9CN3: Human 39S mitoribosome

Human 39S mitoribosome in complex with antibiotic Linezolid. Determined by electron microscopy at 2.62 Å resolution. Released 23 Apr 2025.

Method: Electron microscopy
Resolution: 2.62 Å
Organism: Homo sapiens
Chains: 56
Atoms: 107,417
Mol. weight: 1861.06 kDa
Ligands: ZN, MG, ZLD
Released: 23 Apr 2025

Explore 9CN3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CN3 contains 426 α-helices and 369 β-strands across 54 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 0: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	84-86	3
α-helix	87-94	8
α-helix	97-99	3
α-helix	101-103	3
β-strand	107-108	2	1
β-strand	117-118	2	1
α-helix	124-145	22
β-strand	156-159	4	2
α-helix	164-166	3
β-strand	173-176	4	2
α-helix	180-182	3

Chain 1: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	6
β-strand	29-35	7	6
α-helix	39-41	3
β-strand	42-47	6	6
β-strand	52-58	7	6

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	57-64	8
α-helix	66-70	5
α-helix	73-85	13

Chain 3: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	108-113	6
β-strand	115-116	2	11
β-strand	122-125	4	11
α-helix	133-135	3
α-helix	138-144	7
β-strand	147-149	3	11
α-helix	152-161	10
α-helix	164-167	4
α-helix	169-170	2
β-strand	172	1	12
α-helix	178-181	4

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	19
β-strand	79-84	6	19
β-strand	87-92	6	19
α-helix	96-98	3
β-strand	100-102	3	19

Chain 5: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	22
α-helix	40-47	8
α-helix	48-51	4
α-helix	60-63	4
α-helix	75-77	3
α-helix	84-86	3
α-helix	89-91	3
α-helix	92-94	3
β-strand	98-106	9	23
α-helix	115-123	9
β-strand	125-128	4	24
α-helix	131-132	2
α-helix	133-140	8
α-helix	142-144	3
α-helix	149-158	10
α-helix	159-163	5
α-helix	172-188	17
α-helix	189-191	3
α-helix	197-199	3
β-strand	200-204	5	24
β-strand	208-214	7	23
β-strand	217-223	7	23
β-strand	227-231	5	24
α-helix	234-237	4
α-helix	241-246	6
α-helix	247-249	3
β-strand	258	1	25
β-strand	265-269	5	23
β-strand	286-293	8	24
α-helix	303-304	2
α-helix	305-327	23
β-strand	334-346	13	24
β-strand	350-360	11	24
α-helix	369-370	2
β-strand	371-380	10	24
β-strand	382-386	5	26
β-strand	390-391	2	27
β-strand	396-398	3	27
β-strand	401-405	5	26
α-helix	407-418	12

Chain 6: 18 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	49	1
β-strand	50	1	33
α-helix	55-65	11
α-helix	74-77	4
α-helix	86-88	3
β-strand	89	1	34
α-helix	92-96	5
α-helix	99-115	17
α-helix	118-124	7
α-helix	132-142	11
α-helix	144-155	12
α-helix	157-160	4
β-strand	166	1	34
β-strand	174-176	3	35
β-strand	186	1	35
β-strand	189-192	4	36
α-helix	201-202	2
β-strand	203-205	3	35
β-strand	213-220	8	36
β-strand	231-241	11	36
β-strand	249-252	4	36
β-strand	266-275	10	36
β-strand	297-298	2	36
α-helix	300-306	7
β-strand	311-321	11	36
α-helix	325-329	5
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-345	6	37
α-helix	347-350	4
α-helix	352-355	4
β-strand	362	1	11
α-helix	363-369	7

Chain 7: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	37-57	21
β-strand	64-69	6	39
β-strand	78-82	5	39
α-helix	88-95	8
α-helix	97-102	6
β-strand	105-108	4	40
β-strand	111-113	3	40
α-helix	117-119	3
β-strand	124-125	2	39
β-strand	127-128	2	40
α-helix	136-155	20
β-strand	165-168	4	41
β-strand	179-184	6	41
α-helix	187-189	3
α-helix	196-211	16
β-strand	215	1	42
β-strand	217-222	6	43
α-helix	223-230	8
α-helix	234-245	12
β-strand	251-257	7	43
β-strand	260-262	3	43
β-strand	271	1	42
β-strand	275-285	11	41
β-strand	295-303	9	41
α-helix	307-309	3
α-helix	310-320	11

46 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 L32, mitochondrial	0	protein	188	Homo sapiens	Q9BYC8 (AlphaFold model)
39S ribosomal protein L33, mitochondrial	1	protein	65	Homo sapiens	O75394 (AlphaFold model)
39S ribosomal protein L34, mitochondrial	2	protein	92	Homo sapiens	Q9BQ48 (AlphaFold model)
39S ribosomal protein L35, mitochondrial	3	protein	188	Homo sapiens	Q9NZE8 (AlphaFold model)
39S ribosomal protein L36, mitochondrial	4	protein	103	Homo sapiens	Q9P0J6
39S ribosomal protein L37, mitochondrial	5	protein	423	Homo sapiens	Q9BZE1
39S ribosomal protein L38, mitochondrial	6	protein	380	Homo sapiens	Q96DV4
39S ribosomal protein L39, mitochondrial	7	protein	338	Homo sapiens	Q9NYK5
39S ribosomal protein L40, mitochondrial	8	protein	206	Homo sapiens	Q9NQ50
39S ribosomal protein L41, mitochondrial	9	protein	137	Homo sapiens	Q8IXM3
16S rRNA	A	RNA	1559	Homo sapiens
tRNA	B	RNA	72	Homo sapiens

42 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>9CN3_1 39S ribosomal protein L32, mitochondrial (chains 0)
MALAMLVLVVSPWSAARGVLRNYWERLLRKLPQSRPGFPSPPWGPALAVQGPAMFTEPAN
DTSGSKENSSLLDSIFWMAAPKNRRTIEVNRCRRRNPQKLIKVKNNIDVCPECGHLKQKH
VLCAYCYEKVCKETAEIRRQIGKQEGGPFKAPTIETVVLYTGETPSEQDQGKRIIERDRK
RPSWFTQN

Sequence of entity 2 (1), FASTA

>9CN3_2 39S ribosomal protein L33, mitochondrial (chains 1)
MFLSAVFFAKSKSKNILVRMVSEAGTGFCFNTKRNRLREKLTLLHYDPVVKQRVLFVEKK
KIRSL

Sequence of entity 3 (2), FASTA

>9CN3_3 39S ribosomal protein L34, mitochondrial (chains 2)
MAVLAGSLLGPTSRSAALLGGRWLQPRAWLGFPDAWGLPTPQQARGKARGNEYQPSNIKR
KNKHGWVRRLSTPAGVQVILRRMLKGRKSLSH

Sequence of entity 4 (3), FASTA

>9CN3_4 39S ribosomal protein L35, mitochondrial (chains 3)
MAASAFAGAVRAASGILRPLNILASSTYRNCVKNASLISALSTGRFSHIQTPVVSSTPRL
TTSERNLTCGHTSVILNRMAPVLPSVLKLPVRSLTYFSARKGKRKTVKAVIDRFLRLHCG
LWVRRKAGYKKKLWKKTPARKKRLREFVFCNKTQSKLLDKMTTSFWKRRNWYVDDPYQKY
HDRTNLKV

Sequence of entity 5 (4), FASTA

>9CN3_5 39S ribosomal protein L36, mitochondrial (chains 4)
MANLFIRKMVNPLLYLSRHTVKPRALSTFLFGSIRGAAPVAVEPGAAVRSLLSPGLLPHL
LPALGFKNKTVLKKRCKDCYLVKRRGRWYVYCKTHPRHKQRQM

Sequence of entity 6 (5), FASTA

>9CN3_6 39S ribosomal protein L37, mitochondrial (chains 5)
MALASGPARRALAGSGQLGLGGFGAPRRGAYEWGVRSTRKSEPPPLDRVYEIPGLEPITF
AGKMHFVPWLARPIFPPWDRGYKDPRFYRSPPLHEHPLYKDQACYIFHHRCRLLEGVKQA
LWLTKTKLIEGLPEKVLSLVDDPRNHIENQDECVLNVISHARLWQTTEEIPKRETYCPVI
VDNLIQLCKSQILKHPSLARRICVQNSTFSATWNRESLLLQVRGSGGARLSTKDPLPTIA
SREEIEATKNHVLETFYPISPIIDLHECNIYDVKNDTGFQEGYPYPYPHTLYLLDKANLR
PHRLQPDQLRAKMILFAFGSALAQARLLYGNDAKVLEQPVVVQSVGTDGRVFHFLVFQLN
TTDLDCNEGVKNLAWVDSDQLLYQHFWCLPVIKKRVVVEPVGPVGFKPETFRKFLALYLH
GAA

Sequence of entity 7 (6), FASTA

>9CN3_7 39S ribosomal protein L38, mitochondrial (chains 6)
MAAPWWRAALCECRRWRGFSTSAVLGRRTPPLGPMPNSDIDLSNLERLEKYRSFDRYRRR
AEQEAQAPHWWRTYREYFGEKTDPKEKIDIGLPPPKVSRTQQLLERKQAIQELRANVEEE
RAARLRTASVPLDAVRAEWERTCGPYHKQRLAEYYGLYRDLFHGATFVPRVPLHVAYAVG
EDDLMPVYCGNEVTPTEAAQAPEVTYEAEEGSLWTLLLTSLDGHLLEPDAEYLHWLLTNI
PGNRVAEGQVTCPYLPPFPARGSGIHRLAFLLFKQDQPIDFSEDARPSPCYQLAQRTFRT
FDFYKKHQETMTPAGLSFFQCRWDDSVTYIFHQLLDMREPVFEFVRPPPYHPKQKRFPHR
QPLRYLDRYRDSHEPTYGIY

Sequence of entity 8 (7), FASTA

>9CN3_8 39S ribosomal protein L39, mitochondrial (chains 7)
MEALAMGSRALRLWLVAPGGGIKWRFIATSSASQLSPTELTEMRNDLFNKEKARQLSLTP
RTEKIEVKHVGKTDPGTVFVMNKNISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLT
KSCEIKFLTFKDCDPGEVNKAYWRSCAMMMGCVIERAFKDEYMVNLVRAPEVPVISGAFC
YDVVLDSKLDEWMPTKENLRSFTKDAHALIYKDLPFETLEVEAKVALEIFQHSKYKVDFI
EEKASQNPERIVKLHRIGDFIDVSEGPLIPRTSICFQYEVSAVHNLQPTQPSLIRRFQGV
SLPVHLRAHFTIWDKLLERSRKMVTEDQSKATEECTST

Sequence of entity 9 (8), FASTA

>9CN3_9 39S ribosomal protein L40, mitochondrial (chains 8)
MTASVLRSISLALRPTSGLLGTWQTQLRETHQRASLLSFWELIPMRSEPLRKKKKVDPKK
DQEAKERLKRKIRKLEKATQELIPIEDFITPLKFLDKARERPQVELTFEETERRALLLKK
WSLYKQQERKMERDTIRAMLEAQQEALEELQLESPKLHAEAIKRDPNLFPFEKEGPHYTP
PIPNYQPPEGRYNDITKVYTQVEFKR

Sequence of entity 10 (9), FASTA

>9CN3_10 39S ribosomal protein L41, mitochondrial (chains 9)
MGVLAAAARCLVRGADRMSKWTSKRGPRSFRGRKGRGAKGIGFLTSGWRFVQIKEMVPEF
VVPDLTGFKLKPYVSYLAPESEETPLTAAQLFSEAVAPAIEKDFKDGTFDPDNLEKYGFE
PTQEGKLFQLYPRNFLR

Sequence of entity 11 (A), FASTA

>9CN3_11 16S rRNA (chains A)
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
CCGUAAAUGAUAUCAUCUCAACUUAGUAUUAUACCCACACCCACCCAAGAACAGGGUUU

Sequence of entity 12 (B), FASTA

>9CN3_12 tRNA (chains B)
CAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUGA
CCGCUCUGACCA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
MG	Magnesium ion	Mg	102
ZLD	N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}a…	C16 H20 F N3 O4	1

Primary citation

Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics. Bibel, B., Raskar, T., Couvillion, M. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkaf046 · PubMed

Other PDB entries of the same protein (UniProt Q9BYC8 (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…
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-…

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