› 6eri

Electron Microscopy
3Å resolution

Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor

Released:
DOI: 10.2210/pdb6eri/pdb
PDB entry 6eri coloured by chain, front view.
PDB entry 6eri coloured by chain, side view.
PDB entry 6eri coloured by chain, top view.
Source organism: Spinacia oleracea
Primary publication:
Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor.
Perez Boerema A, Aibara S, Paul B, Tobiasson V, Kimanius D, Forsberg BO, Wallden K, Lindahl E, Amunts A
Nat Plants 4 212-217 (2018)
PMID: 29610536
Related structures: EMD-3941

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 57-mer (preferred)
PDBe Complex ID:
PDB-CPX-129285 (preferred)
Entry contents:
53 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (57 distinct):
Large ribosomal subunit protein uL2cz/uL2cy Chain: AC
Molecule details ›
Chain: AC
Length: 246 amino acids
Theoretical weight: 26.99 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06509 (Residues: 26-271; Coverage: 90%)
Gene names: rpl2-A, rpl2-B
Sequence domains:
Large ribosomal subunit protein uL3c Chain: AD
Molecule details ›
Chain: AD
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: AE
Molecule details ›
Chain: AE
Length: 212 amino acids
Theoretical weight: 23.8 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: O49937 (Residues: 51-262; Coverage: 72%)
Gene names: RPL4, SOVF_029280
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5c Chain: AF
Molecule details ›
Chain: AF
Length: 207 amino acids
Theoretical weight: 23.02 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82192 (Residues: 52-258; Coverage: 80%)
Gene names: PrpL5, RPL5, SOVF_057730
Sequence domains:
Large ribosomal subunit protein uL6c Chain: AG
Molecule details ›
Chain: AG
Length: 172 amino acids
Theoretical weight: 19.13 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82193 (Residues: 44-215; Coverage: 78%)
Gene names: RPL6, SOVF_107200
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9c Chain: AH
Molecule details ›
Chain: AH
Length: 46 amino acids
Theoretical weight: 5.21 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82180 (Residues: 43-88; Coverage: 24%)
Gene names: RPL9, SOVF_040960
Sequence domains: Ribosomal protein L9, N-terminal domain
Large ribosomal subunit protein uL13c Chain: AJ
Molecule details ›
Chain: AJ
Length: 200 amino acids
Theoretical weight: 22.99 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P12629 (Residues: 49-248; Coverage: 80%)
Gene names: RPL13, SOVF_093170
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14c Chain: AK
Molecule details ›
Chain: AK
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
Large ribosomal subunit protein uL15c Chain: AL
Molecule details ›
Chain: AL
Length: 184 amino acids
Theoretical weight: 20.06 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P22798 (Residues: 78-261; Coverage: 68%)
Gene names: RPL15, SOVF_177460
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16c Chain: AM
Molecule details ›
Chain: AM
Length: 134 amino acids
Theoretical weight: 15.27 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P17353 (Residues: 1-134; Coverage: 99%)
Gene name: rpl16
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17c Chain: AN
Molecule details ›
Chain: AN
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
Large ribosomal subunit protein uL18c Chain: AO
Molecule details ›
Chain: AO
Length: 121 amino acids
Theoretical weight: 13.6 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82195 (Residues: 46-166; Coverage: 73%)
Gene names: PRPL18, RPL18, SOVF_159210
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19c Chain: AP
Molecule details ›
Chain: AP
Length: 118 amino acids
Theoretical weight: 13.54 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82413 (Residues: 115-232; Coverage: 51%)
Gene names: PRPL19, RPL19, SOVF_150800
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20c Chain: AQ
Molecule details ›
Chain: AQ
Length: 115 amino acids
Theoretical weight: 14.1 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P28803 (Residues: 2-116; Coverage: 90%)
Gene name: rpl20
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21c Chain: AR
Molecule details ›
Chain: AR
Length: 165 amino acids
Theoretical weight: 18.75 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P24613 (Residues: 72-236; Coverage: 65%)
Gene names: RPL21, SOVF_056040
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22c Chain: AS
Molecule details ›
Chain: AS
Length: 171 amino acids
Theoretical weight: 19.83 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P09594 (Residues: 25-195; Coverage: 86%)
Gene name: rpl22
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23c Chain: AT
Molecule details ›
Chain: AT
Length: 92 amino acids
Theoretical weight: 10.58 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9LWB5 (Residues: 103-194; Coverage: 47%)
Gene names: RPL23, SOVF_109700
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24c Chain: AU
Molecule details ›
Chain: AU
Length: 127 amino acids
Theoretical weight: 14.49 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P27683 (Residues: 49-175; Coverage: 66%)
Gene names: RPL24, SOVF_183870
Sequence domains:
Large ribosomal subunit protein bL27c Chain: AW
Molecule details ›
Chain: AW
Length: 114 amino acids
Theoretical weight: 12.97 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82190 (Residues: 60-173; Coverage: 59%)
Gene names: RPL27, SOVF_107450
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28c Chain: AX
Molecule details ›
Chain: AX
Length: 76 amino acids
Theoretical weight: 8.89 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82245 (Residues: 72-147; Coverage: 51%)
Gene names: RPL28, SOVF_085320
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29c Chain: AY
Molecule details ›
Chain: AY
Length: 99 amino acids
Theoretical weight: 11.9 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82248 (Residues: 59-157; Coverage: 59%)
Gene names: RPL29, SOVF_096810
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein bL31c Chain: AZ
Molecule details ›
Chain: AZ
Length: 66 amino acids
Theoretical weight: 7.62 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82249 (Residues: 37-102; Coverage: 51%)
Gene names: RPL31, SOVF_125040
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32c Chain: Aa
Molecule details ›
Chain: Aa
Length: 48 amino acids
Theoretical weight: 5.6 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P28804 (Residues: 2-49; Coverage: 84%)
Gene name: rpl32
Large ribosomal subunit protein bL33c Chain: Ab
Molecule details ›
Chain: Ab
Length: 60 amino acids
Theoretical weight: 7.02 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P28805 (Residues: 6-65; Coverage: 91%)
Gene name: rpl33
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34c Chain: Ac
Molecule details ›
Chain: Ac
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
Large ribosomal subunit protein bL35c Chain: Ad
Molecule details ›
Chain: Ad
Length: 72 amino acids
Theoretical weight: 8.39 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P23326 (Residues: 88-159; Coverage: 45%)
Gene names: RPL35, SOVF_080710
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36c Chain: Ae
Molecule details ›
Chain: Ae
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 cL38 Chain: Af
Molecule details ›
Chain: Af
Length: 47 amino acids
Theoretical weight: 5.32 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82411 (Residues: 48-94; Coverage: 41%)
Gene names: PSRP6, SOVF_082300
Sequence domains: Family of unknown function (DUF5323)
Large ribosomal subunit protein cL37 gamma Chain: Aw
Molecule details ›
Chain: Aw
Length: 49 amino acids
Theoretical weight: 6.09 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P27684 (Residues: 94-142; Coverage: 35%)
Gene names: PSRP5, RPL40, SOVF_000530
Ribosome-recycling factor, chloroplastic Chain: Az
Molecule details ›
Chain: Az
Length: 191 amino acids
Theoretical weight: 21.64 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82231 (Residues: 79-269; Coverage: 71%)
Gene names: FRRHCP, RRF
Sequence domains: Ribosome recycling factor
Small ribosomal subunit protein uS2c Chain: BB
Molecule details ›
Chain: BB
Length: 215 amino acids
Theoretical weight: 24.17 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P08242 (Residues: 22-236; Coverage: 91%)
Gene name: rps2
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3c Chain: BC
Molecule details ›
Chain: BC
Length: 217 amino acids
Theoretical weight: 24.83 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P09595 (Residues: 2-218; Coverage: 100%)
Gene name: rps3
Sequence domains: Ribosomal protein S3, C-terminal domain
Small ribosomal subunit protein uS4c Chain: BD
Molecule details ›
Chain: BD
Length: 200 amino acids
Theoretical weight: 23.32 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P13788 (Residues: 2-201; Coverage: 100%)
Gene name: rps4
Sequence domains:
Small ribosomal subunit protein uS5c Chain: BE
Molecule details ›
Chain: BE
Length: 158 amino acids
Theoretical weight: 16.99 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9ST69 (Residues: 151-308; Coverage: 51%)
Gene names: SOVF_195380, rps5
Sequence domains:
Small ribosomal subunit protein bS6c epsilon Chain: BF
Molecule details ›
Chain: BF
Length: 113 amino acids
Theoretical weight: 12.97 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82403 (Residues: 99-211; Coverage: 54%)
Gene names: RPS6, SOVF_120630
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7cz/uS7cy Chain: BG
Molecule details ›
Chain: BG
Length: 151 amino acids
Theoretical weight: 16.8 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82129 (Residues: 2-152; Coverage: 97%)
Gene names: rps7-A, rps7-B
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8c Chain: BH
Molecule details ›
Chain: BH
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
Small ribosomal subunit protein uS9c Chain: BI
Molecule details ›
Chain: BI
Length: 141 amino acids
Theoretical weight: 15.48 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82278 (Residues: 67-207; Coverage: 68%)
Gene names: PRPS9, SOVF_016530
Sequence domains: Ribosomal protein S9/S16
30S ribosomal protein S10 beta, chloroplastic Chain: BJ
Molecule details ›
Chain: BJ
Length: 98 amino acids
Theoretical weight: 11.36 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82162 (Residues: 98-195; Coverage: 50%)
Gene names: RPS10, SOVF_026730
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11c Chain: BK
Molecule details ›
Chain: BK
Length: 110 amino acids
Theoretical weight: 11.84 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06506 (Residues: 29-138; Coverage: 80%)
Gene name: rps11
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12cz/uS12cy Chain: BL
Molecule details ›
Chain: BL
Length: 122 amino acids
Theoretical weight: 13.66 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P62128 (Residues: 2-123; Coverage: 99%)
Gene names: rps12-A, rps12-B
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13c Chain: BM
Molecule details ›
Chain: BM
Length: 111 amino acids
Theoretical weight: 13.08 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82163 (Residues: 48-158; Coverage: 65%)
Gene names: RPS13, SOVF_121110
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14c Chain: BN
Molecule details ›
Chain: BN
Length: 99 amino acids
Theoretical weight: 11.73 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06507 (Residues: 2-100; Coverage: 99%)
Gene name: rps14
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15c Chain: BO
Molecule details ›
Chain: BO
Length: 72 amino acids
Theoretical weight: 8.62 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9M3I4 (Residues: 18-89; Coverage: 80%)
Gene name: rps15
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16c Chain: BP
Molecule details ›
Chain: BP
Length: 81 amino acids
Theoretical weight: 9.61 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P28807 (Residues: 1-81; Coverage: 92%)
Gene name: rps16
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17c Chain: BQ
Molecule details ›
Chain: BQ
Length: 84 amino acids
Theoretical weight: 9.69 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82137 (Residues: 58-141; Coverage: 51%)
Gene names: RPS17, SOVF_042540
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18c Chain: BR
Molecule details ›
Chain: BR
Length: 53 amino acids
Theoretical weight: 6.28 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9M3K7 (Residues: 27-79; Coverage: 53%)
Gene name: RPS18
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19c Chain: BS
Molecule details ›
Chain: BS
Length: 81 amino acids
Theoretical weight: 9.28 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06508 (Residues: 5-85; Coverage: 88%)
Gene name: rps19
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20c Chain: BT
Molecule details ›
Chain: BT
Length: 102 amino acids
Theoretical weight: 11.67 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82130 (Residues: 73-174; Coverage: 56%)
Gene name: RPS20
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21c Chain: BU
Molecule details ›
Chain: BU
Length: 59 amino acids
Theoretical weight: 7.35 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82024 (Residues: 83-141; Coverage: 33%)
Gene names: SOVF_070750, rps21
Sequence domains: Ribosomal protein S21
Ribosome-binding factor PSRP1, chloroplastic Chain: BV
Molecule details ›
Chain: BV
Length: 106 amino acids
Theoretical weight: 11.94 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P19954 (Residues: 73-178; Coverage: 35%)
Gene names: PSRP1, RPS22, RPS30, SOVF_177810
Sequence domains: Sigma 54 modulation protein / S30EA ribosomal protein
Small ribosomal subunit protein bTHXc Chain: BW
Molecule details ›
Chain: BW
Length: 37 amino acids
Theoretical weight: 4.1 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P47910 (Residues: 55-91; Coverage: 37%)
Gene names: PSRP4, RPS31, SOVF_048530
Sequence domains: Ribosomal protein S31e
bS1c Chain: BY
Molecule details ›
Chain: BY
Length: 170 amino acids
Theoretical weight: 14.49 KDa
Source organism: Spinacia oleracea
23S ribosomal RNA Chain: AA
Molecule details ›
Chain: AA
Length: 2810 nucleotides
Theoretical weight: 911.34 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
4.5S ribosomal RNA Chain: AB
Molecule details ›
Chain: AB
Length: 106 nucleotides
Theoretical weight: 34.33 KDa
5S ribosomal RNA Chain: Ax
Molecule details ›
Chain: Ax
Length: 118 nucleotides
Theoretical weight: 38.07 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chain: BA
Molecule details ›
Chain: BA
Length: 1481 nucleotides
Theoretical weight: 480.39 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand MG 343 x MG
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3Å
Relevant EMDB volumes: EMD-3941

Quick links

Citations

8 review citations

Stress response as implemented by hibernating ribosomes: a structural overview.
Matzov et al. (2019)
7 more

4 mentions without citation

Structural basis of mitochondrial translation.
Aibara et al. (2020)
3 more