8OIR: 39S ribosomal protein L12, mitochondrial

Name: PDB 8OIR: 55S human mitochondrial ribosome with mtRF1 and P-site tRNA
Published: 2023-06-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

55S human mitochondrial ribosome with mtRF1 and P-site tRNA. Determined by electron microscopy at 3.1 Å resolution. Released 14 Jun 2023.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 94
Atoms: 181,140
Mol. weight: 3149.02 kDa
Ligands: MG, VAL, ZN, FES
Released: 14 Jun 2023

Explore 8OIR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OIR contains 858 α-helices and 603 β-strands across 88 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	57
α-helix	199-217	19
β-strand	221-229	9	57
β-strand	235-243	9	57
α-helix	247-251	5
β-strand	256-262	7	57
α-helix	268-271	4
β-strand	276-286	11	57
α-helix	297-299	3
β-strand	300-305	6	58
α-helix	313-317	5
β-strand	321-326	6	58
β-strand	332-335	4	58
α-helix	341-371	31
β-strand	384-389	6	57
β-strand	394-397	4	57
β-strand	402-405	4	57
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	64
α-helix	152-161	10
β-strand	165-167	3	64
α-helix	179-182	4
β-strand	192-195	4	64
β-strand	199	1	65
β-strand	205	1	65
α-helix	207-214	8
β-strand	219-221	3	64
β-strand	234-235	2	64
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	61
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	62
β-strand	162	1	63
α-helix	166-169	4
β-strand	171-176	6	62
α-helix	177-179	3
α-helix	184-194	11
α-helix	195-197	3
β-strand	198-199	2	62
β-strand	204-209	6	62
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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	10	1	72
α-helix	18-19	2
β-strand	21	1	72
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	70
α-helix	53-56	4
α-helix	59-61	3
β-strand	70-71	2	71
α-helix	73-75	3
α-helix	82-99	18
β-strand	104	1	71
β-strand	109-113	5	71
β-strand	116-124	9	71
α-helix	129-147	19
β-strand	151-158	8	71
β-strand	165-166	2	70

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	81
β-strand	142	1	82
β-strand	146	1	82
β-strand	149-150	2	83
β-strand	153-154	2	83
α-helix	155-157	3
β-strand	158-159	2	81
α-helix	162-184	23
α-helix	187-189	3
β-strand	202-204	3	84
α-helix	206-208	3
β-strand	209	1	85
β-strand	213	1	85
β-strand	219-232	14	84
β-strand	236-248	13	84
β-strand	253-261	9	84
α-helix	264-275	12
β-strand	279-281	3	84
β-strand	285	1	86
β-strand	289	1	86
β-strand	294-298	5	87
β-strand	301-307	7	87
β-strand	314-315	2	87
α-helix	318-327	10
β-strand	332-338	7	87
α-helix	342-354	13
α-helix	356-358	3
α-helix	359-366	8
β-strand	369-373	5	88
β-strand	382-385	4	88
α-helix	390-392	3
α-helix	395-397	3
α-helix	408-414	7

Chain AD: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	131-149	19
α-helix	151-179	29
α-helix	185-186	2

Chain Ae: 37 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	58-60	3
β-strand	61-65	5	119
α-helix	69-77	9
α-helix	100-123	24
α-helix	125-128	4
β-strand	134	1	63
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	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

78 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

77 more molecules are not listed.

Sequence of entity 1 (B1, B2, B3, B4, B5, B6), FASTA

>8OIR_1 39S ribosomal protein L12, mitochondrial (chains B1, B2, B3, B4, B5, B6)
MLPAAARPLWGPCLGLRAAAFRLARRQVPCVCAVRHMRSSGHQRCEALAGAPLDNAPKEY
PPKIQQLVQDIASLTLLEISDLNELLKKTLKIQDVGLVPMGGVMSGAVPAAAAQEAVEED
IPIAKERTHFTVRLTEAKPVDKVKLIKEIKNYIQGINLVQAKKLVESLPQEIKANVAKAE
AEKIKAALEAVGGTVVLE

Sequence of entity 2 (B7), FASTA

>8OIR_2 E-site tRNA (chains B7)
CCA

Sequence of entity 3 (B8), FASTA

>8OIR_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

>8OIR_4 CP Val-tRNA(Val) (chains B9)
CAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUGA
CCGCUCUGACCA

Sequence of entity 5 (BA), FASTA

>8OIR_5 39S ribosomal protein L22, mitochondrial (chains BA)
MAAAVLGQLGALWIHNLRSRGKLALGVLPQSYIHTSASLDISRKWEKKNKIVYPPQLPGE
PRRPAEIYHCRRQIKYSKDKMWYLAKLIRGMSIDQALAQLEFNDKKGAKIIKEVLLEAQD
MAVRDHNVEFRSNLYIAESTSGRGQCLKRIRYHGRGRFGIMEKVYCHYFVKLVEGPPPPP
EPPKTAVAHAKEYIQQLRSRTIVHTL

Sequence of entity 6 (BB), FASTA

>8OIR_6 39S ribosomal protein L23, mitochondrial (chains BB)
MARNVVYPLYRLGGPQLRVFRTNFFIQLVRPGVAQPEDTVQFRIPMEMTRVDLRNYLEGI
YNVPVAAVRTRVQHGSNKRRDHRNVRIKKPDYKVAYVQLAHGQTFTFPDLFPEKDESPEG
SAADDLYSMLEEERQQRQSSDPRRGGVPSWFGL

Sequence of entity 7 (BC), FASTA

>8OIR_7 39S ribosomal protein L24, mitochondrial (chains BC)
MRLSALLALASKVTLPPHYRYGMSPPGSVADKRKNPPWIRRRPVVVEPISDEDWYLFCGD
TVEILEGKDAGKQGKVVQVIRQRNWVVVGGLNTHYRYIGKTMDYRGTMIPSEAPLLHRQV
KLVDPMDRKPTEIEWRFTEAGERVRVSTRSGRIIPKPEFPRADGIVPETWIDGPKDTSVE
DALERTYVPCLKTLQEEVMEAMGIKETRKYKKVYWY

Sequence of entity 8 (BD), FASTA

>8OIR_8 39S ribosomal protein L27, mitochondrial (chains BD)
MASVVLALRTRTAVTSLLSPTPATALAVRYASKKSGGSSKNLGGKSSGRRQGIKKMEGHY
VHAGNIIATQRHFRWHPGAHVGVGKNKCLYALEEGIVRYTKEVYVPHPRNTEAVDLITRL
PKGAVLYKTFVHVVPAKPEGTFKLVAML

Sequence of entity 9 (BE), FASTA

>8OIR_9 39S ribosomal protein L28, mitochondrial (chains BE)
MPLHKYPVWLWKRLQLREGICSRLPGHYLRSLEEERTPTPVHYRPHGAKFKINPKNGQRE
RVEDVPIPIYFPPESQRGLWGGEGWILGQIYANNDKLSKRLKKVWKPQLFEREFYSEILD
KKFTVTVTMRTLDLIDEAYGLDFYILKTPKEDLCSKFGMDLKRGMLLRLARQDPQLHPED
PERRAAIYDKYKEFAIPEEEAEWVGLTLEEAIEKQRLLEEKDPVPLFKIYVAELIQQLQQ
QALSEPAVVQKRASGQ

Sequence of entity 10 (BF), FASTA

>8OIR_10 39S ribosomal protein L47, mitochondrial (chains BF)
MAAAGLALLCRRVSSALKSSRSLITPQVPACTGFFLSLLPKSTPNVTSFHQYRLLHTTLS
RKGLEEFFDDPKNWGQEKVKSGAAWTCQQLRNKSNEDLHKLWYVLLKERNMLLTLEQEAK
RQRLPMPSPERLDKVVDSMDALDKVVQEREDALRLLQTGQERARPGAWRRDIFGRIIWHK
FKQWVIPWHLNKRYNRKRFFALPYVDHFLRLEREKRARIKARKENLERKKAKILLKKFPH
LAEAQKSSLV

Sequence of entity 11 (BG), FASTA

>8OIR_11 39S ribosomal protein L30, mitochondrial (chains BG)
MAGILRLVVQWPPGRLQTVTKGVESLICTDWIRHKFTRSRIPEKVFQASPEDHEKYGGDP
QNPHKLHIVTRIKSTRRRPYWEKDIIKMLGLEKAHTPQVHKNIPSVNAKLKVVKHLIRIK
PLKLPQGLPAEENMSNTCLKSTGELVVQWHLKPVEQKAHES

Sequence of entity 12 (BH), FASTA

>8OIR_12 39S ribosomal protein L32, mitochondrial (chains BH)
MALAMLVLVVSPWSAARGVLRNYWERLLRKLPQSRPGFPSPPWGPALAVQGPAMFTEPAN
DTSGSKENSSLLDSIFWMAAPKNRRTIEVNRCRRRNPQKLIKVKNNIDVCPECGHLKQKH
VLCAYCYEKVCKETAEIRRQIGKQEGGPFKAPTIETVVLYTGETPSEQDQGKRIIERDRK
RPSWFTQN

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	354
VAL	Valine	C5 H11 N O2	1
ZN	Zinc ion	Zn	3
FES	FE2/S2 (inorganic) cluster	Fe2 S2	3
MET	Methionine	C5 H11 N O2 S	1
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 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…

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