8RRI: Human mitochondrial ribosome

Name: PDB 8RRI: Human mitochondrial ribosome in complex with antibiotic tigecycline
Published: 2025-03-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Human mitochondrial ribosome in complex with antibiotic tigecycline. Determined by electron microscopy at 2.4 Å resolution. Released 12 Mar 2025.

Method: Electron microscopy
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 86
Atoms: 175,454
Mol. weight: 2944.82 kDa
Ligands: T1C, GDP, ATP, FES
Released: 12 Mar 2025

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

Secondary structure: helices and β-sheets

8RRI contains 847 α-helices and 565 β-strands across 80 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: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	84-86	3
α-helix	87-94	8
α-helix	101-104	4
β-strand	107-109	3	163
β-strand	116-118	3	163
α-helix	124-145	22
β-strand	156-160	5	164
α-helix	167-169	3
β-strand	173-177	5	164
α-helix	180-182	3

Chain 1: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	165
β-strand	29-35	7	165
α-helix	39-41	3
β-strand	42-47	6	165
β-strand	52-64	13	165

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	108-111	4
β-strand	114-116	3	176
β-strand	122-124	3	176
α-helix	125-126	2
α-helix	133-135	3
α-helix	138-144	7
β-strand	148-149	2	176
α-helix	152-160	9
α-helix	164-167	4
β-strand	172	1	84
α-helix	178-181	4

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	1
β-strand	79-84	6	1
β-strand	87-92	6	1
α-helix	96-98	3
β-strand	100-102	3	1

Chain 5: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	31-32	2
α-helix	36-38	3
α-helix	40-47	8
α-helix	48-50	3
β-strand	59	1	24
β-strand	71	1	24
α-helix	72-73	2
α-helix	75-77	3
α-helix	85-87	3
α-helix	90-92	3
α-helix	93-95	3
β-strand	99-108	10	25
α-helix	117-123	7
β-strand	126-130	5	26
α-helix	134-139	6
α-helix	147	1
α-helix	150-159	10
α-helix	160-164	5
α-helix	173-188	16
α-helix	189-191	3
α-helix	196-199	4
β-strand	201-205	5	26
β-strand	209-215	7	25
β-strand	218-224	7	25
β-strand	228-232	5	26
α-helix	235-238	4
α-helix	242-247	6
α-helix	253-255	3
β-strand	259	1	8
β-strand	266-270	5	25
β-strand	276	1	25
β-strand	279	1	27
β-strand	287-294	8	26
α-helix	300-302	3
α-helix	304-305	2
α-helix	306-328	23
β-strand	335-347	13	26
β-strand	351-361	11	26
β-strand	372-381	10	26
β-strand	385-387	3	28
β-strand	391-393	3	29
β-strand	396-399	4	29
β-strand	402-404	3	28
α-helix	408-419	12

Chain 6: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	50	1	142
α-helix	54-66	13
α-helix	74-78	5
α-helix	86-88	3
β-strand	89	1	35
α-helix	92-96	5
α-helix	99-115	17
α-helix	117-124	8
α-helix	132-141	10
α-helix	144-154	11
α-helix	157-161	5
β-strand	166	1	35
β-strand	173-179	7	36
β-strand	183-186	4	36
β-strand	189-192	4	37
α-helix	201-202	2
β-strand	203-206	4	36
β-strand	213-220	8	37
β-strand	231-241	11	37
α-helix	245-247	3
β-strand	249-252	4	37
α-helix	259-260	2
β-strand	261	1	38
β-strand	266-275	10	37
α-helix	282-284	3
α-helix	285-287	3
α-helix	293-296	4
β-strand	297-298	2	37
α-helix	300-307	8
α-helix	308-310	3
β-strand	311-321	11	37
α-helix	326-329	4
α-helix	330-334	5
β-strand	340-345	6	38
α-helix	346-350	5
α-helix	352-355	4
β-strand	359	1	176
β-strand	362	1	176
α-helix	363-369	7
α-helix	375-376	2

Chain 7: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	37-57	21
β-strand	64-69	6	46
β-strand	78-82	5	46
α-helix	88-95	8
α-helix	97-102	6
β-strand	105-108	4	46
β-strand	111-113	3	46
α-helix	118-119	2
β-strand	123-128	6	46
α-helix	136-155	20
β-strand	158	1	47
β-strand	165-168	4	48
α-helix	174-176	3
β-strand	179-184	6	48
α-helix	196-212	17
β-strand	215	1	49
β-strand	217-222	6	50
α-helix	223-229	7
α-helix	234-246	13
β-strand	251-257	7	50
β-strand	260-263	4	50
β-strand	271	1	49
α-helix	272-274	3
β-strand	275-285	11	48
β-strand	294-303	10	48
α-helix	304-306	3
α-helix	307-309	3
α-helix	310-320	11
α-helix	323-324	2

72 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
mitochondrial tRNAVal	B	RNA	72	Homo sapiens
39S ribosomal protein L2, mitochondrial	D	protein	305	Homo sapiens	Q5T653 (AlphaFold model)
39S ribosomal protein L3, mitochondrial	E	protein	348	Homo sapiens	P09001 (AlphaFold model)
39S ribosomal protein L4, mitochondrial	F	protein	311	Homo sapiens	Q9BYD3 (AlphaFold model)
39S ribosomal protein L9, mitochondrial	H	protein	267	Homo sapiens	Q9BYD2 (AlphaFold model)
39S ribosomal protein L11, mitochondrial	J	protein	192	Homo sapiens	Q9Y3B7
Large ribosomal subunit protein uL13m	K	protein	178	Homo sapiens	Q9BYD1
39S ribosomal protein L14, mitochondrial	L	protein	145	Homo sapiens	Q6P1L8
39S ribosomal protein L15, mitochondrial	M	protein	296	Homo sapiens	Q9P015
39S ribosomal protein L16, mitochondrial	N	protein	251	Homo sapiens	Q9NX20
39S ribosomal protein L17, mitochondrial	O	protein	175	Homo sapiens	Q9NRX2
39S ribosomal protein L18, mitochondrial	P	protein	180	Homo sapiens	Q9H0U6

74 more molecules are not listed.

Sequence of entity 1 (B), FASTA

>8RRI_1 mitochondrial tRNAVal (chains B)
CAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUGA
CCGCUCUGACCA

Sequence of entity 2 (D), FASTA

>8RRI_2 39S ribosomal protein L2, mitochondrial (chains D)
MALCALTRALRSLNLAPPTVAAPAPSLFPAAQMMNNGLLQQPSALMLLPCRPVLTSVALN
ANFVSWKSRTKYTITPVKMRKSGGRDHTGRIRVHGIGGGHKQRYRMIDFLRFRPEETKSG
PFEEKVIQVRYDPCRSADIALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGD
AHPLGALPVGTLINNVESEPGRGAQYIRAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETC
VATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSGRWHRKGGWAGRKIRPLPPMKSYVKLPS
ASAQS

Sequence of entity 3 (E), FASTA

>8RRI_3 39S ribosomal protein L3, mitochondrial (chains E)
MPGWRLLTQVGAQVLGRLGDGLGAALGPGNRTHIWLFVRGLHGKSGTWWDEHLSEENVPF
IKQLVSDEDKAQLASKLCPLKDEPWPIHPWEPGSFRVGLIALKLGMMPLWTKDGQKHVVT
LLQVQDCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEFYRELGLPPKQTVKIFN
ITDNAAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRP
GAVATGDIGRVWPGTKMPGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGHKNCLVKVK
DSKLPAYKDLGKNLPFPTYFPDGDEEELPEDLYDENVCQPGAPSITFA

Sequence of entity 4 (F), FASTA

>8RRI_4 39S ribosomal protein L4, mitochondrial (chains F)
MLQFVRAGARAWLRPTGSQGLSSLAEEAARATENPEQVASEGLPEPVLRKVELPVPTHRR
PVQAWVESLRGFEQERVGLADLHPDVFATAPRLDILHQVAMWQKNFKRISYAKTKTRAEV
RGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRALGLKVALTV
KLAQDDLHIMDSLELPTGDPQYLTELAHYRRWGDSVLLVDLTHEEMPQSIVEATSRLKTF
NLIPAVGLNVHSMLKHQTLVLTLPTVAFLEDKLLWQDSRYRPLYPFSLPYSDFPRPLPHA
TQGPAATPYHC

Sequence of entity 5 (H), FASTA

>8RRI_5 39S ribosomal protein L9, mitochondrial (chains H)
MAAPVVTAPGRALLRAGAGRLLRGGVQELLRPRHEGNAPDLACNFSLSQNRGTVIVERWW
KVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGR
NRLLPQGLAVYASPENKKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNV
KWELNPEIVARHFFKNLGVVVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNF
EKPKTKRYKYWLAQQAAKAMAPTSPQI

Sequence of entity 6 (J), FASTA

>8RRI_6 39S ribosomal protein L11, mitochondrial (chains J)
MSKLGRAARGLRKPEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDI
KEGIPLPTKILVKPDRTFEIKIGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEI
ARIKAQDEAFALQDVPLSSVVRSIIGSARSLGIRVVKDLSSEELAAFQKERAIFLAAQKE
ADLAAQEEAAKK

Sequence of entity 7 (K), FASTA

>8RRI_7 Large ribosomal subunit protein uL13m (chains K)
XSSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIM
NTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRT
MMERLHLFPDEYIPEDILKNLVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDYRL

Sequence of entity 8 (L), FASTA

>8RRI_8 39S ribosomal protein L14, mitochondrial (chains L)
MAFFTGLWGPFTCVSRVLSHHCFSTTGSLSAIQKMTRVRVVDNSALGNSPYHRAPRCIHV
YKKNGVGKVGDQILLAIKGQKKKALIVGHCMPGPRMTPRFDSNNVVLIEDNGNPVGTRIK
TPIPTSLRKREGEYSKVLAIAQNFV

Sequence of entity 9 (M), FASTA

>8RRI_9 39S ribosomal protein L15, mitochondrial (chains M)
MAGPLQGGGARALDLLRGLPRVSLANLKPNPGSKKPERRPRGRRRGRKCGRGHKGERQRG
TRPRLGFEGGQTPFYIRIPKYGFNEGHSFRRQYKPLSLNRLQYLIDLGRVDPSQPIDLTQ
LVNGRGVTIQPLKRDYGVQLVEEGADTFTAKVNIEVQLASELAIAAIEKNGGVVTTAFYD
PRSLDIVCKPVPFFLRGQPIPKRMLPPEELVPYYTDAKNRGYLADPAKFPEARLELARKY
GYILPDITKDELFKMLCTRKDPRQIFFGLAPGWVVNMADKKILKPTDENLLKYYTS

Sequence of entity 10 (N), FASTA

>8RRI_10 39S ribosomal protein L16, mitochondrial (chains N)
MWRLLARASAPLLRVPLSDSWALLPASAGVKTLLPVPSFEDVSIPEKPKLRFIERAPLVP
KVRREPKNLSDIRGPSTEATEFTEGNFAILALGGGYLHWGHFEMMRLTINRSMDPKNMFA
IWRVPAPFKPITRKSVGHRMGGGKGAIDHYVTPVKAGRLVVEMGGRCEFEEVQGFLDQVA
HKLPFAAKAVSRGTLEKMRKDQEERERNNQNPWTFERIATANMLGIRKVLSPYDLTHKGK
YWGKFYMPKRV

Sequence of entity 11 (O), FASTA

>8RRI_11 39S ribosomal protein L17, mitochondrial (chains O)
MRLSVAAAISHGRVFRRMGLGPESRIHLLRNLLTGLVRHERIEAPWARVDEMRGYAEKLI
DYGKLGDTNERAMRMADFWLTEKDLIPKLFQVLAPRYKDQTGGYTRMLQIPNRSLDRAKM
AVIEYKGNCLPPLPLPRRDSHLTLLNQLLQGLRQDLRQSQEASNHSSHTAQTPGI

Sequence of entity 12 (P), FASTA

>8RRI_12 39S ribosomal protein L18, mitochondrial (chains P)
MALRSRFWGLFSVCRNPGCRFAALSTSSEPAAKPEVDPVENEAVAPEFTNRNPRNLELLS
VARKERGWRTVFPSREFWHRLRVIRTQHHVEALVEHQNGKVVVSASTREWAIKKHLYSTR
NVVACESIGRVLAQRCLEAGINFMVYQPTPWEAASDSMKRLQSAMTEGGVVLREPQRIYE

Ligands and cofactors

ID	Name	Formula	Copies
T1C	Tigecycline	C29 H41 N5 O8	3
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
FES	FE2/S2 (inorganic) cluster	Fe2 S2	3
MG	Magnesium ion	Mg	94
VAL	Valine	C5 H11 N O2	1

Water and common crystallization additives (K) are not listed.

Primary citation

T cell toxicity induced by tigecycline binding to the mitochondrial ribosome. Shao, Q., Khawaja, A., Nguyen, M.D. et al. Nat Commun (2025) 16:4080-4080. DOI 10.1038/s41467-025-59388-9 · PubMed

Other PDB entries of the same protein (UniProt Q5T653 (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)
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…
9RU6 2.64 Å, Human mitoribosome bound to TACO1 (Translational activator of COX1), mRNA, A/A-, P/P-…

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