6YWV image
Deposition Date 2020-04-30
Release Date 2020-11-11
Last Version Date 2024-05-22
Entry Detail
PDB ID:
6YWV
Keywords:
TRANSLATION
Title:
The structure of the Atp25 bound assembly intermediate of the mitoribosome from Neurospora crassa
Biological Source:
Source Organism:
Neurospora crassa OR74A (Taxon ID: 367110)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.03 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6YWV validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein
Gene (Uniprot):rtc6
Chain IDs:AA (auth: 0)
Chain Length:124
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S4E7 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial large ribosomal subunit YmL35
Gene (Uniprot):mrpl35
Chain IDs:BA (auth: 1)
Chain Length:449
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7RXV8 Pfam ID:PF01161
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Chain IDs:CA (auth: 2)
Chain Length:370
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):mrpl27
Chain IDs:DA (auth: 3)
Chain Length:103
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S5W0 Pfam ID:PF09809
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L43
Gene (Uniprot):mrpl51
Chain IDs:EA (auth: 4)
Chain Length:138
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S300 Pfam ID:PF05047
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):mrpl3
Chain IDs:FA (auth: 5)
Chain Length:439
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SA88 Pfam ID:PF00035
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal subunit L30
Gene (Uniprot):mrpl17
Chain IDs:GA (auth: 6)
Chain Length:368
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S1Z3 Pfam ID:PF11788, PF00293
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):img2
Chain IDs:HA (auth: 7)
Chain Length:165
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S518 Pfam ID:PF05046
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):mrpl13
Chain IDs:IA (auth: 8)
Chain Length:443
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S711 Pfam ID:PF10501
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNase III domain-containing protein
Gene (Uniprot):mrpl15
Chain IDs:LA (auth: 9)
Chain Length:267
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S1R6 Pfam ID:PF14622
Polymer Type:polyribonucleotide
Molecule:23 S rRNA
Chain IDs:A
Chain Length:3464
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2
Gene (Uniprot):rml2
Chain IDs:B
Chain Length:162
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SCX7 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):mrpl9
Chain IDs:C
Chain Length:110
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K8T6 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4, variant
Gene (Uniprot):yml6
Chain IDs:D
Chain Length:325
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:V5IMN1 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):mrpl7
Chain IDs:E
Chain Length:352
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K6P0 Pfam ID:PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):mrpl6
Chain IDs:F
Chain Length:255
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7RZF0 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L13
Gene (Uniprot):mrpl23
Chain IDs:I (auth: H)
Chain Length:183
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SBV6 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):mrpl38
Chain IDs:J (auth: I)
Chain Length:218
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SBJ8 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal subunit protein L15
Gene (Uniprot):mrpl10
Chain IDs:K (auth: J)
Chain Length:312
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SB98 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16
Gene (Uniprot):mrpl16
Chain IDs:L (auth: K)
Chain Length:249
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:F5HIJ5 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):mrpl8
Chain IDs:M (auth: L)
Chain Length:193
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K8C8 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein
Gene (Uniprot):img1
Chain IDs:N (auth: M)
Chain Length:258
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7RYW8 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Aconitate hydratase
Gene (Uniprot):mrpl49
Chain IDs:O (auth: N)
Chain Length:217
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SGE5 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial large ribosomal subunit
Gene (Uniprot):mrpl22
Chain IDs:P (auth: O)
Chain Length:364
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S5N0 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein subunit L23
Gene (Uniprot):mrp20
Chain IDs:Q (auth: P)
Chain Length:228
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SA60 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:KOW domain-containing protein
Gene (Uniprot):mrpl40
Chain IDs:R (auth: Q)
Chain Length:396
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7RXU7 Pfam ID:PF22682, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):mrp7
Chain IDs:S (auth: R)
Chain Length:447
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K730 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):mrpl24
Chain IDs:T (auth: S)
Chain Length:274
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SC44 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L4, mitochondrial
Gene (Uniprot):mrpl4
Chain IDs:U (auth: T)
Chain Length:263
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7S910 Pfam ID:PF06984
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):mrpl33
Chain IDs:V (auth: U)
Chain Length:161
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K8Y7 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):mrpl36
Chain IDs:W (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:Mitochondrial ribosomal protein subunit L32
Gene (Uniprot):mrpl32
Chain IDs:X (auth: W)
Chain Length:129
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K4P1 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):mrpl39
Chain IDs:Y (auth: X)
Chain Length:59
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:V5IM60 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):mrpl34
Chain IDs:Z (auth: Y)
Chain Length:140
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K7P9 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20
Gene (Uniprot):mrpl20
Chain IDs:MA (auth: a)
Chain Length:3464
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q1K6U7 Pfam ID:PF12824
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial 60S ribosomal protein L25
Gene (Uniprot):mrpl25
Chain IDs:NA (auth: b)
Chain Length:162
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SEK9 Pfam ID:PF18126
Protein Blast
Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L31, mitochondrial
Gene (Uniprot):mrpl31
Chain IDs:OA (auth: c)
Chain Length:110
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:U9W8F2 Pfam ID:PF09784
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):mhr1
Chain IDs:PA (auth: d)
Chain Length:325
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7RYM5 Pfam ID:PF12829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):mrpl11
Chain IDs:G (auth: f)
Chain Length:255
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7RZ62
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19
Gene (Uniprot):mrpl19
Chain IDs:H (auth: g)
Chain Length:158
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7RX40 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein L44
Gene (Uniprot):mrpl44
Chain IDs:JA (auth: h)
Chain Length:183
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SGH0 Pfam ID:PF10780
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):mrpl37
Chain IDs:KA (auth: i)
Chain Length:218
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SCZ3 Pfam ID:PF08561
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ATPase synthesis protein 25, mitochondrial
Gene (Uniprot):atp25
Chain IDs:QA (auth: n)
Chain Length:217
Number of Molecules:1
Biological Source:Neurospora crassa OR74A
UniProt ID:Q7SAC2 Pfam ID:PF02410
Ligand Molecules
K
MG
NAD
SPM
ZN
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
6YWV