7QI4: Human mitochondrial ribosome

Name: PDB 7QI4: Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA)
Published: 2022-07-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA). Determined by electron microscopy at 2.21 Å resolution. Released 13 Jul 2022.

Method: Electron microscopy
Resolution: 2.21 Å
Organism: Homo sapiens
Chains: 94
Atoms: 187,689
Mol. weight: 3115.32 kDa
Ligands: NAD, SPM, SPD, MG
Released: 13 Jul 2022

Explore 7QI4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QI4 contains 918 α-helices and 582 β-strands across 87 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	101-104	4
β-strand	107-109	3	54
β-strand	116-118	3	54
α-helix	124-145	22
β-strand	156-160	5	55
α-helix	167-169	3
β-strand	173-177	5	55
α-helix	180-182	3

Chain 1: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	60
β-strand	29-35	7	60
α-helix	39-41	3
β-strand	42-47	6	60
β-strand	52-64	13	60

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	115-116	2	70
β-strand	122-124	3	70
α-helix	125-126	2
α-helix	133-135	3
α-helix	138-145	8
β-strand	148-149	2	70
α-helix	152-160	9
α-helix	164-167	4
β-strand	172	1	144
α-helix	178-181	4

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	79
β-strand	80-84	5	79
β-strand	87-91	5	79
α-helix	96-98	3
β-strand	100-102	3	79

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	85
β-strand	71	1	85
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	86
α-helix	117-123	7
β-strand	126-130	5	87
α-helix	134-138	5
α-helix	147	1
α-helix	150-159	10
α-helix	160-164	5
α-helix	173-189	17
α-helix	190-192	3
α-helix	196-200	5
β-strand	201-205	5	87
β-strand	209-215	7	86
β-strand	218-224	7	86
β-strand	228-232	5	87
α-helix	235-238	4
α-helix	242-247	6
α-helix	253-255	3
β-strand	259	1	76
β-strand	266-270	5	86
β-strand	276	1	86
β-strand	279	1	88
β-strand	287-294	8	87
α-helix	300-302	3
α-helix	304-305	2
α-helix	306-328	23
β-strand	335-347	13	87
β-strand	351-361	11	87
β-strand	372-381	10	87
β-strand	385-387	3	89
β-strand	391-392	2	90
β-strand	397-399	3	90
β-strand	402-404	3	89
α-helix	408-419	12

Chain 6: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
α-helix	49	1
β-strand	50	1	26
α-helix	54-66	13
α-helix	74-78	5
α-helix	86-88	3
β-strand	89	1	96
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	157-162	6
β-strand	166	1	96
β-strand	174-179	6	97
β-strand	183-187	5	97
β-strand	189-192	4	98
α-helix	201-202	2
β-strand	203-205	3	97
β-strand	213-220	8	98
β-strand	231-241	11	98
α-helix	245-247	3
β-strand	249-252	4	98
α-helix	259-260	2
β-strand	261	1	27
β-strand	266-275	10	98
α-helix	282-284	3
α-helix	293-296	4
β-strand	297-298	2	98
α-helix	300-307	8
α-helix	308-310	3
β-strand	311-321	11	98
α-helix	326-329	4
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-345	6	27
α-helix	346-350	5
α-helix	352-354	3
β-strand	359	1	70
β-strand	362	1	70
α-helix	363-369	7

Chain 7: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	37-57	21
β-strand	64-69	6	106
β-strand	78-82	5	106
α-helix	88-95	8
α-helix	97-102	6
β-strand	105-108	4	106
β-strand	111-113	3	106
α-helix	118-119	2
β-strand	123-128	6	106
α-helix	136-157	22
β-strand	158	1	107
β-strand	165-168	4	108
α-helix	174-176	3
β-strand	179-184	6	108
α-helix	188-190	3
α-helix	196-212	17
β-strand	215	1	109
β-strand	217-222	6	110
α-helix	223-229	7
α-helix	234-246	13
β-strand	251-257	7	110
β-strand	260-263	4	110
β-strand	271	1	109
α-helix	272-274	3
β-strand	275-285	11	108
β-strand	294-303	10	108
α-helix	304-306	3
α-helix	310-320	11

77 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
12S mitochondrial rRNA	AA	RNA	954	Homo sapiens
28S ribosomal protein S2, mitochondrial	AB	protein	296	Homo sapiens	Q9Y399 (AlphaFold model)
28S ribosomal protein S24, mitochondrial	AC	protein	167	Homo sapiens	Q96EL2 (AlphaFold model)
28S ribosomal protein S5, mitochondrial	AD	protein	430	Homo sapiens	P82675 (AlphaFold model)
28S ribosomal protein S6, mitochondrial	AE	protein	125	Homo sapiens	P82932 (AlphaFold model)
28S ribosomal protein S7, mitochondrial	AF	protein	242	Homo sapiens	Q9Y2R9
28S ribosomal protein S9, mitochondrial	AG	protein	396	Homo sapiens	P82933
28S ribosomal protein S10, mitochondrial	AH	protein	201	Homo sapiens	P82664
28S ribosomal protein S11, mitochondrial	AI	protein	194	Homo sapiens	P82912
28S ribosomal protein S12, mitochondrial	AJ	protein	138	Homo sapiens	O15235
28S ribosomal protein S14, mitochondrial	AK	protein	128	Homo sapiens	O60783
28S ribosomal protein S15, mitochondrial	AL	protein	257	Homo sapiens	P82914

77 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>7QI4_1 12S mitochondrial rRNA (chains AA)
AUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCCC
GUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGGACAAGCAUCAAGCACGCA
GCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAAC
CUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCGU
GCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUUU
UAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUGA
CACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACACAAUAGCUAAGACCCAA
ACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAAC
UGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAUA
UCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGC
UCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAGU
ACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAU
UUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUAG
CAGUAAACUGAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCCC
GUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAUA
GAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAACC

Sequence of entity 2 (AB), FASTA

>7QI4_2 28S ribosomal protein S2, mitochondrial (chains AB)
MATSSAALPRILGAGARAPSRWLGFLGKATPRPARPSRRTLGSATALMIRESEDSTDFND
KILNEPLKHSDFFNVKELFSVRSLFDARVHLGHKAGCRHRFMEPYIFGSRLDHDIIDLEQ
TATHLQLALNFTAHMAYRKGIILFISRNRQFSYLIENMARDCGEYAHTRYFRGGMLTNAR
LLFGPTVRLPDLIIFLHTLNNIFEPHVAVRDAAKMNIPTVGIVDTNCNPCLITYPVPGND
DSPLAVHLYCRLFQTAITRAKEKRQQVEALYRLQGQKEPGDQGPAHPPGADMSHSL

Sequence of entity 3 (AC), FASTA

>7QI4_3 28S ribosomal protein S24, mitochondrial (chains AC)
MAASVCSGLLGPRVLSWSRELPCAWRALHTSPVCAKNRAARVRVSKGDKPVTYEEAHAPH
YIAHRKGWLSLHTGNLDGEDHAAERTVEDVFLRKFMWGTFPGCLADQLVLKRRGNQLEIC
AVVLRQLSPHKYYFLVGYSETLLSYFYKCPVRLHLQTVPSKVVYKYL

Sequence of entity 4 (AD), FASTA

>7QI4_4 28S ribosomal protein S5, mitochondrial (chains AD)
MATAVRAVGCLPVLCSGTAGHLLGRQCSLNTLPAASILAWKSVLGNGHLSSLGTRDTHPY
ASLSRALQTQCCISSPSHLMSQQYRPYSFFTKLTADELWKGALAETGAGAKKGRGKRTKK
KKRKDLNRGQIIGEGRYGFLWPGLNVPLMKNGAVQTIAQRSKEEQEKVEADMIQQREEWD
RKKKMKVKRERGWSGNSWGGISLGPPDPGPCGETYEDFDTRILEVRNVFTMTAKEGRKKS
IRVLVAVGNGKGAAGFSIGKATDRMDAFRKAKNRAVHHLHYIERYEDHTIFHDISLRFKR
THIKMKKQPKGYGLRCHRAIITICRLIGIKDMYAKVSGSINMLSLTQGLFRGLSRQETHQ
QLADKKGLHVVEIREECGPLPIVVASPRGPLRKDPEPEDEVPDVKLDWEDVKTAQGMKRS
VWSNLKRAAT

Sequence of entity 5 (AE), FASTA

>7QI4_5 28S ribosomal protein S6, mitochondrial (chains AE)
MPRYELALILKAMQRPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNR
GGYFLVDFYAPTAAVESMVEHLSRDIDVIRGNIVKHPLTQELKECEGIVPVPLAEKLYST
KKRKK

Sequence of entity 6 (AF), FASTA

>7QI4_6 28S ribosomal protein S7, mitochondrial (chains AF)
MAAPAVKVARGWSGLALGVRRAVLQLPGLTQVRWSRYSPEFKDPLIDKEYYRKPVEELTE
EEKYVRELKKTQLIKAAPAGKTSSVFEDPVISKFTNMMMIGGNKVLARSLMIQTLEAVKR
KQFEKYHAASAEEQATIERNPYTIFHQALKNCEPMIGLVPILKGGRFYQVPVPLPDRRRR
FLAMKWMITECRDKKHQRTLMPEKLSHKLLEAFHNQGPVIKRKHDLHKMAEANRALAHYR
WW

Sequence of entity 7 (AG), FASTA

>7QI4_7 28S ribosomal protein S9, mitochondrial (chains AG)
MAAPCVSYGGAVSYRLLLWGRGSLARKQGLWKTAAPELQTNVRSQILRLRHTAFVIPKKN
VPTSKRETYTEDFIKKQIEEFNIGKRHLANMMGEDPETFTQEDIDRAIAYLFPSGLFEKR
ARPVMKHPEQIFPRQRAIQWGEDGRPFHYLFYTGKQSYYSLMHDVYGMLLNLEKHQSHLQ
AKSLLPEKTVTRDVIGSRWLIKEELEEMLVEKLSDLDYMQFIRLLEKLLTSQCGAAEEEF
VQRFRRSVTLESKKQLIEPVQYDEQGMAFSKSEGKRKTAKAEAIVYKHGSGRIKVNGIDY
QLYFPITQDREQLMFPFHFVDRLGKHDVTCTVSGGGRSAQAGAIRLAMAKALCSFVTEDE
VEWMRQAGLLTTDPRVRERKKPGQEGARRKFTWKKR

Sequence of entity 8 (AH), FASTA

>7QI4_8 28S ribosomal protein S10, mitochondrial (chains AH)
MAARTAFGAVCRRLWQGLGNFSVNTSKGNTAKNGGLLLSTNMKWVQFSNLHVDVPKDLTK
PVVTISDEPDILYKRLSVLVKGHDKAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTL
LQSVHIYKKHRVQYEMRTLYRCLELEHLTGSTADVYLEYIQRNLPEGVAMEVTKTQLEQL
PEHIKEPIWETLSEEKEESKS

Sequence of entity 9 (AI), FASTA

>7QI4_9 28S ribosomal protein S11, mitochondrial (chains AI)
MQAVRNAGSRFLRSWTWPQTAGRVVARTPAGTICTGARQLQDAAAKQKVEQNAAPSHTKF
SIYPPIPGEESSLRWAGKKFEEIPIAHIKASHNNTQIQVVSASNEPLAFASCGTEGFRNA
KKGTGIAAQTAGIAAAARAKQKGVIHIRVVVKGLGPGRLSAMHGLIMGGLEVISITDNTP
IPHXGCRPRKARKL

Sequence of entity 10 (AJ), FASTA

>7QI4_10 28S ribosomal protein S12, mitochondrial (chains AJ)
MSWSGLLHGLNTSLTCGPALVPRLWATCSMATLNQMHRLGPPKRPPRKLGPTEGRPQLKG
VVLCTFTRKPKKPNSANRKCCRVRLSTGREAVCFIPGEGHTLQEHQIVLVEGGRTQDLPG
VKLTVVRGKYDCGHVQKK

Sequence of entity 11 (AK), FASTA

>7QI4_11 28S ribosomal protein S14, mitochondrial (chains AK)
MAAFMLGSLLRTFKQMVPSSASGQVRSHYVDWRMWRDVKRRKMAYEYADERLRINSLRKN
TILPKILQDVADEEIAALPRDSCPVRIRNRCVMTSRPRGVKRRWRLSRIVFRHLADHGQL
SGIQRATW

Sequence of entity 12 (AL), FASTA

>7QI4_12 28S ribosomal protein S15, mitochondrial (chains AL)
MLRVAWRTLSLIRTRAVTQVLVPGLPGGGSAKFPFNQWGLQPRSLLLQAARGYVVRKPAQ
SRLDDDPPPSTLLKDYQNVPGIEKVDDVVKRLLSLEMANKKEMLKIKQEQFMKKIVANPE
DTRSLEARIIALSVKIRSYEEHLEKHRKDKAHKRYLLMSIDQRKKMLKNLRNTNYDVFEK
ICWGLGIEYTFPPLYYRRAHRRFVTKKALCIRVFQETQKLKKRRRALKAAAAAQKQAKRR
NPDSPAKAIPKTLKDSQ

Ligands and cofactors

ID	Name	Formula	Copies
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	1
SPM	Spermine	C10 H26 N4	1
SPD	Spermidine	C7 H19 N3	4
MG	Magnesium ion	Mg	206
ZN	Zinc ion	Zn	3
FES	FE2/S2 (inorganic) cluster	Fe2 S2	3
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
PUT	1,4-diaminobutane	C4 H12 N2	1
VAL	Valine	C5 H11 N O2	1

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

Primary citation

Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk. Singh, V., Itoh, Y., Del'Olio, S. et al. Nat Commun (2024) 15:4272-4272. DOI 10.1038/s41467-024-48163-x · PubMed

Other PDB entries of the same protein (UniProt Q9Y399 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8CSS 2.36 Å, Human mitochondrial small subunit assembly intermediate (State D)
7P2E 2.4 Å, Human mitochondrial ribosome small subunit in complex with IF3, GMPPMP and streptomycin
8RRI 2.4 Å, Human mitochondrial ribosome in complex with antibiotic tigecycline
9OLF 2.46 Å, Membrane-associated human mitoribosome in complex with TACO1
9OJM 2.5 Å, Human mitochondrial 28S PIC with tRNA and mtIF2
8CSQ 2.54 Å, Human mitochondrial small subunit assembly intermediate (State B)
8CSR 2.54 Å, Human mitochondrial small subunit assembly intermediate (State C)
6ZM6 2.59 Å, Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA
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-…
8CSP 2.66 Å, Human mitochondrial small subunit assembly intermediate (State A)
7PNX 2.76 Å, Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in…

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