6YW5 image
Deposition Date 2020-04-29
Release Date 2020-11-11
Last Version Date 2024-11-06
Entry Detail
PDB ID:
6YW5
Keywords:
TRANSLATION
Title:
The structure of the small subunit of the mitoribosome from Neurospora crassa
Biological Source:
Source Organism:
Neurospora crassa OR74A (Taxon ID: 367110)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.85 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6YW5 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mS47
Gene (Uniprot):inh1
Chain IDs:IA (auth: 00), JA (auth: 99)
Chain Length:95
Number of Molecules:2
Biological Source:Neurospora crassa OR74A
UniProt ID:V5IRA3 Pfam ID:PF04568
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein mrp10, mitochondrial
Gene (Uniprot):mrp10
Chain IDs:AA (auth: 11)
Chain Length:90
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S4Y4
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DUF1713 domain-containing protein
Gene (Uniprot):cox24
Chain IDs:BA (auth: 22)
Chain Length:344
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SHR6 Pfam ID:PF08213
Protein Blast
Polymer Type:polypeptide(L)
Molecule:IGR domain-containing protein
Gene (Uniprot):fyv4
Chain IDs:CA (auth: 33)
Chain Length:236
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K6Q3 Pfam ID:PF09597
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Fe superoxide dismutase
Gene (Uniprot):rsm26
Chain IDs:DA (auth: 44), EA (auth: 55)
Chain Length:310
Number of Molecules:2
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S2H6 Pfam ID:PF02777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mS42
Gene (Uniprot):mrps35
Chain IDs:FA (auth: 66)
Chain Length:348
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SHB2 Pfam ID:PF12298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mS46
Gene (Uniprot):rsm28
Chain IDs:GA (auth: 77)
Chain Length:414
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SG49
Protein Blast
Polymer Type:polypeptide(L)
Molecule:3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
Gene (Uniprot):ehd3
Chain IDs:HA (auth: 88)
Chain Length:508
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K7A4 Pfam ID:PF16113
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS2m
Gene (Uniprot):mrp51
Chain IDs:A (auth: AA)
Chain Length:470
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:A7UWX2 Pfam ID:PF11709
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mito ribosomal protein S2
Gene (Uniprot):mrp4
Chain IDs:B (auth: BB)
Chain Length:428
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:V5ILE0 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S5, mitochondrial
Gene (Uniprot):var1
Chain IDs:C (auth: CC)
Chain Length:508
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:P23351
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mito ribosomal protein S4
Gene (Uniprot):NAM9
Chain IDs:D (auth: DD)
Chain Length:453
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SA90 Pfam ID:PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S5
Gene (Uniprot):mrps5
Chain IDs:E (auth: EE)
Chain Length:477
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K548 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mito ribosomal protein S6
Gene (Uniprot):mrp17
Chain IDs:F (auth: FF)
Chain Length:117
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SB95 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal_S7 domain-containing protein
Gene (Uniprot):rsm7
Chain IDs:G (auth: GG)
Chain Length:309
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S6M9 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):mrps8
Chain IDs:H (auth: HH)
Chain Length:161
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SHF3 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS9m
Gene (Uniprot):mrp-9
Chain IDs:I (auth: II)
Chain Length:315
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S7R6 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S10, mitochondrial
Gene (Uniprot):mrp-10
Chain IDs:J (auth: JJ)
Chain Length:268
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7RYL4 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein subunit S18
Gene (Uniprot):mrps18
Chain IDs:K (auth: KK)
Chain Length:376
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SGU0 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial 30S ribosomal protein S12
Gene (Uniprot):mrps12
Chain IDs:L (auth: LL)
Chain Length:174
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S9I4 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):sws2
Chain IDs:M (auth: MM)
Chain Length:119
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S2C2 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial 40S ribosomal protein MRP2
Gene (Uniprot):mrp2
Chain IDs:N (auth: NN)
Chain Length:113
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SF85 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S15
Gene (Uniprot):mrps28
Chain IDs:O (auth: OO)
Chain Length:320
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K5G1 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S16, mitochondrial
Gene (Uniprot):cyt-21
Chain IDs:P (auth: PP)
Chain Length:107
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:P08580 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial 37S ribosomal protein S17
Gene (Uniprot):mrps17
Chain IDs:Q (auth: QQ)
Chain Length:165
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S4E0 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mito ribosomal protein S18
Gene (Uniprot):rsm18
Chain IDs:R (auth: RR)
Chain Length:256
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K8E0 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein S19
Gene (Uniprot):rsm19
Chain IDs:S (auth: SS)
Chain Length:91
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K8V2 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mito ribosomal protein S21
Gene (Uniprot):mrp21
Chain IDs:T (auth: TT)
Chain Length:236
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SAJ1 Pfam ID:PF01165
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S25, mitochondrial
Gene (Uniprot):rsm25
Chain IDs:U (auth: UU)
Chain Length:253
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q873E4 Pfam ID:PF13741
Protein Blast
Polymer Type:polypeptide(L)
Molecule:IF1
Gene (Uniprot):mrpl36
Chain IDs:LA (auth: V)
Chain Length:219
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K7L7 Pfam ID:PF21492
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mS26
Gene (Uniprot):pet123
Chain IDs:V (auth: VV)
Chain Length:316
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SHR9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mS27
Gene (Uniprot):mrp13
Chain IDs:W (auth: WW)
Chain Length:396
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7RYW7
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein DAP3
Gene (Uniprot):rsm23
Chain IDs:X (auth: XX)
Chain Length:469
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SD06 Pfam ID:PF10236
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mS33
Gene (Uniprot):rsm27
Chain IDs:Y (auth: YY)
Chain Length:108
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K5R0 Pfam ID:PF08293
Protein Blast
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S24, mitochondrial
Gene (Uniprot):rsm24
Chain IDs:Z (auth: ZZ)
Chain Length:382
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K5Z0 Pfam ID:PF10213
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:KA (auth: aa)
Chain Length:470
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Ligand Molecules
ATP
K
MG
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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Disease

Primary Citation of related structures
6YW5