8OIT: 39S ribosomal protein L12, mitochondrial
39S human mitochondrial large ribosomal subunit with mtRF1 and P-site tRNA. Determined by electron microscopy at 2.9 Å resolution. Released 14 Jun 2023.
- Method
- Electron microscopy
- Resolution
- 2.9 Å
- Organism
- Homo sapiens
- Chains
- 62
- Atoms
- 113,095
- Mol. weight
- 1994.31 kDa
- Ligands
- MG, VAL, ZN, FES
- Released
- 14 Jun 2023
Explore 8OIT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8OIT contains 522 α-helices and 420 β-strands across 58 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, 12 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 | 44 |
| α-helix | 199-217 | 19 | |
| β-strand | 221-229 | 9 | 44 |
| β-strand | 235-243 | 9 | 44 |
| α-helix | 247-251 | 5 | |
| β-strand | 256-262 | 7 | 44 |
| α-helix | 268-271 | 4 | |
| β-strand | 276-283 | 8 | 44 |
| β-strand | 286 | 1 | 44 |
| α-helix | 297-299 | 3 | |
| β-strand | 300-305 | 6 | 45 |
| α-helix | 313-317 | 5 | |
| β-strand | 321-326 | 6 | 45 |
| β-strand | 332-335 | 4 | 45 |
| α-helix | 341-371 | 31 | |
| β-strand | 384-389 | 6 | 44 |
| β-strand | 394-397 | 4 | 44 |
| β-strand | 402-405 | 4 | 44 |
| α-helix | 407-410 | 4 | |
| α-helix | 415-444 | 30 | |
Chain B1: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 48-53 | 6 | |
| α-helix | 57-58 | 2 | |
| α-helix | 62-73 | 12 | |
| α-helix | 76-90 | 15 | |
Chain B2: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 62-73 | 12 | |
| α-helix | 76-90 | 15 | |
Chains B3 and B4: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-73 | 10 | |
| α-helix | 76-84 | 9 | |
| α-helix | 85-89 | 5 | |
Chains B5 and B6: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 62-73 | 12 | |
| α-helix | 76-84 | 9 | |
| α-helix | 85-89 | 5 | |
Chain Ba: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-30 | 6 | |
| α-helix | 42-45 | 4 | |
| β-strand | 49-51 | 3 | 40 |
| α-helix | 55 | 1 | |
| β-strand | 56 | 1 | 40 |
| α-helix | 57-60 | 4 | |
| α-helix | 61-106 | 46 | |
| α-helix | 110-111 | 2 | |
Chain BA: 8 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-49 | 4 | |
| α-helix | 53-57 | 5 | |
| α-helix | 61-65 | 5 | |
| β-strand | 66-74 | 9 | 42 |
| α-helix | 78-87 | 10 | |
| β-strand | 92 | 1 | 42 |
| α-helix | 93-101 | 9 | |
| α-helix | 106-125 | 20 | |
| β-strand | 134-143 | 10 | 42 |
| β-strand | 147-152 | 6 | 43 |
| β-strand | 158-163 | 6 | 43 |
| β-strand | 166-174 | 9 | 42 |
| α-helix | 177-185 | 9 | |
| α-helix | 186-197 | 12 | |
Chain Bb: 6 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-8 | 6 | |
| β-strand | 13-20 | 8 | 49 |
| α-helix | 28-37 | 10 | |
| α-helix | 40-44 | 5 | |
| β-strand | 50-55 | 6 | 49 |
| α-helix | 60-62 | 3 | |
| β-strand | 63-68 | 6 | 49 |
| β-strand | 73-76 | 4 | 49 |
| α-helix | 78-80 | 3 | |
| α-helix | 83-101 | 19 | |
48 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 L12, mitochondrial | B1, B2, B3, B4, B5, B6 | protein | 198 | Homo sapiens | P52815 (AlphaFold model) |
| E-site tRNA | B7 | RNA | 3 | Homo sapiens | |
| 16S rRNA | B8 | RNA | 1561 | Homo sapiens | |
| CP Val-tRNA(Val) | B9 | RNA | 72 | Homo sapiens | |
| 39S ribosomal protein L22, mitochondrial | BA | protein | 206 | Homo sapiens | Q9NWU5 (AlphaFold model) |
| 39S ribosomal protein L23, mitochondrial | BB | protein | 153 | Homo sapiens | Q16540 (AlphaFold model) |
| 39S ribosomal protein L24, mitochondrial | BC | protein | 216 | Homo sapiens | Q96A35 (AlphaFold model) |
| 39S ribosomal protein L27, mitochondrial | BD | protein | 148 | Homo sapiens | Q9P0M9 |
| 39S ribosomal protein L28, mitochondrial | BE | protein | 256 | Homo sapiens | Q13084 |
| 39S ribosomal protein L47, mitochondrial | BF | protein | 250 | Homo sapiens | Q9HD33 |
| 39S ribosomal protein L30, mitochondrial | BG | protein | 161 | Homo sapiens | Q8TCC3 |
| 39S ribosomal protein L32, mitochondrial | BH | protein | 188 | Homo sapiens | Q9BYC8 |
45 more molecules are not listed.
Sequence of entity 1 (B1, B2, B3, B4, B5, B6), FASTA
>8OIT_1 39S ribosomal protein L12, mitochondrial (chains B1, B2, B3, B4, B5, B6)
MLPAAARPLWGPCLGLRAAAFRLARRQVPCVCAVRHMRSSGHQRCEALAGAPLDNAPKEY
PPKIQQLVQDIASLTLLEISDLNELLKKTLKIQDVGLVPMGGVMSGAVPAAAAQEAVEED
IPIAKERTHFTVRLTEAKPVDKVKLIKEIKNYIQGINLVQAKKLVESLPQEIKANVAKAE
AEKIKAALEAVGGTVVLE
Sequence of entity 2 (B7), FASTA
>8OIT_2 E-site tRNA (chains B7)
CCA
Sequence of entity 3 (B8), FASTA
>8OIT_3 16S rRNA (chains B8)
GCUAAACCUAGCCCCAAACCCACUCCACCUUACUACCAGACAACCUUAGCCAAACCAUUU
ACCCAAAUAAAGUAUAGGCGAUAGAAAUUGAAACCUGGCGCAAUAGAUAUAGUACCGCAA
GGGAAAGAUGAAAAAUUAUAACCAAGCAUAAUAUAGCAAGGACUAACCCCUAUACCUUCU
GCAUAAUGAAUUAACUAGAAAUAACUUUGCAAGGAGAGCCAAAGCUAAGACCCCCGAAAC
CAGACGAGCUACCUAAGAACAGCUAAAAGAGCACACCCGUCUAUGUAGCAAAAUAGUGGG
AAGAUUUAUAGGUAGAGGCGACAAACCUACCGAGCCUGGUGAUAGCUGGUUGUCCAAGAU
AGAAUCUUAGUUCAACUUUAAAUUUGCCCACAGAACCCUCUAAAUCCCCUUGUAAAUUUA
ACUGUUAGUCCAAAGAGGAACAGCUCUUUGGACACUAGGAAAAAACCUUGUAGAGAGAGU
AAAAAAUUUAACACCCAUAGUAGGCCUAAAAGCAGCCACCAAUUAAGAAAGCGUUCAAGC
UCAACACCCACUACCUAAAAAAUCCCAAACAUAUAACUGAACUCCUCACACCCAAUUGGA
CCAAUCUAUCACCCUAUAGAAGAACUAAUGUUAGUAUAAGUAACAUGAAAACAUUCUCCU
CCGCAUAAGCCUGCGUCAGAUUAAAACACUGAACUGACAAUUAACAGCCCAAUAUCUACA
AUCAACCAACAAGUCAUUAUUACCCUCACUGUCAACCCAACACAGGCAUGCUCAUAAGGA
AAGGUUAAAAAAAGUAAAAGGAACUCGGCAAAUCUUACCCCGCCUGUUUACCAAAAACAU
CACCUCUAGCAUCACCAGUAUUAGAGGCACCGCCUGCCCAGUGACACAUGUUUAACGGCC
GCGGUACCCUAACCGUGCAAAGGUAGCAUAAUCACUUGUUCCUUAAAUAGGGACCUGUAU
GAAUGGCUCCACGAGGGUUCAGCUGUCUCUUACUUUUAACCAGUGAAAUUGACCUGCCCG
UGAAGAGGCGGGCAUAACACAGCAAGACGAGAAGACCCUAUGGAGCUUUAAUUUAUUAAU
GCAAACAGUACCUAACAAACCCACAGGUCCUAAACUACCAAACCUGCAUUAAAAAUUUCG
GUUGGGGCGACCUCGGAGCAGAACCCAACCUCCGAGCAGUACAUGCUAAGACUUCACCAG
UCAAAGCGAACUACUAUACUCAAUUGAUCCAAUAACUUGACCAACGGAACAAGUUACCCU
AGGGAUAACAGCGCAAUCCUAUUCUAGAGUCCAUAUCAACAAUAGGGUUUACGACCUCGA
UGUUGGAUCAGGACAUCCCGAUGGUGCAGCCGCUAUUAAAGGUUCGUUUGUUCAACGAUU
AAAGUCCUACGUGAUCUGAGUUCAGACCGGAGUAAUCCAGGUCGGUUUCUAUCUACUUUC
AAAUUCCUCCCUGUACGAAAGGACAAGAGAAAUAAGGCCUACUUCACAAAGCGCCUUCCC
CCGUAAAUGAUAUCAUCUCAACUUAGUAUUAUACCCACACCCACCCAAGAACAGGGUUUG
U
Sequence of entity 4 (B9), FASTA
>8OIT_4 CP Val-tRNA(Val) (chains B9)
CAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUGA
CCGCUCUGACCA
Sequence of entity 5 (BA), FASTA
>8OIT_5 39S ribosomal protein L22, mitochondrial (chains BA)
MAAAVLGQLGALWIHNLRSRGKLALGVLPQSYIHTSASLDISRKWEKKNKIVYPPQLPGE
PRRPAEIYHCRRQIKYSKDKMWYLAKLIRGMSIDQALAQLEFNDKKGAKIIKEVLLEAQD
MAVRDHNVEFRSNLYIAESTSGRGQCLKRIRYHGRGRFGIMEKVYCHYFVKLVEGPPPPP
EPPKTAVAHAKEYIQQLRSRTIVHTL
Sequence of entity 6 (BB), FASTA
>8OIT_6 39S ribosomal protein L23, mitochondrial (chains BB)
MARNVVYPLYRLGGPQLRVFRTNFFIQLVRPGVAQPEDTVQFRIPMEMTRVDLRNYLEGI
YNVPVAAVRTRVQHGSNKRRDHRNVRIKKPDYKVAYVQLAHGQTFTFPDLFPEKDESPEG
SAADDLYSMLEEERQQRQSSDPRRGGVPSWFGL
Sequence of entity 7 (BC), FASTA
>8OIT_7 39S ribosomal protein L24, mitochondrial (chains BC)
MRLSALLALASKVTLPPHYRYGMSPPGSVADKRKNPPWIRRRPVVVEPISDEDWYLFCGD
TVEILEGKDAGKQGKVVQVIRQRNWVVVGGLNTHYRYIGKTMDYRGTMIPSEAPLLHRQV
KLVDPMDRKPTEIEWRFTEAGERVRVSTRSGRIIPKPEFPRADGIVPETWIDGPKDTSVE
DALERTYVPCLKTLQEEVMEAMGIKETRKYKKVYWY
Sequence of entity 8 (BD), FASTA
>8OIT_8 39S ribosomal protein L27, mitochondrial (chains BD)
MASVVLALRTRTAVTSLLSPTPATALAVRYASKKSGGSSKNLGGKSSGRRQGIKKMEGHY
VHAGNIIATQRHFRWHPGAHVGVGKNKCLYALEEGIVRYTKEVYVPHPRNTEAVDLITRL
PKGAVLYKTFVHVVPAKPEGTFKLVAML
Sequence of entity 9 (BE), FASTA
>8OIT_9 39S ribosomal protein L28, mitochondrial (chains BE)
MPLHKYPVWLWKRLQLREGICSRLPGHYLRSLEEERTPTPVHYRPHGAKFKINPKNGQRE
RVEDVPIPIYFPPESQRGLWGGEGWILGQIYANNDKLSKRLKKVWKPQLFEREFYSEILD
KKFTVTVTMRTLDLIDEAYGLDFYILKTPKEDLCSKFGMDLKRGMLLRLARQDPQLHPED
PERRAAIYDKYKEFAIPEEEAEWVGLTLEEAIEKQRLLEEKDPVPLFKIYVAELIQQLQQ
QALSEPAVVQKRASGQ
Sequence of entity 10 (BF), FASTA
>8OIT_10 39S ribosomal protein L47, mitochondrial (chains BF)
MAAAGLALLCRRVSSALKSSRSLITPQVPACTGFFLSLLPKSTPNVTSFHQYRLLHTTLS
RKGLEEFFDDPKNWGQEKVKSGAAWTCQQLRNKSNEDLHKLWYVLLKERNMLLTLEQEAK
RQRLPMPSPERLDKVVDSMDALDKVVQEREDALRLLQTGQERARPGAWRRDIFGRIIWHK
FKQWVIPWHLNKRYNRKRFFALPYVDHFLRLEREKRARIKARKENLERKKAKILLKKFPH
LAEAQKSSLV
Sequence of entity 11 (BG), FASTA
>8OIT_11 39S ribosomal protein L30, mitochondrial (chains BG)
MAGILRLVVQWPPGRLQTVTKGVESLICTDWIRHKFTRSRIPEKVFQASPEDHEKYGGDP
QNPHKLHIVTRIKSTRRRPYWEKDIIKMLGLEKAHTPQVHKNIPSVNAKLKVVKHLIRIK
PLKLPQGLPAEENMSNTCLKSTGELVVQWHLKPVEQKAHES
Sequence of entity 12 (BH), FASTA
>8OIT_12 39S ribosomal protein L32, mitochondrial (chains BH)
MALAMLVLVVSPWSAARGVLRNYWERLLRKLPQSRPGFPSPPWGPALAVQGPAMFTEPAN
DTSGSKENSSLLDSIFWMAAPKNRRTIEVNRCRRRNPQKLIKVKNNIDVCPECGHLKQKH
VLCAYCYEKVCKETAEIRRQIGKQEGGPFKAPTIETVVLYTGETPSEQDQGKRIIERDRK
RPSWFTQN
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 228 |
| VAL | Valine | C5 H11 N O2 | 1 |
| ZN | Zinc ion | Zn | 2 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 1 |
| MET | Methionine | C5 H11 N O2 S | 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 P52815 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7QI4 2.21 Å, Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA)
- 9OLF 2.46 Å, Membrane-associated human mitoribosome in complex with TACO1
- 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,…
- 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…
- 9RU6 2.64 Å, Human mitoribosome bound to TACO1 (Translational activator of COX1), mRNA, A/A-, P/P-…
- 9PR4 2.77 Å, In Situ Structure of the Human Mitochondrial Large Subunit 39S in Complex with TACO1
- 9PRA 2.83 Å, In Situ Structure of the Human Mitoribosome Large Subunit 39S in Complex with EF-Tu
- 8ANY 2.85 Å, Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-site, P-site, E-site tRNAs…
- 6ZM5 2.89 Å, Human mitochondrial ribosome in complex with OXA1L, mRNA, A/A tRNA, P/P tRNA and nascent…
Browse structure collections
About this viewer
MolViewer shows 8OIT directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.