PDBsum entry 5oom

Ribosome

PDB id: 5oom

Contents

Protein chains

220 a.a.

285 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.

141 a.a.

217 a.a.

140 a.a.

156 a.a.

159 a.a.

139 a.a.

192 a.a.

109 a.a.

243 a.a.

176 a.a.

120 a.a.

108 a.a.

52 a.a.

43 a.a.

95 a.a.

387 a.a.

324 a.a.

287 a.a.

99 a.a.

117 a.a.

82 a.a.

148 a.a.

275 a.a.

211 a.a.

217 a.a.

116 a.a.

129 a.a.

100 a.a.

97 a.a.

85 a.a.

80 a.a.

23 a.a.

45 a.a.

79 a.a.

127 a.a.

128 a.a.

146 a.a.

370 a.a.

28 a.a.

111 a.a.

69 a.a.

79 a.a.

DNA/RNA

Ligands

PNS

Metals

_MG ×49

_ZN ×2

PDB id:

5oom

Name:

Ribosome

Title:

Structure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rrna

Structure:

16s ribosomal RNA. Chain: a. Mitochondrial trnaval. Chain: b. 39s ribosomal protein l2, mitochondrial. Chain: d. Synonym: mrp-l2,mitochondrial large ribosomal subunit protein ul2m. 39s ribosomal protein l3, mitochondrial. Chain: e.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Organism_taxid: 9606

Authors:

A.Brown,S.Rathore,D.Kimanius,S.Aibara,X.C.Bai,J.Rorbach,A.Amunts, V.Ramakrishnan

Key ref:

A.Brown et al. (2017). Structures of the human mitochondrial ribosome in native states of assembly. Nat Struct Mol Biol, 24, 866-869. PubMed id: 28892042

Date:

08-Aug-17 Release date: 13-Sep-17

Protein chain

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

Seq: 305 a.a.

Struc: 220 a.a.

Protein chain

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

Seq: 348 a.a.

Struc: 285 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: 141 a.a.

Protein chain

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

Seq: 292 a.a.

Struc: 217 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: 159 a.a.

Protein chain

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

Seq: 153 a.a.

Struc: 139 a.a.

Protein chain

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

Seq: 216 a.a.

Struc: 192 a.a.

Protein chain

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

Seq: 148 a.a.

Struc: 109 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: 108 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

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

Seq: 423 a.a.

Struc: 387 a.a.

Protein chain

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

Seq: 380 a.a.

Struc: 324 a.a.

Protein chain

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

Seq: 338 a.a.

Struc: 287 a.a.

Protein chain

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

Seq: 206 a.a.

Struc: 99 a.a.

Protein chain

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

Seq: 137 a.a.

Struc: 117 a.a.

Protein chain

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

Seq: 142 a.a.

Struc: 82 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: 211 a.a.

Protein chain

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

Seq: 279 a.a.

Struc: 217 a.a.

Protein chain

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

Seq: 212 a.a.

Struc: 116 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: 97 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: 80 a.a.

Protein chain

Q6P161  (RM54_HUMAN) -  Large ribosomal subunit protein mL54 from Homo sapiens

Seq: 138 a.a.

Struc: 23 a.a.

Protein chain

Q7Z7F7  (RM55_HUMAN) -  Large ribosomal subunit protein mL55 from Homo sapiens

Seq: 128 a.a.

Struc: 45 a.a.

Protein chain

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

Seq: 102 a.a.

Struc: 79 a.a.

Protein chain

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

Seq: 206 a.a.

Struc: 127 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: 28 a.a.

Protein chain

Q96EH3  (MASU1_HUMAN) -  Mitochondrial assembly of ribosomal large subunit protein 1 from Homo sapiens

Seq: 234 a.a.

Struc: 111 a.a.

Protein chain

L0R8F8  (MIDUO_HUMAN) -  Mitochondrial ribosome and complex I assembly factor AltMIEF1 from Homo sapiens

Seq: 70 a.a.

Struc: 69 a.a.

Protein chain

O14561  (ACPM_HUMAN) -  Acyl carrier protein, mitochondrial from Homo sapiens

Seq: 156 a.a.

Struc: 79 a.a.

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-A- ... 1092 bases

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-A- 56 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

Nat Struct Mol Biol 24:866-869 (2017)

PubMed id: 28892042

Structures of the human mitochondrial ribosome in native states of assembly.

A.Brown, S.Rathore, D.Kimanius, S.Aibara, X.C.Bai, J.Rorbach, A.Amunts, V.Ramakrishnan.

ABSTRACT

Mammalian mitochondrial ribosomes (mitoribosomes) have less rRNA content and 36 additional proteins compared with the evolutionarily related bacterial ribosome. These differences make the assembly of mitoribosomes more complex than the assembly of bacterial ribosomes, but the molecular details of mitoribosomal biogenesis remain elusive. Here, we report the structures of two late-stage assembly intermediates of the human mitoribosomal large subunit (mt-LSU) isolated from a native pool within a human cell line and solved by cryo-EM to ∼3-Å resolution. Comparison of the structures reveals insights into the timing of rRNA folding and protein incorporation during the final steps of ribosomal maturation and the evolutionary adaptations that are required to preserve biogenesis after the structural diversification of mitoribosomes. Furthermore, the structures redefine the ribosome silencing factor (RsfS) family as multifunctional biogenesis factors and identify two new assembly factors (L0R8F8 and mt-ACP) not previously implicated in mitoribosomal biogenesis.