› 5x8p

Electron Microscopy
3.4Å resolution

Structure of the 70S chloroplast ribosome from spinach

Released:
DOI: 10.2210/pdb5x8p/pdb
PDB entry 5x8p coloured by chain, front view.
PDB entry 5x8p coloured by chain, side view.
PDB entry 5x8p 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-6709

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 58-mer (preferred)
PDBe Complex ID:
PDB-CPX-129283 (preferred)
Entry contents:
54 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (58 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
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
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:
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:
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Small ribosomal subunit protein uS13c Chain: m
Molecule details ›
Chain: m
Length: 126 amino acids
Theoretical weight: 14.42 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82163 (Residues: 27-40, 41-155; Coverage: 69%)
Gene names: RPS13, SOVF_121110
Sequence domains: Ribosomal protein S13/S18
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
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
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
protein S20 Chain: t
Molecule details ›
Chain: t
Length: 108 amino acids
Theoretical weight: 12.18 KDa
Source organism: Spinacia oleracea
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:
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
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
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
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: 3.4Å
Relevant EMDB volumes: EMD-6709

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

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)
1 more