6YW5 image
Entry Detail
PDB ID:
6YW5
EMDB ID:
Keywords:
Title:
The structure of the small subunit of the mitoribosome from Neurospora crassa
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2020-04-29
Release Date:
2020-11-11
Method Details:
Experimental Method:
Resolution:
2.85 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:mS47
Chain IDs:IA (auth: 00), JA (auth: 99)
Chain Length:95
Number of Molecules:2
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:37S ribosomal protein mrp10, mitochondrial
Chain IDs:AA (auth: 11)
Chain Length:90
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:DUF1713 domain-containing protein
Chain IDs:BA (auth: 22)
Chain Length:344
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:IGR domain-containing protein
Chain IDs:CA (auth: 33)
Chain Length:236
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Fe superoxide dismutase
Chain IDs:DA (auth: 44), EA (auth: 55)
Chain Length:310
Number of Molecules:2
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:mS42
Chain IDs:FA (auth: 66)
Chain Length:348
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:mS46
Chain IDs:GA (auth: 77)
Chain Length:414
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
Chain IDs:HA (auth: 88)
Chain Length:508
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:uS2m
Chain IDs:A (auth: AA)
Chain Length:470
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Mito ribosomal protein S2
Chain IDs:B (auth: BB)
Chain Length:428
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Ribosomal protein S5, mitochondrial
Chain IDs:C (auth: CC)
Chain Length:508
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Mito ribosomal protein S4
Chain IDs:D (auth: DD)
Chain Length:453
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:37S ribosomal protein S5
Chain IDs:E (auth: EE)
Chain Length:477
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Mito ribosomal protein S6
Chain IDs:F (auth: FF)
Chain Length:117
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Ribosomal_S7 domain-containing protein
Chain IDs:G (auth: GG)
Chain Length:309
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S8
Chain IDs:H (auth: HH)
Chain Length:161
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:uS9m
Chain IDs:I (auth: II)
Chain Length:315
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:37S ribosomal protein S10, mitochondrial
Chain IDs:J (auth: JJ)
Chain Length:268
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein subunit S18
Chain IDs:K (auth: KK)
Chain Length:376
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Mitochondrial 30S ribosomal protein S12
Chain IDs:L (auth: LL)
Chain Length:174
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S13
Chain IDs:M (auth: MM)
Chain Length:119
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Mitochondrial 40S ribosomal protein MRP2
Chain IDs:N (auth: NN)
Chain Length:113
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Ribosomal protein S15
Chain IDs:O (auth: OO)
Chain Length:320
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Ribosomal protein S16, mitochondrial
Chain IDs:P (auth: PP)
Chain Length:107
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Mitochondrial 37S ribosomal protein S17
Chain IDs:Q (auth: QQ)
Chain Length:165
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Mito ribosomal protein S18
Chain IDs:R (auth: RR)
Chain Length:256
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein S19
Chain IDs:S (auth: SS)
Chain Length:91
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Mito ribosomal protein S21
Chain IDs:T (auth: TT)
Chain Length:236
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:37S ribosomal protein S25, mitochondrial
Chain IDs:U (auth: UU)
Chain Length:253
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:IF1
Chain IDs:LA (auth: V)
Chain Length:219
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:mS26
Chain IDs:V (auth: VV)
Chain Length:316
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:mS27
Chain IDs:W (auth: WW)
Chain Length:396
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:Mitochondrial ribosomal protein DAP3
Chain IDs:X (auth: XX)
Chain Length:469
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:mS33
Chain IDs:Y (auth: YY)
Chain Length:108
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polypeptide(L)
Description:37S ribosomal protein S24, mitochondrial
Chain IDs:Z (auth: ZZ)
Chain Length:382
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Polymer Type:polyribonucleotide
Description:16S rRNA
Chain IDs:KA (auth: aa)
Chain Length:470
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Primary Citation
Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.
Nat Commun 11 5187 5187 (2020)
PMID: 33056988 DOI: 10.1038/s41467-020-18830-w

Abstact

Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each other is not understood. We report models of the translating fungal mitoribosome with mRNA, tRNA and nascent polypeptide, as well as an assembly intermediate. Nicotinamide adenine dinucleotide (NAD) is found in the central protuberance of the large subunit, and the ATPase inhibitory factor 1 (IF1) in the small subunit. The models of the active mitoribosome explain how mRNA binds through a dedicated protein platform on the small subunit, tRNA is translocated with the help of the protein mL108, bridging it with L1 stalk on the large subunit, and nascent polypeptide paths through a newly shaped exit tunnel involving a series of structural rearrangements. An assembly intermediate is modeled with the maturation factor Atp25, providing insight into the biogenesis of the mitoribosomal large subunit and translation regulation.

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Primary Citation of related structures