ISDA: 8APN

Deposition Date 2022-08-10

Release Date 2022-11-16

Last Version Date 2024-10-16

Entry Detail

PDB ID:

8APN

Keywords:

RIBOSOME

Title:

Structure of the mitochondrial ribosome from Polytomella magna with tRNA bound to the P site

Biological Source:

Source Organism:

Polytomella magna (Taxon ID: 353565)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.10 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:mtLSU-1
Chain IDs:A (auth: A1)
Chain Length:109
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polyribonucleotide
Molecule:mtLSU-2
Chain IDs:B (auth: A2)
Chain Length:81
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polyribonucleotide
Molecule:mtLSU-3
Chain IDs:C (auth: A3)
Chain Length:207
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polyribonucleotide
Molecule:mtLSU-4
Chain IDs:D (auth: A4)
Chain Length:73
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polyribonucleotide
Molecule:mtLSU-5
Chain IDs:E (auth: A5)
Chain Length:136
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polyribonucleotide
Molecule:mtLSU-6
Chain IDs:F (auth: A6)
Chain Length:109
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polyribonucleotide
Molecule:mtLSU-7
Chain IDs:G (auth: A7)
Chain Length:534
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polyribonucleotide
Molecule:mtLSU-8
Chain IDs:H (auth: A8)
Chain Length:350
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polyribonucleotide
Molecule:mt-5S
Chain IDs:I (auth: A9)
Chain Length:69
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bL33m
Chain IDs:IA (auth: AA)
Chain Length:50
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bL34m
Chain IDs:JA (auth: AB)
Chain Length:50
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bL35m
Chain IDs:KA (auth: AC)
Chain Length:139
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bL36m
Chain IDs:LA (auth: AD)
Chain Length:47
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL40
Chain IDs:MA (auth: AE)
Chain Length:242
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL41
Chain IDs:NA (auth: AF)
Chain Length:56
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL43
Chain IDs:OA (auth: AG)
Chain Length:121
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL46
Chain IDs:PA (auth: AH)
Chain Length:186
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL63
Chain IDs:QA (auth: AI)
Chain Length:64
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL64
Chain IDs:RA (auth: AJ)
Chain Length:206
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL87
Chain IDs:SA (auth: AK)
Chain Length:166
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL116
Chain IDs:TA (auth: AL)
Chain Length:394
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL116
Chain IDs:UA (auth: AM)
Chain Length:114
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL116
Chain IDs:VA (auth: AN)
Chain Length:170
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL118
Chain IDs:WA (auth: AO)
Chain Length:117
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uL2m
Chain IDs:J (auth: Aa)
Chain Length:50
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uL3m
Chain IDs:K (auth: Ab)
Chain Length:50
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uL4m
Chain IDs:L (auth: Ac)
Chain Length:139
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uL5m
Chain IDs:M (auth: Ad)
Chain Length:47
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uL6m
Chain IDs:N (auth: Ae)
Chain Length:242
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uL9m
Chain IDs:O (auth: Af)
Chain Length:56
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uL13m
Chain IDs:P (auth: Ah)
Chain Length:186
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:Hypothetical protein
Chain IDs:Q (auth: Ai)
Chain Length:64
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uL15m
Chain IDs:R (auth: Aj)
Chain Length:206
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uL16m
Chain IDs:S (auth: Ak)
Chain Length:166
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bL17m
Chain IDs:T (auth: Al)
Chain Length:394
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uL18m
Chain IDs:U (auth: Am)
Chain Length:114
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bL19m
Chain IDs:V (auth: An)
Chain Length:170
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bL20m
Chain IDs:W (auth: Ao)
Chain Length:117
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bL21m
Chain IDs:X (auth: Ap)
Chain Length:200
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uL22m
Chain IDs:Y (auth: Aq)
Chain Length:188
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uL23m
Chain IDs:Z (auth: Ar)
Chain Length:155
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bL24m
Chain IDs:AA (auth: As)
Chain Length:115
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bL25m
Chain IDs:BA (auth: At)
Chain Length:253
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bL27m
Chain IDs:CA (auth: Au)
Chain Length:142
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bL28m
Chain IDs:DA (auth: Av)
Chain Length:129
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uL29m
Chain IDs:EA (auth: Aw)
Chain Length:123
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uL30m
Chain IDs:FA (auth: Ax)
Chain Length:176
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bL31m
Chain IDs:GA (auth: Ay)
Chain Length:72
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bL32m
Chain IDs:HA (auth: Az)
Chain Length:59
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polyribonucleotide
Molecule:mtSSU-1
Chain IDs:HB (auth: B1)
Chain Length:102
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polyribonucleotide
Molecule:mtSSU-2
Chain IDs:IB (auth: B2)
Chain Length:210
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polyribonucleotide
Molecule:mtSSU-3
Chain IDs:JB (auth: B3)
Chain Length:379
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polyribonucleotide
Molecule:mtSSU-4
Chain IDs:KB (auth: B4)
Chain Length:337
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS35
Chain IDs:LC (auth: BA)
Chain Length:242
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS37
Chain IDs:MC (auth: BB)
Chain Length:236
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS45
Chain IDs:NC (auth: BC)
Chain Length:289
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS38
Chain IDs:OC (auth: BD)
Chain Length:31
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS106
Chain IDs:PC (auth: BE)
Chain Length:171
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS107
Chain IDs:QC (auth: BF)
Chain Length:370
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bS1m
Chain IDs:LB (auth: Ba)
Chain Length:242
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS2m
Chain IDs:MB (auth: Bb)
Chain Length:236
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS3m
Chain IDs:NB (auth: Bc)
Chain Length:289
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS4m
Chain IDs:OB (auth: Bd)
Chain Length:31
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS5m
Chain IDs:PB (auth: Be)
Chain Length:171
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS6m
Chain IDs:QB (auth: Bf)
Chain Length:370
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS7m
Chain IDs:RB (auth: Bg)
Chain Length:112
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS8m
Chain IDs:SB (auth: Bh)
Chain Length:374
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS9m
Chain IDs:TB (auth: Bi)
Chain Length:282
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS10m
Chain IDs:UB (auth: Bj)
Chain Length:401
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS11m
Chain IDs:VB (auth: Bk)
Chain Length:116
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS12m
Chain IDs:WB (auth: Bl)
Chain Length:123
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS13m
Chain IDs:XB (auth: Bm)
Chain Length:113
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS14m
Chain IDs:YB (auth: Bn)
Chain Length:118
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS15m
Chain IDs:ZB (auth: Bo)
Chain Length:167
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bS16m
Chain IDs:AC (auth: Bp)
Chain Length:123
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS17m
Chain IDs:BC (auth: Bq)
Chain Length:130
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bS18m
Chain IDs:CC (auth: Br)
Chain Length:90
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bS19m
Chain IDs:DC (auth: Bs)
Chain Length:92
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:bS21m
Chain IDs:EC (auth: Bt)
Chain Length:75
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS23
Chain IDs:FC (auth: Bu)
Chain Length:167
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS26
Chain IDs:GC (auth: Bv)
Chain Length:164
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS29
Chain IDs:HC (auth: Bw)
Chain Length:349
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS31
Chain IDs:IC (auth: Bx)
Chain Length:621
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS33
Chain IDs:JC (auth: By)
Chain Length:80
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS34
Chain IDs:KC (auth: Bz)
Chain Length:119
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:DD (auth: C1)
Chain Length:73
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:ED (auth: C3)
Chain Length:4
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:Unknown
Chain IDs:GD (auth: Ua)
Chain Length:32
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL105
Chain IDs:FD (auth: Ub)
Chain Length:130
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:Unknown
Chain IDs:HD (auth: Ud)
Chain Length:43
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:Unknown
Chain IDs:ID (auth: Ue)
Chain Length:47
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:Unknown
Chain IDs:JD (auth: Uf)
Chain Length:73
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:Unknown
Chain IDs:KD (auth: Ug)
Chain Length:63
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:Unknown
Chain IDs:LD (auth: Uh)
Chain Length:48
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:Unknown
Chain IDs:MD (auth: Ui)
Chain Length:26
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:Unknown
Chain IDs:ND (auth: Uj)
Chain Length:9
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:Unknown
Chain IDs:OD (auth: Uk)
Chain Length:23
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:Unknown
Chain IDs:PD (auth: Ul)
Chain Length:16
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:Unknown
Chain IDs:QD (auth: Um)
Chain Length:11
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL120
Chain IDs:XA (auth: Xa)
Chain Length:199
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL121
Chain IDs:YA (auth: Xb)
Chain Length:244
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL122
Chain IDs:ZA (auth: Xc)
Chain Length:57
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL123
Chain IDs:AB (auth: Xd)
Chain Length:413
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL124
Chain IDs:BB (auth: Xe)
Chain Length:483
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL125
Chain IDs:CB (auth: Xf)
Chain Length:201
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL126
Chain IDs:DB (auth: Xg)
Chain Length:410
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL127
Chain IDs:EB (auth: Xh)
Chain Length:143
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL128
Chain IDs:FB (auth: Xi)
Chain Length:24
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mL129
Chain IDs:GB (auth: Xj)
Chain Length:71
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS4m-2
Chain IDs:RC (auth: Ya)
Chain Length:180
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS108
Chain IDs:SC (auth: Yb)
Chain Length:50
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS109
Chain IDs:TC (auth: Yc)
Chain Length:159
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS110
Chain IDs:UC (auth: Yd)
Chain Length:95
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS3m-2
Chain IDs:VC (auth: Ye)
Chain Length:106
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS111
Chain IDs:WC (auth: Yf)
Chain Length:150
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS112
Chain IDs:XC (auth: Yg)
Chain Length:67
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS113
Chain IDs:YC (auth: Yh)
Chain Length:65
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS114
Chain IDs:ZC (auth: Yi)
Chain Length:132
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS115
Chain IDs:AD (auth: Yj)
Chain Length:386
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:mS116
Chain IDs:BD (auth: Yk)
Chain Length:92
Number of Molecules:1
Biological Source:Polytomella magna

Polymer Type:polypeptide(L)
Molecule:uS7m-2
Chain IDs:CD (auth: Yl)
Chain Length:84
Number of Molecules:1
Biological Source:Polytomella magna

Ligand Molecules

ATP

Primary Citation

Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.

Tobiasson, V, Berzina, I, Amunts, A.Show

Nat Commun 13 6132 6132 (2022)

PMID: 36253367 DOI: 10.1038/s41467-022-33582-5

Abstact

Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature. Here, we report a 2.9 Å resolution structure of the mitoribosome from the alga Polytomella magna harbouring a reduced rRNA split into 13 fragments. We found that the rRNA contains a non-canonical reduced form of the 5S, as well as a permutation of the LSU domain I. The mt-5S rRNA is stabilised by mL40 that is also found in mitoribosomes lacking the 5S, which suggests an evolutionary pathway. Through comparison to other ribosomes with fragmented rRNAs, we observe that the pattern is shared across large evolutionary distances, and between cellular compartments, indicating an evolutionary convergence and supporting the concept of a primordial fragmented ribosome. On the protein level, eleven peripherally associated HEAT-repeat proteins are involved in the binding of 3' rRNA termini, and the structure features a prominent pseudo-trimer of one of them (mL116). Finally, in the exit tunnel, mL128 constricts the tunnel width of the vestibular area, and mL105, a homolog of a membrane targeting component mediates contacts with an inner membrane bound insertase. Together, the structural analysis provides insight into the evolution of the ribosomal machinery in mitochondria.

Legend

Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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