 1-128; Coverage: 100%)
Gene name: rpl20
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21c Chain: T
Molecule details ›
Chain: T
Length: 256 amino acids
Theoretical weight: 28.44 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P24613 (Residues: 1-256; Coverage: 100%)
Gene names: RPL21, SOVF_056040
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22c Chain: U
Molecule details ›
Chain: U
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: V
Molecule details ›
Chain: V
Length: 198 amino acids
Theoretical weight: 21.83 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9LWB5 (Residues: 1-198; Coverage: 100%)
Gene names: RPL23, SOVF_109700
Sequence domains: Ribosomal protein L23
Structure domains: Alpha-Beta Plaits
Large ribosomal subunit protein uL24c Chain: W
Molecule details ›
Chain: W
Length: 191 amino acids
Theoretical weight: 21.48 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P27683 (Residues: 1-192; Coverage: 100%)
Gene names: RPL24, SOVF_183870
Sequence domains:
Large ribosomal subunit protein bL27c Chain: X
Molecule details ›
Chain: X
Length: 194 amino acids
Theoretical weight: 21.37 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82190 (Residues: 1-194; Coverage: 100%)
Gene names: RPL27, SOVF_107450
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28c Chain: Y
Molecule details ›
Chain: Y
Length: 148 amino acids
Theoretical weight: 16.46 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82245 (Residues: 1-148; Coverage: 100%)
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: 168 amino acids
Theoretical weight: 19.08 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82248 (Residues: 1-168; Coverage: 100%)
Gene names: RPL29, SOVF_096810
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein bL32c Chain: 2
Molecule details ›
Chain: 2
Length: 57 amino acids
Theoretical weight: 6.65 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P28804 (Residues: 1-57; Coverage: 100%)
Gene name: rpl32
Large ribosomal subunit protein bL33c Chain: 3
Molecule details ›
Chain: 3
Length: 66 amino acids
Theoretical weight: 7.67 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P28805 (Residues: 1-66; Coverage: 100%)
Gene name: rpl33
Sequence domains: Ribosomal protein L33
Structure domains: Ribosomal protein L33
Large ribosomal subunit protein bL34c Chain: 4
Molecule details ›
Chain: 4
Length: 152 amino acids
Theoretical weight: 16.13 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82244 (Residues: 1-152; Coverage: 100%)
Gene names: RPL34, SOVF_073030
Sequence domains: Ribosomal protein L34
Structure domains: Helix Hairpins
Large ribosomal subunit protein bL35c Chain: 5
Molecule details ›
Chain: 5
Length: 159 amino acids
Theoretical weight: 17.38 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P23326 (Residues: 1-159; Coverage: 100%)
Gene names: RPL35, SOVF_080710
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36c Chain: 6
Molecule details ›
Chain: 6
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
Ribosome-recycling factor, chloroplastic Chain: 9
Molecule details ›
Chain: 9
Length: 271 amino acids
Theoretical weight: 30.48 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82231 (Residues: 1-271; Coverage: 100%)
Gene names: FRRHCP, RRF
Sequence domains: Ribosome recycling factor
Structure domains: Ribosome-recycling factor
Large ribosomal subunit protein cL37 alpha Chain: 7
Molecule details ›
Chain: 7
Length: 142 amino acids
Theoretical weight: 15.35 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: 8
Molecule details ›
Chain: 8
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)
23S ribosomal RNA, chloroplastic Chain: A
Molecule details ›
Chain: A
Length: 2811 nucleotides
Theoretical weight: 911.65 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA, chloroplastic Chain: B
Molecule details ›
Chain: B
Length: 121 nucleotides
Theoretical weight: 39.01 KDa
Sequence domains: 5S ribosomal RNA
4.8S ribosomal RNA, chloroplastic Chain: C
Molecule details ›
Chain: C
Length: 103 nucleotides
Theoretical weight: 33.33 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-3525

Quick links

Citations

5 review citations

Ribosome Hibernation.
Prossliner et al. (2018)
4 more

1 mention without citation

Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions.
Graf et al. (2017)