PDBsum entry 5mlc

Ribosome

PDB id: 5mlc

Contents

Protein chains

246 a.a.

219 a.a.

205 a.a.

179 a.a.

178 a.a.

45 a.a.

196 a.a.

120 a.a.

182 a.a.

135 a.a.

116 a.a.

118 a.a.

114 a.a.

116 a.a.

134 a.a.

152 a.a.

91 a.a.

129 a.a.

108 a.a.

75 a.a.

94 a.a.

42 a.a.

60 a.a.

61 a.a.

70 a.a.

37 a.a.

107 a.a.

46 a.a.

47 a.a.

DNA/RNA

PDB id:

5mlc

Name:

Ribosome

Title:

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

Structure:

23s ribosomal RNA, chloroplastic. Chain: a. 5s ribosomal RNA, chloroplastic. Chain: b. 4.8s ribosomal RNA, chloroplastic. Chain: c. 50s ribosomal protein l2, chloroplastic. Chain: d. Synonym: ribosomal protein cs-l4.

Source:

Spinacia oleracea. Spinach. Organism_taxid: 3562. Organism_taxid: 3562

Authors:

M.Graf,S.Arenz,P.Huter,A.Doenhoefer,J.Novacek,D.N.Wilson

Key ref:

M.Graf et al. (2017). Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions. Nucleic Acids Res, 45, 2887-2896. PubMed id: 27986857

Date:

06-Dec-16 Release date: 28-Dec-16

Protein chain

P06509  (RK2_SPIOL) -  Large ribosomal subunit protein uL2cz/uL2cy from Spinacia oleracea

Seq: 272 a.a.

Struc: 246 a.a.

Protein chain

P82191  (RK3_SPIOL) -  Large ribosomal subunit protein uL3c from Spinacia oleracea

Seq: 305 a.a.

Struc: 219 a.a.

Protein chain

O49937  (RK4_SPIOL) -  Large ribosomal subunit protein uL4c from Spinacia oleracea

Seq: 293 a.a.

Struc: 205 a.a.

Protein chain

P82192  (RK5_SPIOL) -  Large ribosomal subunit protein uL5c from Spinacia oleracea

Seq: 258 a.a.

Struc: 179 a.a.

Protein chain

P82193  (RK6_SPIOL) -  Large ribosomal subunit protein uL6c from Spinacia oleracea

Seq: 220 a.a.

Struc: 178 a.a.

Protein chain

P82180  (RK9_SPIOL) -  Large ribosomal subunit protein bL9c from Spinacia oleracea

Seq: 196 a.a.

Struc: 45 a.a.

Protein chain

P12629  (RK13_SPIOL) -  Large ribosomal subunit protein uL13c from Spinacia oleracea

Seq: 250 a.a.

Struc: 196 a.a.

Protein chain

P09596  (RK14_SPIOL) -  Large ribosomal subunit protein uL14c from Spinacia oleracea

Seq: 121 a.a.

Struc: 120 a.a.

Protein chain

P22798  (RK15_SPIOL) -  Large ribosomal subunit protein uL15c from Spinacia oleracea

Seq: 271 a.a.

Struc: 182 a.a.

Protein chain

P17353  (RK16_SPIOL) -  Large ribosomal subunit protein uL16c from Spinacia oleracea

Seq: 135 a.a.

Struc: 135 a.a.

Protein chain

P82194  (RK17_SPIOL) -  Large ribosomal subunit protein bL17c from Spinacia oleracea

Seq: 126 a.a.

Struc: 116 a.a.

Protein chain

P82195  (RK18_SPIOL) -  Large ribosomal subunit protein uL18c from Spinacia oleracea

Seq: 166 a.a.

Struc: 118 a.a.

Protein chain

P82413  (RK19_SPIOL) -  Large ribosomal subunit protein bL19c from Spinacia oleracea

Seq: 233 a.a.

Struc: 114 a.a.

Protein chain

P28803  (RK20_SPIOL) -  Large ribosomal subunit protein bL20c from Spinacia oleracea

Seq: 128 a.a.

Struc: 116 a.a.

Protein chain

P24613  (RK21_SPIOL) -  Large ribosomal subunit protein bL21c from Spinacia oleracea

Seq: 256 a.a.

Struc: 134 a.a.

Protein chain

P09594  (RK22_SPIOL) -  Large ribosomal subunit protein uL22c from Spinacia oleracea

Seq: 199 a.a.

Struc: 152 a.a.

Protein chain

Q9LWB5  (RK23_SPIOL) -  Large ribosomal subunit protein uL23c from Spinacia oleracea

Seq: 198 a.a.

Struc: 91 a.a.

Protein chain

P27683  (RK24_SPIOL) -  Large ribosomal subunit protein uL24c from Spinacia oleracea

Seq: 192 a.a.

Struc: 129 a.a.*

Protein chain

P82190  (RK27_SPIOL) -  Large ribosomal subunit protein bL27c from Spinacia oleracea

Seq: 194 a.a.

Struc: 108 a.a.

Protein chain

P82245  (RK28_SPIOL) -  Large ribosomal subunit protein bL28c from Spinacia oleracea

Seq: 148 a.a.

Struc: 75 a.a.

Protein chain

P82248  (RK29_SPIOL) -  Large ribosomal subunit protein uL29c from Spinacia oleracea

Seq: 168 a.a.

Struc: 94 a.a.

Protein chain

P28804  (RK32_SPIOL) -  Large ribosomal subunit protein bL32c from Spinacia oleracea

Seq: 57 a.a.

Struc: 42 a.a.

Protein chain

P28805  (RK33_SPIOL) -  Large ribosomal subunit protein bL33c from Spinacia oleracea

Seq: 66 a.a.

Struc: 60 a.a.

Protein chain

P82244  (RK34_SPIOL) -  Large ribosomal subunit protein bL34c from Spinacia oleracea

Seq: 152 a.a.

Struc: 61 a.a.

Protein chain

P23326  (RK35_SPIOL) -  Large ribosomal subunit protein bL35c from Spinacia oleracea

Seq: 159 a.a.

Struc: 70 a.a.

Protein chain

P12230  (RK36_SPIOL) -  Large ribosomal subunit protein bL36c from Spinacia oleracea

Seq: 37 a.a.

Struc: 37 a.a.

Protein chain

P82231  (RRFC_SPIOL) -  Ribosome-recycling factor, chloroplastic from Spinacia oleracea

Seq: 271 a.a.

Struc: 107 a.a.*

Protein chain

P27684  (PSRP5_SPIOL) -  Large ribosomal subunit protein cL37 alpha from Spinacia oleracea

Seq: 142 a.a.

Struc: 46 a.a.*

Protein chain

P82411  (PSRP6_SPIOL) -  Large ribosomal subunit protein cL38 from Spinacia oleracea

Seq: 116 a.a.

Struc: 47 a.a.

* PDB and UniProt seqs differ at 38 residue positions (black crosses)

DNA/RNA chains

U-U-C-A-A-A-C-G-A-G-G-A-A-A-G-G-C-U-U-A-C-G-G-U-G-G-A-U-A-C-C-U-A-G-G-C-A-C-C- ... 2750 bases

A-U-U-C-U-G-G-U-G-U-C-C-U-A-G-G-C-G-U-A-G-A-G-G-A-A-C-C-A-C-A-C-C-A-A-U-C-C-A- 120 bases

G-A-A-G-G-U-C-A-C-G-G-C-G-A-G-A-C-G-A-G-C-C-G-U-U-A-U-A-G-G-U-G-U-C-A-A-G-U-G- 93 bases

Nucleic Acids Res 45:2887-2896 (2017)

PubMed id: 27986857

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

M.Graf, S.Arenz, P.Huter, A.Dönhöfer, J.Novácek, D.N.Wilson.

ABSTRACT

Ribosomes are the protein synthesizing machines of the cell. Recent advances in cryo-EM have led to the determination of structures from a variety of species, including bacterial 70S and eukaryotic 80S ribosomes as well as mitoribosomes from eukaryotic mitochondria, however, to date high resolution structures of plastid 70S ribosomes have been lacking. Here we present a cryo-EM structure of the spinach chloroplast 70S ribosome, with an average resolution of 5.4 Å for the small 30S subunit and 3.6 Å for the large 50S ribosomal subunit. The structure reveals the location of the plastid-specific ribosomal proteins (RPs) PSRP1, PSRP4, PSRP5 and PSRP6 as well as the numerous plastid-specific extensions of the RPs. We discover many features by which the plastid-specific extensions stabilize the ribosome via establishing additional interactions with surrounding ribosomal RNA and RPs. Moreover, we identify a large conglomerate of plastid-specific protein mass adjacent to the tunnel exit site that could facilitate interaction of the chloroplast ribosome with the thylakoid membrane and the protein-targeting machinery. Comparing the Escherichia coli 70S ribosome with that of the spinach chloroplast ribosome provides detailed insight into the co-evolution of RP and rRNA.