ISDA

Deposition Date 2023-03-23

Release Date 2023-06-14

Last Version Date 2024-06-26

Entry Detail

PDB ID:

8OIT

Keywords:

RIBOSOME

Title:

39S human mitochondrial large ribosomal subunit with mtRF1 and P-site tRNA

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Homo sapiens

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.90 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:P-site Met-tRNA(Met)
Chain IDs:IB (auth: AG)
Chain Length:71
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Peptide chain release factor 1, mitochondrial
Gene (Uniprot):MTRF1
Mutagens:311GGQ313 > AAQ
Chain IDs:JB (auth: Aa)
Chain Length:484
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O75570 Pfam ID:PF03462, PF00472

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L12, mitochondrial
Gene (Uniprot):MRPL12
Chain IDs:A (auth: B1), B (auth: B2), C (auth: B3), D (auth: B4), E (auth: B5), F (auth: B6)
Chain Length:198
Number of Molecules:6
Biological Source:Homo sapiens

UniProt ID:P52815 Pfam ID:PF16320, PF00542

Polymer Type:polyribonucleotide
Molecule:E-site tRNA
Chain IDs:G (auth: B7)
Chain Length:3
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:H (auth: B8)
Chain Length:1561
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:CP Val-tRNA(Val)
Chain IDs:I (auth: B9)
Chain Length:72
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L22, mitochondrial
Gene (Uniprot):MRPL22
Chain IDs:J (auth: BA)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NWU5 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L23, mitochondrial
Gene (Uniprot):MRPL23
Chain IDs:K (auth: BB)
Chain Length:153
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q16540 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L24, mitochondrial
Gene (Uniprot):MRPL24
Chain IDs:L (auth: BC)
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96A35 Pfam ID:PF00467, PF17136

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L27, mitochondrial
Gene (Uniprot):MRPL27
Chain IDs:M (auth: BD)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9P0M9 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L28, mitochondrial
Gene (Uniprot):MRPL28
Chain IDs:N (auth: BE)
Chain Length:102
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q13084 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L47, mitochondrial
Gene (Uniprot):MRPL47
Chain IDs:O (auth: BF)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9HD33 Pfam ID:PF06984

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L30, mitochondrial
Gene (Uniprot):MRPL30
Chain IDs:P (auth: BG)
Chain Length:161
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8TCC3 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L32, mitochondrial
Gene (Uniprot):MRPL32
Chain IDs:Q (auth: BH)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BYC8 Pfam ID:PF01783

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L33, mitochondrial
Gene (Uniprot):MRPL33
Chain IDs:R (auth: BI)
Chain Length:439
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O75394 Pfam ID:PF00471

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L34, mitochondrial
Gene (Uniprot):MRPL34
Chain IDs:S (auth: BJ)
Chain Length:325
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BQ48 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L35, mitochondrial
Gene (Uniprot):MRPL35
Chain IDs:T (auth: BK)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NZE8 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L2, mitochondrial
Gene (Uniprot):MRPL2
Chain IDs:U (auth: BL)
Chain Length:103
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q5T653 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L3, mitochondrial
Gene (Uniprot):MRPL3
Chain IDs:V (auth: BM)
Chain Length:423
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P09001 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L4, mitochondrial
Gene (Uniprot):MRPL4
Chain IDs:W (auth: BN)
Chain Length:311
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BYD3 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L9, mitochondrial
Gene (Uniprot):MRPL9
Chain IDs:X (auth: BO)
Chain Length:338
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BYD2 Pfam ID:PF01281, PF22078

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L10, mitochondrial
Gene (Uniprot):MRPL10
Chain IDs:Y (auth: BP)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q7Z7H8 Pfam ID:PF00466

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L11, mitochondrial
Gene (Uniprot):MRPL11
Chain IDs:Z (auth: BQ)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y3B7 Pfam ID:PF03946, PF00298

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L13, mitochondrial
Gene (Uniprot):MRPL13
Chain IDs:AA (auth: BR)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BYD1 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L14, mitochondrial
Gene (Uniprot):MRPL14
Chain IDs:BA (auth: BS)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q6P1L8 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L15, mitochondrial
Gene (Uniprot):MRPL15
Chain IDs:CA (auth: BT)
Chain Length:332
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9P015 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L16, mitochondrial
Gene (Uniprot):MRPL16
Chain IDs:DA (auth: BU)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NX20 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L17, mitochondrial
Gene (Uniprot):MRPL17
Chain IDs:EA (auth: BV)
Chain Length:279
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NRX2 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L18, mitochondrial
Gene (Uniprot):MRPL18
Chain IDs:FA (auth: BW)
Chain Length:180
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9H0U6 Pfam ID:PF00861

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L19, mitochondrial
Gene (Uniprot):MRPL19
Chain IDs:GA (auth: BX)
Chain Length:292
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P49406 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L20, mitochondrial
Gene (Uniprot):MRPL20
Chain IDs:HA (auth: BY)
Chain Length:149
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BYC9 Pfam ID:PF00453

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L21, mitochondrial
Gene (Uniprot):MRPL21
Chain IDs:IA (auth: BZ)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q7Z2W9 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L52, mitochondrial
Gene (Uniprot):MRPL52
Chain IDs:JA (auth: Ba)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q86TS9 Pfam ID:PF18699

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L53, mitochondrial
Gene (Uniprot):MRPL53
Chain IDs:KA (auth: Bb)
Chain Length:153
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96EL3 Pfam ID:PF10780

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L54, mitochondrial
Gene (Uniprot):MRPL54
Chain IDs:LA (auth: Bc)
Chain Length:138
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q6P161 Pfam ID:PF08561

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L55, mitochondrial
Gene (Uniprot):MRPL55
Chain IDs:MA (auth: Bd)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q7Z7F7 Pfam ID:PF09776

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein 63, mitochondrial
Gene (Uniprot):MRPL57
Chain IDs:NA (auth: Be)
Chain Length:102
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BQC6 Pfam ID:PF14978

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Peptidyl-tRNA hydrolase ICT1, mitochondrial
Gene (Uniprot):MRPL58
Chain IDs:OA (auth: Bf)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q14197 Pfam ID:PF00472 EC:3.1.1.29

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Growth arrest and DNA damage-inducible proteins-interacting protein 1
Gene (Uniprot):GADD45GIP1
Chain IDs:PA (auth: Bg)
Chain Length:161
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8TAE8 Pfam ID:PF10147

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein S18a, mitochondrial
Gene (Uniprot):MRPS18A
Chain IDs:QA (auth: Bh)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NVS2 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein S30, mitochondrial
Gene (Uniprot):MRPS30
Chain IDs:RA (auth: Bi)
Chain Length:439
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NP92 Pfam ID:PF07147

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L1, mitochondrial
Gene (Uniprot):MRPL1
Chain IDs:SA (auth: Bj)
Chain Length:325
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BYD6 Pfam ID:PF00687

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L36, mitochondrial
Gene (Uniprot):MRPL36
Chain IDs:TA (auth: Bl)
Chain Length:103
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9P0J6 Pfam ID:PF00444

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L37, mitochondrial
Gene (Uniprot):MRPL37
Chain IDs:UA (auth: Bm)
Chain Length:423
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BZE1 Pfam ID:PF07147

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L38, mitochondrial
Gene (Uniprot):MRPL38
Chain IDs:VA (auth: Bn)
Chain Length:311
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96DV4 Pfam ID:PF01161

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L39, mitochondrial
Gene (Uniprot):MRPL39
Chain IDs:WA (auth: Bo)
Chain Length:338
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NYK5

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L40, mitochondrial
Gene (Uniprot):MRPL40
Chain IDs:XA (auth: Bp)
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NQ50 Pfam ID:PF09812

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L41, mitochondrial
Gene (Uniprot):MRPL41
Chain IDs:YA (auth: Bq)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8IXM3 Pfam ID:PF09809

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L42, mitochondrial
Gene (Uniprot):MRPL42
Chain IDs:ZA (auth: Br)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y6G3 Pfam ID:PF10210

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein mL43
Gene (Uniprot):MRPL43
Chain IDs:AB (auth: Bs)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8N983 Pfam ID:PF05047

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L44, mitochondrial
Gene (Uniprot):MRPL44
Chain IDs:BB (auth: Bt)
Chain Length:332
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9H9J2 Pfam ID:PF22935, PF22892

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L45, mitochondrial
Gene (Uniprot):MRPL45
Chain IDs:CB (auth: Bu)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BRJ2 Pfam ID:PF04280

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L46, mitochondrial
Gene (Uniprot):MRPL46
Chain IDs:DB (auth: Bv)
Chain Length:279
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9H2W6 Pfam ID:PF11788

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L48, mitochondrial
Gene (Uniprot):MRPL48
Chain IDs:EB (auth: Bw)
Chain Length:180
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96GC5 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L49, mitochondrial
Gene (Uniprot):MRPL49
Chain IDs:FB (auth: Bx)
Chain Length:292
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q13405 Pfam ID:PF05046

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L50, mitochondrial
Gene (Uniprot):MRPL50
Chain IDs:GB (auth: By)
Chain Length:149
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q8N5N7 Pfam ID:PF10501

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L51, mitochondrial
Gene (Uniprot):MRPL51
Chain IDs:HB (auth: Bz)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q4U2R6 Pfam ID:PF10244

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
1MA	H	A	modified residue
2MG	I	G	modified residue
AYA	K	ALA	modified residue
OMG	H	G	modified residue
OMU	H	U	modified residue
PSU	H	U	modified residue
RSQ	IB	C	modified residue
SAC	AA	SER	modified residue

Ligand Molecules

FS2

MET

VAL

Primary Citation

Molecular basis of translation termination at noncanonical stop codons in human mitochondria.

Saurer, M, Leibundgut, M, Nadimpalli, H.P, Scaiola, A, Schonhut, T, Lee, R.G, Siira, S.J, Rackham, O, Dreos, R, Lenarcic, T, Kummer, E, Gatfield, D, Filipovska, A, Ban, N.Show

Science 380 531 536 (2023)

PMID: 37141370 DOI: 10.1126/science.adf9890

Abstact

The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the standard genetic code, including the reassignment of two arginine codons to stop codons. The protein required for translation termination at these noncanonical stop codons to release the newly synthesized polypeptides is not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo-electron microscopy to establish that mitochondrial release factor 1 (mtRF1) detects noncanonical stop codons in human mitochondria by a previously unknown mechanism of codon recognition. We discovered that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual conformation in the messenger RNA in which the ribosomal RNA participates in specific recognition of the noncanonical stop codons.

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Protein

Chemical

Disease

Primary Citation of related structures