ISDA

Deposition Date 2020-04-29

Release Date 2020-11-11

Last Version Date 2024-11-06

Entry Detail

PDB ID:

6YWE

Keywords:

TRANSLATION

Title:

The structure of the mitoribosome from Neurospora crassa in the P/E tRNA bound state

Biological Source:

Source Organism:

Neurospora crassa (Taxon ID: 5141)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.99 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein
Gene (Uniprot):rtc6
Chain IDs:CA (auth: 0)
Chain Length:124
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q7S4E7 Pfam ID:PF00444

Polymer Type:polypeptide(L)
Molecule:IF1
Chain IDs:CC (auth: 00), DC (auth: 99)
Chain Length:95
Number of Molecules:2
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:PEBP-like protein
Chain IDs:DA (auth: 1)
Chain Length:449
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein mrp10, mitochondrial
Chain IDs:UB (auth: 11)
Chain Length:90
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:mL40
Chain IDs:EA (auth: 2)
Chain Length:370
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DUF1713 domain-containing protein
Gene (Uniprot):cox24
Chain IDs:VB (auth: 22)
Chain Length:344
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q7SHR6 Pfam ID:PF08213

Polymer Type:polypeptide(L)
Molecule:mL41
Chain IDs:FA (auth: 3)
Chain Length:103
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Protein FYV4, mitochondrial
Gene (Uniprot):B2F7.100
Chain IDs:WB (auth: 33)
Chain Length:236
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q9HE52 Pfam ID:PF09597

Polymer Type:polypeptide(L)
Molecule:L51_S25_CI-B8 domain-containing protein
Chain IDs:GA (auth: 4)
Chain Length:138
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:Manganese and iron superoxide dismutase
Chain IDs:XB (auth: 44), YB (auth: 55)
Chain Length:310
Number of Molecules:2
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:Ribonuclease III
Chain IDs:HA (auth: 5)
Chain Length:439
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:MRP-L46 domain-containing protein
Chain IDs:IA (auth: 6)
Chain Length:368
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS45
Gene (Uniprot):mrps35
Chain IDs:ZB (auth: 66)
Chain Length:348
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q7SHB2 Pfam ID:PF12298

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL49
Gene (Uniprot):img2
Chain IDs:JA (auth: 7)
Chain Length:165
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q7S518 Pfam ID:PF05046

Polymer Type:polypeptide(L)
Molecule:mS46
Chain IDs:AC (auth: 77)
Chain Length:414
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mL50
Gene (Uniprot):mrpl13
Chain IDs:KA (auth: 8)
Chain Length:443
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q7S711 Pfam ID:PF10501

Protein Blast

Polymer Type:polypeptide(L)
Molecule:3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
Gene (Uniprot):B18D24.230
Chain IDs:BC (auth: 88)
Chain Length:508
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q9C251 Pfam ID:PF16113

Polymer Type:polypeptide(L)
Molecule:RNase III domain-containing protein
Chain IDs:NA (auth: 9)
Chain Length:267
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:A
Chain Length:225
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:bS1m
Chain IDs:UA (auth: AA)
Chain Length:1864
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2, mitochondrial
Chain IDs:C (auth: B)
Chain Length:383
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mito ribosomal protein S2
Gene (Uniprot):mrp4
Chain IDs:VA (auth: BB)
Chain Length:428
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:V5ILE0 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Related to ribosomal protein L3, mitochondrial
Gene (Uniprot):B24N11.110
Chain IDs:D (auth: C)
Chain Length:110
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q873B3 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S5
Gene (Uniprot):rps3
Chain IDs:WA (auth: CC)
Chain Length:508
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:A0A1W5YJW8

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4, variant
Gene (Uniprot):yml6
Chain IDs:E (auth: D)
Chain Length:292
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:V5IMN1 Pfam ID:PF00573

Polymer Type:polypeptide(L)
Molecule:S4 RNA-binding domain-containing protein
Chain IDs:XA (auth: DD)
Chain Length:453
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Related to ribosomal protein L5, mitochondrial
Gene (Uniprot):B7A16.090
Chain IDs:F (auth: E)
Chain Length:303
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q96U12 Pfam ID:PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Related to ribosomal protein S5 (Mitochondrial)
Gene (Uniprot):B1K11.100
Chain IDs:YA (auth: EE)
Chain Length:11
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q8X048 Pfam ID:PF00333, PF03719

Polymer Type:polypeptide(L)
Molecule:uL6m
Chain IDs:G (auth: F)
Chain Length:255
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S6
Chain IDs:ZA (auth: FF)
Chain Length:117
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL_L9 domain-containing protein
Chain IDs:H (auth: G)
Chain Length:158
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:Ribosomal_S7 domain-containing protein
Chain IDs:AB (auth: GG)
Chain Length:309
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:uL13m
Chain IDs:K (auth: H)
Chain Length:98
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:uS8m
Chain IDs:BB (auth: HH)
Chain Length:161
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L14
Chain IDs:L (auth: I)
Chain Length:218
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:uS9m
Chain IDs:CB (auth: II)
Chain Length:315
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L15
Chain IDs:M (auth: J)
Chain Length:201
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10, mitochondrial
Chain IDs:DB (auth: JJ)
Chain Length:268
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Related to ribosomal protein L16, mitochondrial
Gene (Uniprot):B14D6.470
Chain IDs:N (auth: K)
Chain Length:249
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q8X081 Pfam ID:PF00252

Polymer Type:polypeptide(L)
Molecule:Translational machinery component
Chain IDs:EB (auth: KK)
Chain Length:376
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:uL17m
Chain IDs:O (auth: L)
Chain Length:193
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S12
Chain IDs:FB (auth: LL)
Chain Length:174
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:bL19m
Chain IDs:P (auth: M)
Chain Length:258
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Probable ribosomal protein S13
Gene (Uniprot):B11E5.360
Chain IDs:GB (auth: MM)
Chain Length:119
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q6MVY0 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Related to ribosomal protein YmL49, mitochondrial
Gene (Uniprot):B20J13.280
Chain IDs:Q (auth: N)
Chain Length:217
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q6MVF2 Pfam ID:PF00829

Polymer Type:polypeptide(L)
Molecule:Mitochondrial 37S ribosomal protein MRP2
Chain IDs:HB (auth: NN)
Chain Length:113
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial large ribosomal subunit
Gene (Uniprot):mrpl22
Chain IDs:R (auth: O)
Chain Length:364
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q7S5N0 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Related to ribosomal protein S15 (Mitochondrial)
Gene (Uniprot):B19C19.050
Chain IDs:IB (auth: OO)
Chain Length:320
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q8X067 Pfam ID:PF00312

Polymer Type:polypeptide(L)
Molecule:uL23m
Chain IDs:S (auth: P)
Chain Length:228
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:bS16m
Chain IDs:JB (auth: PP)
Chain Length:107
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:KOW domain-containing protein
Chain IDs:T (auth: Q)
Chain Length:396
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:uS17m
Chain IDs:KB (auth: QQ)
Chain Length:165
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Related to 60s ribosomal protein L2 (Mitochondrial)
Gene (Uniprot):5E6.150
Chain IDs:U (auth: R)
Chain Length:447
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q8X0Q2 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S18
Gene (Uniprot):B11O8.090
Chain IDs:LB (auth: RR)
Chain Length:256
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q872A7 Pfam ID:PF01084

Polymer Type:polypeptide(L)
Molecule:bL28m
Chain IDs:V (auth: S)
Chain Length:274
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S19/S15
Chain IDs:MB (auth: SS)
Chain Length:91
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L4, mitochondrial
Chain IDs:W (auth: T)
Chain Length:263
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:bS21m
Chain IDs:NB (auth: TT)
Chain Length:236
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Related to ribosomal protein L30
Gene (Uniprot):B14D6.300
Chain IDs:X (auth: U)
Chain Length:161
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q8X098 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S25, mitochondrial
Gene (Uniprot):rsm25
Chain IDs:OB (auth: UU)
Chain Length:253
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q873E4 Pfam ID:PF13741

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Related to ribosomal protein YmL36, mitochondrial
Gene (Uniprot):9G6.200
Chain IDs:Y (auth: V)
Chain Length:219
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q9C2E5 Pfam ID:PF21492

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS26
Gene (Uniprot):pet123
Chain IDs:PB (auth: VV)
Chain Length:316
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q7SHR9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Related to ribosomal protein YmL32 (Mitochondrial),Mitochondrial ribosomal protein subunit L32
Gene (Uniprot):B11E6.060
Chain IDs:Z (auth: W)
Chain Length:129
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q9HFL0 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS27
Gene (Uniprot):mrp13
Chain IDs:QB (auth: WW)
Chain Length:396
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q7RYW7

Polymer Type:polypeptide(L)
Molecule:bL33m
Chain IDs:AA (auth: X)
Chain Length:59
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein DAP3
Gene (Uniprot):rsm23
Chain IDs:RB (auth: XX)
Chain Length:469
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q7SD06 Pfam ID:PF10236

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Related to ribosomal protein L34, mitochondrial
Gene (Uniprot):B11N2.075
Chain IDs:BA (auth: Y)
Chain Length:140
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q96U95 Pfam ID:PF00468

Polymer Type:polypeptide(L)
Molecule:mS33
Chain IDs:SB (auth: YY)
Chain Length:108
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S24, mitochondrial
Gene (Uniprot):B23L21.370
Chain IDs:TB (auth: ZZ)
Chain Length:382
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q9P5J2 Pfam ID:PF10213

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Related to ribosomal protein YmL20, mitochondrial
Gene (Uniprot):G15D1.090
Chain IDs:OA (auth: a)
Chain Length:225
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q8NIR6 Pfam ID:PF12824

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:EC (auth: aa)
Chain Length:1864
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:Mitoc_mL59 domain-containing protein
Chain IDs:PA (auth: b)
Chain Length:383
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polyribonucleotide
Molecule:tRNA P/E state
Chain IDs:TA (auth: bb)
Chain Length:428
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:54S ribosomal protein L31, mitochondrial
Chain IDs:QA (auth: c)
Chain Length:110
Number of Molecules:1
Biological Source:Neurospora crassa

Polymer Type:polypeptide(L)
Molecule:mL67
Chain IDs:RA (auth: d)
Chain Length:292
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L1, mitochondrial
Gene (Uniprot):B14A21.170
Chain IDs:B (auth: e)
Chain Length:303
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q870V5 Pfam ID:PF00687

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:FC (auth: ee)
Chain Length:11
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Related to ribosomal protein YmL11, mitochondrial
Gene (Uniprot):29E8.010
Chain IDs:I (auth: f)
Chain Length:255
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q6M9C4

Polymer Type:polypeptide(L)
Molecule:uL11m
Chain IDs:J (auth: g)
Chain Length:158
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Probable ribosomal protein YmL44, mitochondrial
Gene (Uniprot):B20J13.030
Chain IDs:LA (auth: h)
Chain Length:98
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q6MVH6 Pfam ID:PF10780

Polymer Type:polypeptide(L)
Molecule:mL54
Chain IDs:MA (auth: i)
Chain Length:218
Number of Molecules:1
Biological Source:Neurospora crassa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:L51_S25_CI-B8 domain-containing protein
Gene (Uniprot):mrp49
Chain IDs:SA (auth: j)
Chain Length:201
Number of Molecules:1
Biological Source:Neurospora crassa

UniProt ID:Q7RWZ7 Pfam ID:PF05047

Ligand Molecules

ATP

NAD

SPM

Primary Citation

Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.

Itoh, Y, Naschberger, A, Mortezaei, N, Herrmann, J.M, Amunts, A.Show

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures