8OIS: 39S ribosomal protein L19, mitochondrial
28S human mitochondrial small ribosomal subunit with mtRF1 and P-site tRNA. Determined by electron microscopy at 3.0 Å resolution. Released 14 Jun 2023.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organism
- Homo sapiens
- Chains
- 36
- Atoms
- 72,671
- Mol. weight
- 1282.56 kDa
- Ligands
- MG, MET, ZN, FES
- Released
- 14 Jun 2023
Explore 8OIS in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8OIS contains 351 α-helices and 193 β-strands across 33 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain Aa: 13 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 66-71 | 6 | |
| α-helix | 73-94 | 22 | |
| α-helix | 100-138 | 39 | |
| α-helix | 142-144 | 3 | |
| α-helix | 145-174 | 30 | |
| β-strand | 185-191 | 7 | 1 |
| α-helix | 199-217 | 19 | |
| β-strand | 221-229 | 9 | 1 |
| β-strand | 235-243 | 9 | 1 |
| α-helix | 247-251 | 5 | |
| β-strand | 256-262 | 7 | 1 |
| α-helix | 268-271 | 4 | |
| β-strand | 276-286 | 11 | 1 |
| α-helix | 297-299 | 3 | |
| β-strand | 300-305 | 6 | 2 |
| α-helix | 312-317 | 6 | |
| β-strand | 321-326 | 6 | 2 |
| β-strand | 332-335 | 4 | 2 |
| α-helix | 341-371 | 31 | |
| β-strand | 384-389 | 6 | 1 |
| β-strand | 394-397 | 4 | 1 |
| β-strand | 402-405 | 4 | 1 |
| α-helix | 407-410 | 4 | |
| α-helix | 415-444 | 30 | |
Chain Ab: 11 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 54-62 | 9 | |
| α-helix | 66-68 | 3 | |
| α-helix | 75-77 | 3 | |
| α-helix | 81-86 | 6 | |
| β-strand | 91-94 | 4 | 6 |
| α-helix | 95-97 | 3 | |
| α-helix | 100-105 | 6 | |
| β-strand | 106-109 | 4 | 6 |
| β-strand | 113-116 | 4 | 6 |
| α-helix | 118-137 | 20 | |
| β-strand | 142-145 | 4 | 7 |
| α-helix | 152-161 | 10 | |
| β-strand | 165-167 | 3 | 7 |
| α-helix | 179-182 | 4 | |
| β-strand | 192-195 | 4 | 7 |
| β-strand | 199 | 1 | 8 |
| β-strand | 205 | 1 | 8 |
| α-helix | 207-214 | 8 | |
| β-strand | 219-221 | 3 | 7 |
| β-strand | 234-235 | 2 | 7 |
| α-helix | 243-276 | 34 | |
Chain AB: 20 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 50-55 | 6 | |
| α-helix | 56-59 | 4 | |
| α-helix | 66-69 | 4 | |
| β-strand | 86 | 1 | 3 |
| α-helix | 89-91 | 3 | |
| α-helix | 96-98 | 3 | |
| α-helix | 103-106 | 4 | |
| α-helix | 116-126 | 11 | |
| α-helix | 127-129 | 3 | |
| α-helix | 132-134 | 3 | |
| α-helix | 140-146 | 7 | |
| β-strand | 149-157 | 9 | 4 |
| β-strand | 162 | 1 | 5 |
| α-helix | 166-169 | 4 | |
| β-strand | 171-176 | 6 | 4 |
| α-helix | 177-179 | 3 | |
| α-helix | 184-194 | 11 | |
| α-helix | 195-197 | 3 | |
| β-strand | 198-199 | 2 | 4 |
| β-strand | 204-209 | 6 | 4 |
| α-helix | 215-234 | 20 | |
| α-helix | 238-242 | 5 | |
| α-helix | 257-272 | 16 | |
| α-helix | 280-284 | 5 | |
| α-helix | 287-301 | 15 | |
| α-helix | 306-319 | 14 | |
Chain Ac: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 18-19 | 2 | |
| α-helix | 34-41 | 8 | |
| α-helix | 46-58 | 13 | |
| α-helix | 64-66 | 3 | |
| α-helix | 67-86 | 20 | |
| α-helix | 87-91 | 5 | |
| α-helix | 92-94 | 3 | |
| α-helix | 99-100 | 2 | |
| α-helix | 101-110 | 10 | |
Chain AC: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-44 | 3 | |
| β-strand | 50-51 | 2 | 9 |
| α-helix | 53-56 | 4 | |
| α-helix | 59-61 | 3 | |
| β-strand | 70-71 | 2 | 10 |
| α-helix | 73-75 | 3 | |
| α-helix | 82-99 | 18 | |
| β-strand | 104 | 1 | 10 |
| β-strand | 109-113 | 5 | 10 |
| β-strand | 116-124 | 9 | 10 |
| α-helix | 129-147 | 19 | |
| β-strand | 151-158 | 8 | 10 |
| β-strand | 165-166 | 2 | 9 |
Chain Ad: 15 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 95-103 | 9 | |
| α-helix | 108-110 | 3 | |
| α-helix | 121-123 | 3 | |
| β-strand | 139-140 | 2 | 11 |
| β-strand | 142 | 1 | 12 |
| β-strand | 146 | 1 | 12 |
| β-strand | 149-150 | 2 | 13 |
| β-strand | 153-154 | 2 | 13 |
| α-helix | 155-157 | 3 | |
| β-strand | 158-159 | 2 | 11 |
| α-helix | 162-184 | 23 | |
| α-helix | 187-189 | 3 | |
| β-strand | 202-204 | 3 | 14 |
| α-helix | 206-208 | 3 | |
| β-strand | 209 | 1 | 15 |
| β-strand | 213 | 1 | 15 |
| β-strand | 219-232 | 14 | 14 |
| β-strand | 236-248 | 13 | 14 |
| β-strand | 253-261 | 9 | 14 |
| α-helix | 264-275 | 12 | |
| β-strand | 279-281 | 3 | 14 |
| β-strand | 285 | 1 | 16 |
| β-strand | 289 | 1 | 16 |
| β-strand | 294-298 | 5 | 17 |
| β-strand | 301-307 | 7 | 17 |
| β-strand | 314-315 | 2 | 17 |
| α-helix | 318-327 | 10 | |
| β-strand | 332-338 | 7 | 17 |
| α-helix | 342-354 | 13 | |
| α-helix | 356-358 | 3 | |
| α-helix | 359-366 | 8 | |
| β-strand | 369-373 | 5 | 18 |
| β-strand | 382-385 | 4 | 18 |
| α-helix | 390-392 | 3 | |
| α-helix | 395-396 | 2 | |
| α-helix | 408-414 | 7 | |
Chain AD: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 131-149 | 19 | |
| α-helix | 151-179 | 29 | |
| α-helix | 185-186 | 2 | |
Chain Ae: 38 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 58-60 | 3 | |
| β-strand | 61-65 | 5 | 30 |
| α-helix | 69-77 | 9 | |
| α-helix | 100-123 | 24 | |
| α-helix | 125-128 | 4 | |
| β-strand | 134 | 1 | 5 |
| α-helix | 138-140 | 3 | |
| α-helix | 154-162 | 9 | |
| α-helix | 166-178 | 13 | |
| α-helix | 185-198 | 14 | |
| α-helix | 202-204 | 3 | |
| α-helix | 243-250 | 8 | |
| α-helix | 256-268 | 13 | |
| α-helix | 272-284 | 13 | |
| α-helix | 291-304 | 14 | |
| α-helix | 309-325 | 17 | |
| α-helix | 332-341 | 10 | |
| α-helix | 342-344 | 3 | |
| α-helix | 350-363 | 14 | |
| α-helix | 369-379 | 11 | |
| α-helix | 387-400 | 14 | |
| α-helix | 412-414 | 3 | |
| α-helix | 415-426 | 12 | |
| α-helix | 429-439 | 11 | |
| α-helix | 444-447 | 4 | |
| α-helix | 451-467 | 17 | |
| α-helix | 471-481 | 11 | |
| α-helix | 487-489 | 3 | |
| α-helix | 490-503 | 14 | |
| α-helix | 509-518 | 10 | |
| α-helix | 525-537 | 13 | |
| α-helix | 542-560 | 19 | |
| α-helix | 563-566 | 4 | |
| α-helix | 573-585 | 13 | |
| α-helix | 589-601 | 13 | |
| α-helix | 605-607 | 3 | |
| α-helix | 608-621 | 14 | |
| α-helix | 624-636 | 13 | |
| α-helix | 640-652 | 13 | |
| α-helix | 656-665 | 10 | |
25 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| 39S ribosomal protein L19, mitochondrial | BX | protein | 292 | Homo sapiens | P49406 (AlphaFold model) |
| 39S ribosomal protein L55, mitochondrial | Bd | protein | 128 | Homo sapiens | Q7Z7F7 (AlphaFold model) |
| 12S rRNA | AA | RNA | 955 | Homo sapiens | |
| 28S ribosomal protein S35, mitochondrial | AB | protein | 323 | Homo sapiens | P82673 (AlphaFold model) |
| 28S ribosomal protein S24, mitochondrial | AC | protein | 167 | Homo sapiens | Q96EL2 (AlphaFold model) |
| Aurora kinase A-interacting protein | AD | protein | 199 | Homo sapiens | Q9NWT8 |
| 28S ribosomal protein S6, mitochondrial | AE | protein | 125 | Homo sapiens | P82932 |
| 28S ribosomal protein S7, mitochondrial | AF | protein | 242 | Homo sapiens | Q9Y2R9 |
| P-site Met-tRNA(Met) | AG | RNA | 71 | Homo sapiens | |
| 28S ribosomal protein S10, mitochondrial | AH | protein | 201 | Homo sapiens | P82664 |
| mRNA | AI | RNA | 33 | Homo sapiens | |
| 28S ribosomal protein S12, mitochondrial | AJ | protein | 138 | Homo sapiens | O15235 |
24 more molecules are not listed.
Sequence of entity 1 (BX), FASTA
>8OIS_1 39S ribosomal protein L19, mitochondrial (chains BX)
MAACIAAGHWAAMGLGRSFQAARTLLPPPASIACRVHAGPVRQQSTGPSEPGAFQPPPKP
VIVDKHRPVEPERRFLSPEFIPRRGRTDPLKFQIERKDMLERRKVLHIPEFYVGSILRVT
TADPYASGKISQFLGICIQRSGRGLGATFILRNVIEGQGVEICFELYNPRVQEIQVVKLE
KRLDDSLLYLRDALPEYSTFDVNMKPVVQEPNQKVPVNELKVKMKPKPWSKRWERPNFNI
KGIRFDLCLTEQQMKEAQKWNQPWLEFDMMREYDTSKIEAAIWKEIEASKRS
Sequence of entity 2 (Bd), FASTA
>8OIS_2 39S ribosomal protein L55, mitochondrial (chains Bd)
MAAVGSLLGRLRQSTVKATGPALRRLHTSSWRADSSRASLTRVHRQAYARLYPVLLVKQD
GSTIHIRYREPRRMLAMPIDLDTLSPEERRARLRKREAQLQSRKEYEQELSDDLHVERYR
QFWTRTKK
Sequence of entity 3 (AA), FASTA
>8OIS_3 12S rRNA (chains AA)
AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCC
CGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGGACAAGCAUCAAGCACGC
AGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAA
CCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCG
UGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUU
UUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUG
ACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACACAAUAGCUAAGACCCA
AACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAA
CUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAU
AUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUG
CUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAG
UACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACA
UUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUA
GCAGUAAACUGAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCC
CGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAU
AGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAACC
Sequence of entity 4 (AB), FASTA
>8OIS_4 28S ribosomal protein S35, mitochondrial (chains AB)
MAAAALPAWLSLQSRARTLRAFSTAVYSATPVPTPSLPERTPGNERPPRRKALPPRTEKM
AVDQDWPSVYPVAAPFKPSAVPLPVRMGYPVKKGVPMAKEGNLELLKIPNFLHLTPVAIK
KHCEALKDFCTEWPAALDSDEKCEKHFPIEIDSTDYVSSGPSVRNPRARVVVLRVKLSSL
NLDDHAKKKLIKLVGERYCKTTDVLTIKTDRCPLRRQNYDYAVYLLTVLYHESWNTEEWE
KSKTEADMEEYIWENSSSERNILETLLQMKAAEKNMEINKEELLGTKEIEEYKKSVVSLK
NEEENENSISQYKESVKRLLNVT
Sequence of entity 5 (AC), FASTA
>8OIS_5 28S ribosomal protein S24, mitochondrial (chains AC)
MAASVCSGLLGPRVLSWSRELPCAWRALHTSPVCAKNRAARVRVSKGDKPVTYEEAHAPH
YIAHRKGWLSLHTGNLDGEDHAAERTVEDVFLRKFMWGTFPGCLADQLVLKRRGNQLEIC
AVVLRQLSPHKYYFLVGYSETLLSYFYKCPVRLHLQTVPSKVVYKYL
Sequence of entity 6 (AD), FASTA
>8OIS_6 Aurora kinase A-interacting protein (chains AD)
MLLGRLTSQLLRAVPWAGGRPPWPVSGVLGSRVCGPLYSTSPAGPGRAASLPRKGAQLEL
EEMLVPRKMSVSPLESWLTARCFLPRLDTGTAGTVAPPQSYQCPPSQIGEGAEQGDEGVA
DAPQIQCKNVLKIRRRKMNHHKYRKLVKKTRFLRRKVQEGRLRRKQIKFEKDLRRIWLKA
GLKEAPEGWQTPKIYLRGK
Sequence of entity 7 (AE), FASTA
>8OIS_7 28S ribosomal protein S6, mitochondrial (chains AE)
MPRYELALILKAMQRPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNR
GGYFLVDFYAPTAAVESMVEHLSRDIDVIRGNIVKHPLTQELKECEGIVPVPLAEKLYST
KKRKK
Sequence of entity 8 (AF), FASTA
>8OIS_8 28S ribosomal protein S7, mitochondrial (chains AF)
MAAPAVKVARGWSGLALGVRRAVLQLPGLTQVRWSRYSPEFKDPLIDKEYYRKPVEELTE
EEKYVRELKKTQLIKAAPAGKTSSVFEDPVISKFTNMMMIGGNKVLARSLMIQTLEAVKR
KQFEKYHAASAEEQATIERNPYTIFHQALKNCEPMIGLVPILKGGRFYQVPVPLPDRRRR
FLAMKWMITECRDKKHQRTLMPEKLSHKLLEAFHNQGPVIKRKHDLHKMAEANRALAHYR
WW
Sequence of entity 9 (AG), FASTA
>8OIS_9 P-site Met-tRNA(Met) (chains AG)
AGUAAGGUCAGCUAAAUAAGCUAUCGGGCCXAUACCCCGAAAAUGUUGGUUAUACCCUUC
CCGUACUACCA
Sequence of entity 10 (AH), FASTA
>8OIS_10 28S ribosomal protein S10, mitochondrial (chains AH)
MAARTAFGAVCRRLWQGLGNFSVNTSKGNTAKNGGLLLSTNMKWVQFSNLHVDVPKDLTK
PVVTISDEPDILYKRLSVLVKGHDKAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTL
LQSVHIYKKHRVQYEMRTLYRCLELEHLTGSTADVYLEYIQRNLPEGVAMEVTKTQLEQL
PEHIKEPIWETLSEEKEESKS
Sequence of entity 11 (AI), FASTA
>8OIS_11 mRNA (chains AI)
NNNNAUGAGGXNNNNNNNNNNNNNNNNNNNNNN
Sequence of entity 12 (AJ), FASTA
>8OIS_12 28S ribosomal protein S12, mitochondrial (chains AJ)
MSWSGLLHGLNTSLTCGPALVPRLWATCSMATLNQMHRLGPPKRPPRKLGPTEGRPQLKG
VVLCTFTRKPKKPNSANRKCCRVRLSTGREAVCFIPGEGHTLQEHQIVLVEGGRTQDLPG
VKLTVVRGKYDCGHVQKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 126 |
| MET | Methionine | C5 H11 N O2 S | 1 |
| ZN | Zinc ion | Zn | 1 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 2 |
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 1 |
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 1 |
Water and common crystallization additives (K) are not listed.
Primary citation
Molecular basis of translation termination at noncanonical stop codons in human mitochondria. Saurer, M., Leibundgut, M., Nadimpalli, H.P. et al. Science (2023) 380:531-536. DOI 10.1126/science.adf9890 · PubMed
Other PDB entries of the same protein (UniProt P49406 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7OF0 2.2 Å, Structure of a human mitochondrial ribosome large subunit assembly intermediate in…
- 7QI4 2.21 Å, Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA)
- 8RRI 2.4 Å, Human mitochondrial ribosome in complex with antibiotic tigecycline
- 8QU5 2.42 Å, mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2
- 9OLF 2.46 Å, Membrane-associated human mitoribosome in complex with TACO1
- 7OF7 2.5 Å, Structure of a human mitochondrial ribosome large subunit assembly intermediate in…
- 7PO4 2.56 Å, Assembly intermediate of human mitochondrial ribosome large subunit (largely unfolded…
- 6ZM6 2.59 Å, Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA
- 7O9M 2.6 Å, Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4,…
- 7OF6 2.6 Å, Structure of mature human mitochondrial ribosome large subunit in complex with GTPBP6…
- 9CN3 2.62 Å, Human 39S mitoribosome in complex with antibiotic Linezolid
- 7QI5 2.63 Å, Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A…
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