PDBsum entry 3j7y

Ribosome

PDB id: 3j7y

Contents

Protein chains

236 a.a.

300 a.a.

250 a.a.

95 a.a.

158 a.a.

140 a.a.

177 a.a.

115 a.a.

287 a.a.

205 a.a.

152 a.a.

133 a.a.

204 a.a.

140 a.a.

156 a.a.

166 a.a.

111 a.a.

189 a.a.

107 a.a.

243 a.a.

176 a.a.

120 a.a.

98 a.a.

52 a.a.

43 a.a.

95 a.a.

36 a.a.

376 a.a.

325 a.a.

266 a.a.

57 a.a.

109 a.a.

39 a.a.

148 a.a.

275 a.a.

162 a.a.

134 a.a.

95 a.a.

129 a.a.

100 a.a.

96 a.a.

85 a.a.

84 a.a.

94 a.a.

83 a.a.

128 a.a.

146 a.a.

370 a.a.

123 a.a.

DNA/RNA

Ligands

AMP

Metals

_MG ×66

_ZN ×3

PDB id:

3j7y

Name:

Ribosome

Title:

Structure of the large ribosomal subunit from human mitochondria

Structure:

16s rrna. Chain: a. Mt-trnaval. Chain: b. Ul2. Chain: d. Ul3. Chain: e. Ul4.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cell_line: hek293. Cell_line: hek293

Authors:

A.Brown,A.Amunts,X.C.Bai,Y.Sugimoto,P.C.Edwards,G.Murshudov, S.H.W.Scheres,V.Ramakrishnan

Key ref:

A.Brown et al. (2014). Structure of the large ribosomal subunit from human mitochondria. Science, 346, 718-722. PubMed id: 25278503 DOI: 10.1126/science.1258026

Date:

26-Aug-14 Release date: 15-Oct-14

Protein chain

Q5T653  (RM02_HUMAN) -  Large ribosomal subunit protein uL2m from Homo sapiens

Seq: 305 a.a.

Struc: 236 a.a.

Protein chain

P09001  (RM03_HUMAN) -  Large ribosomal subunit protein uL3m from Homo sapiens

Seq: 348 a.a.

Struc: 300 a.a.

Protein chain

Q9BYD3  (RM04_HUMAN) -  Large ribosomal subunit protein uL4m from Homo sapiens

Seq: 311 a.a.

Struc: 250 a.a.

Protein chain

Q9BYD2  (RM09_HUMAN) -  Large ribosomal subunit protein bL9m from Homo sapiens

Seq: 267 a.a.

Struc: 95 a.a.

Protein chain

Q7Z7H8  (RM10_HUMAN) -  Large ribosomal subunit protein uL10m from Homo sapiens

Seq: 261 a.a.

Struc: 158 a.a.

Protein chain

Q9Y3B7  (RM11_HUMAN) -  Large ribosomal subunit protein uL11m from Homo sapiens

Seq: 192 a.a.

Struc: 140 a.a.

Protein chain

Q9BYD1  (RM13_HUMAN) -  Large ribosomal subunit protein uL13m from Homo sapiens

Seq: 178 a.a.

Struc: 177 a.a.

Protein chain

Q6P1L8  (RM14_HUMAN) -  Large ribosomal subunit protein uL14m from Homo sapiens

Seq: 145 a.a.

Struc: 115 a.a.

Protein chain

Q9P015  (RM15_HUMAN) -  Large ribosomal subunit protein uL15m from Homo sapiens

Seq: 296 a.a.

Struc: 287 a.a.

Protein chain

Q9NX20  (RM16_HUMAN) -  Large ribosomal subunit protein uL16m from Homo sapiens

Seq: 251 a.a.

Struc: 205 a.a.

Protein chain

Q9NRX2  (RM17_HUMAN) -  Large ribosomal subunit protein bL17m from Homo sapiens

Seq: 175 a.a.

Struc: 152 a.a.

Protein chain

Q9H0U6  (RM18_HUMAN) -  Large ribosomal subunit protein uL18m from Homo sapiens

Seq: 180 a.a.

Struc: 133 a.a.

Protein chain

P49406  (RM19_HUMAN) -  Large ribosomal subunit protein bL19m from Homo sapiens

Seq: 292 a.a.

Struc: 204 a.a.

Protein chain

Q9BYC9  (RM20_HUMAN) -  Large ribosomal subunit protein bL20m from Homo sapiens

Seq: 149 a.a.

Struc: 140 a.a.

Protein chain

Q7Z2W9  (RM21_HUMAN) -  Large ribosomal subunit protein bL21m from Homo sapiens

Seq: 205 a.a.

Struc: 156 a.a.

Protein chain

Q9NWU5  (RM22_HUMAN) -  Large ribosomal subunit protein uL22m from Homo sapiens

Seq: 206 a.a.

Struc: 166 a.a.

Protein chain

Q16540  (RM23_HUMAN) -  Large ribosomal subunit protein uL23m from Homo sapiens

Seq: 153 a.a.

Struc: 111 a.a.

Protein chain

Q96A35  (RM24_HUMAN) -  Large ribosomal subunit protein uL24m from Homo sapiens

Seq: 216 a.a.

Struc: 189 a.a.

Protein chain

Q9P0M9  (RM27_HUMAN) -  Large ribosomal subunit protein bL27m from Homo sapiens

Seq: 148 a.a.

Struc: 107 a.a.

Protein chain

Q13084  (RM28_HUMAN) -  Large ribosomal subunit protein bL28m from Homo sapiens

Seq: 256 a.a.

Struc: 243 a.a.*

Protein chain

Q9HD33  (RM47_HUMAN) -  Large ribosomal subunit protein uL29m from Homo sapiens

Seq: 250 a.a.

Struc: 176 a.a.

Protein chain

Q8TCC3  (RM30_HUMAN) -  Large ribosomal subunit protein uL30m from Homo sapiens

Seq: 161 a.a.

Struc: 120 a.a.

Protein chain

Q9BYC8  (RM32_HUMAN) -  Large ribosomal subunit protein bL32m from Homo sapiens

Seq: 188 a.a.

Struc: 98 a.a.

Protein chain

O75394  (RM33_HUMAN) -  Large ribosomal subunit protein bL33m from Homo sapiens

Seq: 65 a.a.

Struc: 52 a.a.

Protein chain

Q9BQ48  (RM34_HUMAN) -  Large ribosomal subunit protein bL34m from Homo sapiens

Seq: 92 a.a.

Struc: 43 a.a.

Protein chain

Q9NZE8  (RM35_HUMAN) -  Large ribosomal subunit protein bL35m from Homo sapiens

Seq: 188 a.a.

Struc: 95 a.a.

Protein chain

Q9P0J6  (RM36_HUMAN) -  Large ribosomal subunit protein bL36m from Homo sapiens

Seq: 103 a.a.

Struc: 36 a.a.

Protein chain

Q9BZE1  (RM37_HUMAN) -  Large ribosomal subunit protein mL37 from Homo sapiens

Seq: 423 a.a.

Struc: 376 a.a.

Protein chain

Q96DV4  (RM38_HUMAN) -  Large ribosomal subunit protein mL38 from Homo sapiens

Seq: 380 a.a.

Struc: 325 a.a.

Protein chain

Q9NYK5  (RM39_HUMAN) -  Large ribosomal subunit protein mL39 from Homo sapiens

Seq: 338 a.a.

Struc: 266 a.a.

Protein chain

Q9NQ50  (RM40_HUMAN) -  Large ribosomal subunit protein mL40 from Homo sapiens

Seq: 206 a.a.

Struc: 57 a.a.

Protein chain

Q8IXM3  (RM41_HUMAN) -  Large ribosomal subunit protein mL41 from Homo sapiens

Seq: 137 a.a.

Struc: 109 a.a.

Protein chain

Q9Y6G3  (RM42_HUMAN) -  Large ribosomal subunit protein mL42 from Homo sapiens

Seq: 142 a.a.

Struc: 39 a.a.

Protein chain

Q8N983  (RM43_HUMAN) -  Large ribosomal subunit protein mL43 from Homo sapiens

Seq: 215 a.a.

Struc: 148 a.a.

Protein chain

Q9H9J2  (RM44_HUMAN) -  Large ribosomal subunit protein mL44 from Homo sapiens

Seq: 332 a.a.

Struc: 275 a.a.

Protein chain

Q9BRJ2  (RM45_HUMAN) -  Large ribosomal subunit protein mL45 from Homo sapiens

Seq: 306 a.a.

Struc: 162 a.a.

Protein chain

Q9H2W6  (RM46_HUMAN) -  Large ribosomal subunit protein mL46 from Homo sapiens

Seq: 279 a.a.

Struc: 134 a.a.

Protein chain

Q96GC5  (RM48_HUMAN) -  Large ribosomal subunit protein mL48 from Homo sapiens

Seq: 212 a.a.

Struc: 95 a.a.*

Protein chain

Q13405  (RM49_HUMAN) -  Large ribosomal subunit protein mL49 from Homo sapiens

Seq: 166 a.a.

Struc: 129 a.a.

Protein chain

Q8N5N7  (RM50_HUMAN) -  Large ribosomal subunit protein mL50 from Homo sapiens

Seq: 158 a.a.

Struc: 100 a.a.

Protein chain

Q4U2R6  (RM51_HUMAN) -  Large ribosomal subunit protein mL51 from Homo sapiens

Seq: 128 a.a.

Struc: 96 a.a.

Protein chain

Q86TS9  (RM52_HUMAN) -  Large ribosomal subunit protein mL52 from Homo sapiens

Seq: 123 a.a.

Struc: 85 a.a.

Protein chain

Q96EL3  (RM53_HUMAN) -  Large ribosomal subunit protein mL53 from Homo sapiens

Seq: 112 a.a.

Struc: 84 a.a.

Protein chain

Q9BQC6  (RT63_HUMAN) -  Large ribosomal subunit protein mL63 from Homo sapiens

Seq: 102 a.a.

Struc: 94 a.a.

Protein chain

Q14197  (ICT1_HUMAN) -  Large ribosomal subunit protein mL62 from Homo sapiens

Seq: 206 a.a.

Struc: 83 a.a.

Protein chain

Q8TAE8  (G45IP_HUMAN) -  Large ribosomal subunit protein mL64 from Homo sapiens

Seq: 222 a.a.

Struc: 128 a.a.

Protein chain

Q9NVS2  (RT18A_HUMAN) -  Large ribosomal subunit protein mL66 from Homo sapiens

Seq: 196 a.a.

Struc: 146 a.a.

Protein chain

Q9NP92  (RT30_HUMAN) -  Large ribosomal subunit protein mL65 from Homo sapiens

Seq: 439 a.a.

Struc: 370 a.a.

Protein chain

No UniProt id for this chain

Struc: 123 a.a.

* PDB and UniProt seqs differ at 19 residue positions (black crosses)

DNA/RNA chains

G-C-U-A-A-A-C-C-U-A-G-C-C-C-C-A-A-A-C-C-C-A-C-U-C-C-A-C-C-U-U-A-C-U-A-C-C-A-G- ... 1472 bases

C-A-G-A-G-U-G-U-A-G-C-U-U-A-A-A-A-G-C-A-C-C-C-A-A-C-U-U-A-C-A-C-U-U-A-G-G-A-G- 57 bases

Enzyme reactions

• Enzyme class 2: Chain c: E.C.3.1.26.- - ?????
• Enzyme class 3: Chain p: E.C.3.1.1.29 - peptidyl-tRNA hydrolase.
• Reaction: an N-acyl-L-alpha-aminoacyl-tRNA + H2O = an N-acyl-L-amino acid + a tRNA + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1126/science.1258026

Science 346:718-722 (2014)

PubMed id: 25278503

Structure of the large ribosomal subunit from human mitochondria.

A.Brown, A.Amunts, X.C.Bai, Y.Sugimoto, P.C.Edwards, G.Murshudov, S.H.Scheres, V.Ramakrishnan.

ABSTRACT

Human mitochondrial ribosomes are highly divergent from all other known ribosomes and are specialized to exclusively translate membrane proteins. They are linked with hereditary mitochondrial diseases and are often the unintended targets of various clinically useful antibiotics. Using single-particle cryogenic electron microscopy, we have determined the structure of its large subunit to 3.4 angstrom resolution, revealing 48 proteins, 21 of which are specific to mitochondria. The structure unveils an adaptation of the exit tunnel for hydrophobic nascent peptides, extensive remodeling of the central protuberance, including recruitment of mitochondrial valine transfer RNA (tRNA(Val)) to play an integral structural role, and changes in the tRNA binding sites related to the unusual characteristics of mitochondrial tRNAs.