› 4v61

Electron Microscopy
9.4Å resolution

Homology model for the Spinach chloroplast 30S subunit fitted to 9.4A cryo-EM map of the 70S chlororibosome.

Released:
DOI: 10.2210/pdb4v61/pdb
PDB entry 4v61 coloured by chain, front view.
PDB entry 4v61 coloured by chain, side view.
PDB entry 4v61 coloured by chain, top view.
Source organism: Spinacia oleracea
Primary publication:
Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins.
Sharma MR, Wilson DN, Datta PP, Barat C, Schluenzen F, Fucini P, Agrawal RK
Proc Natl Acad Sci U S A 104 19315-20 (2007)
PMID: 18042701
Related structures: EMD-1417

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 53-mer (preferred)
PDBe Complex ID:
PDB-CPX-129286 (preferred)
Entry contents:
49 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (53 distinct):
Small ribosomal subunit protein uS2c Chain: AB
Molecule details ›
Chain: AB
Length: 231 amino acids
Theoretical weight: 26.09 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P08242 (Residues: 5-235; Coverage: 98%)
Gene name: rps2
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3c Chain: AC
Molecule details ›
Chain: AC
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 uS4c Chain: AD
Molecule details ›
Chain: AD
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 uS5c Chain: AE
Molecule details ›
Chain: AE
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: AF
Molecule details ›
Chain: AF
Length: 168 amino acids
Theoretical weight: 18.87 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82403 (Residues: 44-211; Coverage: 80%)
Gene names: RPS6, SOVF_120630
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7cz/uS7cy Chain: AG
Molecule details ›
Chain: AG
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: AH
Molecule details ›
Chain: AH
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: AI
Molecule details ›
Chain: AI
Length: 197 amino acids
Theoretical weight: 21.35 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82278 (Residues: 12-208; Coverage: 95%)
Gene names: PRPS9, SOVF_016530
Sequence domains: Ribosomal protein S9/S16
Ribosomal Protein S10 Chain: AJ
Molecule details ›
Chain: AJ
Length: 197 amino acids
Theoretical weight: 21.63 KDa
Source organism: Spinacia oleracea
Small ribosomal subunit protein uS11c Chain: AK
Molecule details ›
Chain: AK
Length: 140 amino acids
Theoretical weight: 15.09 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06506 (Residues: 1-22, 23-138; Coverage: 100%)
Gene name: rps11
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12cz/uS12cy Chain: AL
Molecule details ›
Chain: AL
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: AM
Molecule details ›
Chain: AM
Length: 145 amino acids
Theoretical weight: 16.31 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P82163 (Residues: 5-40, 41-155; Coverage: 79%)
Gene names: RPS13, SOVF_121110
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14c Chain: AN
Molecule details ›
Chain: AN
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 uS15c Chain: AO
Molecule details ›
Chain: AO
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: AP
Molecule details ›
Chain: AP
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
Ribosomal Protein S17 Chain: AQ
Molecule details ›
Chain: AQ
Length: 142 amino acids
Theoretical weight: 15.83 KDa
Source organism: Spinacia oleracea
Small ribosomal subunit protein bS18c Chain: AR
Molecule details ›
Chain: AR
Length: 103 amino acids
Theoretical weight: 12.34 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9M3K7 (Residues: 1-80, 81-101; Coverage: 100%)
Gene name: RPS18
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19c Chain: AS
Molecule details ›
Chain: AS
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
Ribosomal Protein S20 Chain: AT
Molecule details ›
Chain: AT
Length: 202 amino acids
Theoretical weight: 21.87 KDa
Source organism: Spinacia oleracea
Ribosomal Protein S21 Chain: AU
Molecule details ›
Chain: AU
Length: 190 amino acids
Theoretical weight: 21.7 KDa
Source organism: Spinacia oleracea
Large ribosomal subunit protein uL1c Chain: BD
Molecule details ›
Chain: BD
Length: 352 amino acids
Theoretical weight: 38.68 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9LE95 (Residues: 1-352; Coverage: 100%)
Gene names: RPL1, SOVF_186350
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL2cz/uL2cy Chain: BE
Molecule details ›
Chain: BE
Length: 269 amino acids
Theoretical weight: 29.48 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06509 (Residues: 1-269; Coverage: 99%)
Gene names: rpl2-A, rpl2-B
Sequence domains:
Ribosomal Protein L3 Chain: BF
Molecule details ›
Chain: BF
Length: 259 amino acids
Theoretical weight: 28.42 KDa
Source organism: Spinacia oleracea
Large ribosomal subunit protein uL4c Chain: BG
Molecule details ›
Chain: BG
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: BH
Molecule details ›
Chain: BH
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:
Ribosomal Protein L6 Chain: BI
Molecule details ›
Chain: BI
Length: 223 amino acids
Theoretical weight: 24.75 KDa
Source organism: Spinacia oleracea
Ribosomal Protein L9 Chain: BJ
Molecule details ›
Chain: BJ
Length: 197 amino acids
Theoretical weight: 22.17 KDa
Source organism: Spinacia oleracea
Large ribosomal subunit protein uL11c Chain: BK
Molecule details ›
Chain: BK
Length: 224 amino acids
Theoretical weight: 23.69 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P31164 (Residues: 1-224; Coverage: 100%)
Gene names: SOVF_048900, rpl11
Sequence domains:
Large ribosomal subunit protein uL13c Chain: BL
Molecule details ›
Chain: BL
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: BM
Molecule details ›
Chain: BM
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
Ribosomal Protein L15 Chain: BN
Molecule details ›
Chain: BN
Length: 257 amino acids
Theoretical weight: 27.49 KDa
Source organism: Spinacia oleracea
Large ribosomal subunit protein uL16c Chain: BO
Molecule details ›
Chain: BO
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
Ribosomal Protein L17 Chain: BP
Molecule details ›
Chain: BP
Length: 205 amino acids
Theoretical weight: 22.98 KDa
Source organism: Spinacia oleracea
Ribosomal Protein L18 Chain: BQ
Molecule details ›
Chain: BQ
Length: 161 amino acids
Theoretical weight: 17.85 KDa
Source organism: Spinacia oleracea
Large ribosomal subunit protein bL19c Chain: BR
Molecule details ›
Chain: BR
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: BS
Molecule details ›
Chain: BS
Length: 119 amino acids
Theoretical weight: 14.62 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P28803 (Residues: 1-119; Coverage: 93%)
Gene name: rpl20
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21c Chain: BT
Molecule details ›
Chain: BT
Length: 257 amino acids
Theoretical weight: 28.55 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P24613 (Residues: 1-122, 124-256; Coverage: 100%)
Gene names: RPL21, SOVF_056040
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22c Chain: BU
Molecule details ›
Chain: BU
Length: 199 amino acids
Theoretical weight: 23.28 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: BV
Molecule details ›
Chain: BV
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
Large ribosomal subunit protein uL24c Chain: BW
Molecule details ›
Chain: BW
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:
Ribosomal Protein L27 Chain: BX
Molecule details ›
Chain: BX
Length: 198 amino acids
Theoretical weight: 21.77 KDa
Source organism: Spinacia oleracea
Ribosomal Protein L28 Chain: BY
Molecule details ›
Chain: BY
Length: 151 amino acids
Theoretical weight: 16.73 KDa
Source organism: Spinacia oleracea
Ribosomal Protein L29 Chain: BZ
Molecule details ›
Chain: BZ
Length: 173 amino acids
Theoretical weight: 19.42 KDa
Source organism: Spinacia oleracea
Ribosomal Protein L31 Chain: B1
Molecule details ›
Chain: B1
Length: 144 amino acids
Theoretical weight: 16.06 KDa
Source organism: Spinacia oleracea
Large ribosomal subunit protein bL32c Chain: B2
Molecule details ›
Chain: B2
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: B3
Molecule details ›
Chain: B3
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
Large ribosomal subunit protein bL34c Chain: B4
Molecule details ›
Chain: B4
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
Large ribosomal subunit protein bL35c Chain: B5
Molecule details ›
Chain: B5
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
Ribosomal Protein L36 Chain: B6
Molecule details ›
Chain: B6
Length: 104 amino acids
Theoretical weight: 11.51 KDa
Source organism: Spinacia oleracea
16S ribosomal RNA Chain: AA
Molecule details ›
Chain: AA
Length: 1491 nucleotides
Theoretical weight: 483.49 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23S ribosomal RNA Chain: BA
Molecule details ›
Chain: BA
Length: 2810 nucleotides
Theoretical weight: 911.37 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: BB
Molecule details ›
Chain: BB
Length: 117 nucleotides
Theoretical weight: 37.74 KDa
Sequence domains: 5S ribosomal RNA
4.8S rRNA Chain: BC
Molecule details ›
Chain: BC
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: 9.4Å
Relevant EMDB volumes: EMD-1417

Quick links

Citations

15 review citations

The translational apparatus of plastids and its role in plant development.
Tiller et al. (2014)
14 more

1 mention without citation

Cryo-EM structure of the large subunit of the spinach chloroplast ribosome.
Ahmed et al. (2016)