7L08 image
Entry Detail
PDB ID:
7L08
EMDB ID:
Keywords:
Title:
Cryo-EM structure of the human 55S mitoribosome-RRFmt complex.
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2020-12-11
Release Date:
2021-05-12
Method Details:
Experimental Method:
Resolution:
3.49 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L32, mitochondrial
Chain IDs:VA (auth: 0)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L33, mitochondrial
Chain IDs:WA (auth: 1)
Chain Length:65
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L34, mitochondrial
Chain IDs:XA (auth: 2)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L35, mitochondrial
Chain IDs:YA (auth: 3)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L36, mitochondrial
Chain IDs:ZA (auth: 4)
Chain Length:103
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L37, mitochondrial
Chain IDs:RB (auth: 5)
Chain Length:423
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L38, mitochondrial
Chain IDs:SB (auth: 6)
Chain Length:380
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L39, mitochondrial
Chain IDs:TB (auth: 7)
Chain Length:338
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L40, mitochondrial
Chain IDs:AB (auth: 8)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L41, mitochondrial
Chain IDs:UB (auth: 9)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:16S RRNA
Chain IDs:FA (auth: A)
Chain Length:1559
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S34, mitochondrial
Chain IDs:Z (auth: A0)
Chain Length:218
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S35, mitochondrial
Chain IDs:Y (auth: A1)
Chain Length:323
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
Chain IDs:P (auth: A2)
Chain Length:118
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Aurora kinase A-interacting protein
Chain IDs:AA (auth: A3)
Chain Length:199
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Pentatricopeptide repeat domain-containing protein 3, mitochondrial
Chain IDs:BA (auth: A4)
Chain Length:689
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:12S rRNA
Chain IDs:A (auth: AA)
Chain Length:954
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S2, mitochondrial
Chain IDs:B (auth: AB)
Chain Length:296
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S24, mitochondrial
Chain IDs:C (auth: AC)
Chain Length:167
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S5, mitochondrial
Chain IDs:CA (auth: AD)
Chain Length:430
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S6, mitochondrial
Chain IDs:D (auth: AE)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S7, mitochondrial
Chain IDs:DA (auth: AF)
Chain Length:242
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S9, mitochondrial
Chain IDs:EA (auth: AG)
Chain Length:396
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S10, mitochondrial
Chain IDs:Q (auth: AH)
Chain Length:201
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S11, mitochondrial
Chain IDs:E (auth: AI)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S12, mitochondrial
Chain IDs:F (auth: AJ)
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S14, mitochondrial
Chain IDs:G (auth: AK)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S15, mitochondrial
Chain IDs:R (auth: AL)
Chain Length:257
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S16, mitochondrial
Chain IDs:H (auth: AM)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S17, mitochondrial
Chain IDs:I (auth: AN)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S18b, mitochondrial
Chain IDs:J (auth: AO)
Chain Length:258
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S18c, mitochondrial
Chain IDs:K (auth: AP)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S21, mitochondrial
Chain IDs:L (auth: AQ)
Chain Length:87
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S22, mitochondrial
Chain IDs:S (auth: AR)
Chain Length:360
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S23, mitochondrial
Chain IDs:T (auth: AS)
Chain Length:190
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S25, mitochondrial
Chain IDs:M (auth: AT)
Chain Length:173
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S26, mitochondrial
Chain IDs:U (auth: AU)
Chain Length:205
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S27, mitochondrial
Chain IDs:V (auth: AV)
Chain Length:414
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S28, mitochondrial
Chain IDs:N (auth: AW)
Chain Length:187
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S29, mitochondrial
Chain IDs:O (auth: AX)
Chain Length:398
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S31, mitochondrial
Chain IDs:W (auth: AY)
Chain Length:395
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:28S ribosomal protein S33, mitochondrial
Chain IDs:X (auth: AZ)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:tRNAVAL
Chain IDs:GA (auth: B)
Chain Length:73
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L2, mitochondrial
Chain IDs:HA (auth: D)
Chain Length:305
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L3, mitochondrial
Chain IDs:QB (auth: E)
Chain Length:348
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L4, mitochondrial
Chain IDs:IA (auth: F)
Chain Length:311
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L9, mitochondrial
Chain IDs:JA (auth: H)
Chain Length:267
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L10, mitochondrial
Chain IDs:LB (auth: I)
Chain Length:261
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L11, mitochondrial
Chain IDs:KB (auth: J)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L13, mitochondrial
Chain IDs:KA (auth: K)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L14, mitochondrial
Chain IDs:LA (auth: L)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L15, mitochondrial
Chain IDs:MA (auth: M)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L16, mitochondrial
Chain IDs:MB (auth: N)
Chain Length:251
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L17, mitochondrial
Chain IDs:NA (auth: O)
Chain Length:102
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein L18, isoform CRA_b
Chain IDs:NB (auth: P)
Chain Length:179
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L19, mitochondrial
Chain IDs:EC (auth: Q)
Chain Length:222
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L20, mitochondrial
Chain IDs:OA (auth: R)
Chain Length:149
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L21, mitochondrial
Chain IDs:PA (auth: S)
Chain Length:439
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L22, mitochondrial
Chain IDs:QA (auth: T)
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L12, mitochondrial
Chain IDs:GC (auth: TA), HC (auth: TB)
Chain Length:198
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L23, mitochondrial
Chain IDs:OB (auth: U)
Chain Length:65
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L24, mitochondrial
Chain IDs:PB (auth: V)
Chain Length:216
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L27, mitochondrial
Chain IDs:RA (auth: W)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L28, mitochondrial
Chain IDs:SA (auth: X)
Chain Length:256
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L47, mitochondrial
Chain IDs:TA (auth: Y)
Chain Length:250
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L30, mitochondrial
Chain IDs:UA (auth: Z)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L42, mitochondrial
Chain IDs:VB (auth: a)
Chain Length:1559
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L43, mitochondrial
Chain IDs:BB (auth: b)
Chain Length:73
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L44, mitochondrial
Chain IDs:WB (auth: c)
Chain Length:332
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L45, mitochondrial
Chain IDs:XB (auth: d)
Chain Length:305
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L46, mitochondrial
Chain IDs:CB (auth: e)
Chain Length:348
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L48, mitochondrial
Chain IDs:YB (auth: f)
Chain Length:311
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L49, mitochondrial
Chain IDs:DB (auth: g)
Chain Length:166
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L50, mitochondrial
Chain IDs:ZB (auth: h)
Chain Length:267
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L51, mitochondrial
Chain IDs:EB (auth: i)
Chain Length:261
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNA
Chain IDs:FB (auth: j)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L53, mitochondrial
Chain IDs:AC (auth: k)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L54, mitochondrial
Chain IDs:BC (auth: l)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein L55, mitochondrial
Chain IDs:GB (auth: m)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosomal protein 63, mitochondrial
Chain IDs:HB (auth: o)
Chain Length:102
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Peptidyl-tRNA hydrolase ICT1, mitochondrial
Chain IDs:CC (auth: p)
Chain Length:179
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Growth arrest and DNA damage-inducible proteins-interacting protein 1
Chain IDs:IB (auth: q)
Chain Length:222
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein S18a, mitochondrial
Chain IDs:JB (auth: r)
Chain Length:149
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:39S ribosomal protein S30, mitochondrial
Chain IDs:DC (auth: s)
Chain Length:439
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:P-site finger
Chain IDs:FC (auth: u)
Chain Length:65
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosome-recycling factor, mitochondrial
Chain IDs:IC (auth: z)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Distinct mechanisms of the human mitoribosome recycling and antibiotic resistance.
Nat Commun 12 3607 3607 (2021)
PMID: 34127662 DOI: 10.1038/s41467-021-23726-4

Abstact

Ribosomes are recycled for a new round of translation initiation by dissociation of ribosomal subunits, messenger RNA and transfer RNA from their translational post-termination complex. Here we present cryo-EM structures of the human 55S mitochondrial ribosome (mitoribosome) and the mitoribosomal large 39S subunit in complex with mitoribosome recycling factor (RRFmt) and a recycling-specific homolog of elongation factor G (EF-G2mt). These structures clarify an unusual role of a mitochondria-specific segment of RRFmt, identify the structural distinctions that confer functional specificity to EF-G2mt, and show that the deacylated tRNA remains with the dissociated 39S subunit, suggesting a distinct sequence of events in mitoribosome recycling. Furthermore, biochemical and structural analyses reveal that the molecular mechanism of antibiotic fusidic acid resistance for EF-G2mt is markedly different from that of mitochondrial elongation factor EF-G1mt, suggesting that the two human EF-Gmts have evolved diversely to negate the effect of a bacterial antibiotic.

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Primary Citation of related structures