6ZM6: Human mitochondrial ribosome

Name: PDB 6ZM6: Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA
Published: 2021-01-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA. Determined by electron microscopy at 2.59 Å resolution. Released 13 Jan 2021.

Method: Electron microscopy
Resolution: 2.59 Å
Organism: Homo sapiens
Chains: 92
Atoms: 176,756
Mol. weight: 3069.3 kDa
Ligands: GTP, ATP, FES, ZN
Released: 13 Jan 2021

Explore 6ZM6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZM6 contains 818 α-helices and 562 β-strands across 86 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: 5 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	170
β-strand	116-118	3	170
α-helix	124-145	22
β-strand	156-160	5	171
β-strand	173-177	5	171
α-helix	180-182	3

Chain 1: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	174
β-strand	29-35	7	174
α-helix	39-41	3
β-strand	44-47	4	175
β-strand	52-55	4	175
β-strand	56-64	9	174

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	57-63	7
α-helix	66-69	4
α-helix	73-85	13

Chain 3: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	108-111	4
β-strand	115-116	2	2
β-strand	122-124	3	2
α-helix	133-135	3
α-helix	138-144	7
β-strand	148-149	2	2
α-helix	152-160	9
α-helix	164-167	4
β-strand	172	1	93
α-helix	178-181	4

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	68-69	2	11
β-strand	80-84	5	11
β-strand	87-91	5	11
α-helix	96-98	3
β-strand	100-102	3	11

Chain 5: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	40-47	8
α-helix	48-51	4
β-strand	59	1	18
β-strand	71	1	18
α-helix	72-73	2
α-helix	75-78	4
α-helix	85-87	3
α-helix	90-92	3
α-helix	93-95	3
β-strand	104-107	4	19
α-helix	117-123	7
β-strand	126-130	5	20
α-helix	134-138	5
α-helix	147	1
α-helix	150-159	10
α-helix	160-164	5
α-helix	173-188	16
α-helix	189-192	4
α-helix	196-198	3
β-strand	201-205	5	20
β-strand	208-214	7	19
β-strand	219-225	7	19
β-strand	228-232	5	20
α-helix	235-238	4
α-helix	242-246	5
α-helix	247-249	3
β-strand	259	1	8
β-strand	266-268	3	19
β-strand	276	1	19
β-strand	279	1	21
β-strand	287-294	8	20
α-helix	304-305	2
α-helix	306-329	24
β-strand	335-347	13	20
β-strand	351-361	11	20
β-strand	372-381	10	20
β-strand	385-387	3	22
β-strand	391-392	2	23
β-strand	397-399	3	23
β-strand	402-404	3	22
α-helix	408-419	12

Chain 6: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	45-47	3
β-strand	50	1	155
α-helix	54-65	12
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	117-125	9
α-helix	132-142	11
α-helix	144-155	12
α-helix	157-162	6
β-strand	166	1	35
β-strand	174-179	6	36
β-strand	183-187	5	36
β-strand	189-192	4	37
β-strand	203-205	3	36
β-strand	213-220	8	37
β-strand	231-241	11	37
β-strand	249-252	4	37
α-helix	259-260	2
β-strand	261	1	38
β-strand	266-275	10	37
α-helix	293-296	4
β-strand	297-298	2	37
α-helix	300-305	6
β-strand	311-321	11	37
α-helix	326-329	4
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-345	6	38
α-helix	346-350	5
α-helix	352-354	3
β-strand	362	1	2
α-helix	363-369	7

Chain 7: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	37-58	22
β-strand	64-69	6	42
β-strand	78-82	5	42
α-helix	88-95	8
α-helix	97-102	6
β-strand	105-108	4	42
β-strand	111-113	3	42
α-helix	118-119	2
β-strand	124-128	5	42
α-helix	136-157	22
β-strand	158	1	43
β-strand	165-168	4	44
β-strand	179-184	6	44
α-helix	187-189	3
α-helix	196-211	16
α-helix	214	1
β-strand	215	1	45
β-strand	216-222	7	46
α-helix	223-229	7
α-helix	234-246	13
β-strand	251-257	7	46
β-strand	260-263	4	46
β-strand	271	1	45
α-helix	272-274	3
β-strand	275-285	11	44
β-strand	295-303	9	44
α-helix	310-321	12

76 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
16S mitochondrial rRNA	A	RNA	1561	Homo sapiens
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 L10, mitochondrial	I	protein	261	Homo sapiens	Q7Z7H8
39S ribosomal protein L11, mitochondrial	J	protein	192	Homo sapiens	Q9Y3B7
39S ribosomal protein L13, mitochondrial	K	protein	177	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

75 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>6ZM6_1 16S mitochondrial 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
CCGUAAAUGAUAUCAUCUCAACUUAGUAUUAUACCCACACCCACCCAAGAACAGGGUUUG
U

Sequence of entity 2 (B), FASTA

>6ZM6_2 mitochondrial tRNAVal (chains B)
CAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUGA
CCGCUCUGACCA

Sequence of entity 3 (D), FASTA

>6ZM6_3 39S ribosomal protein L2, mitochondrial (chains D)
MALCALTRALRSLNLAPPTVAAPAPSLFPAAQMMNNGLLQQPSALMLLPCRPVLTSVALN
ANFVSWKSRTKYTITPVKMRKSGGRDHTGRIRVHGIGGGHKQRYRMIDFLRFRPEETKSG
PFEEKVIQVRYDPCRSADIALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGD
AHPLGALPVGTLINNVESEPGRGAQYIRAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETC
VATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSGRWHRKGGWAGRKIRPLPPMKSYVKLPS
ASAQS

Sequence of entity 4 (E), FASTA

>6ZM6_4 39S ribosomal protein L3, mitochondrial (chains E)
MPGWRLLTQVGAQVLGRLGDGLGAALGPGNRTHIWLFVRGLHGKSGTWWDEHLSEENVPF
IKQLVSDEDKAQLASKLCPLKDEPWPIHPWEPGSFRVGLIALKLGMMPLWTKDGQKHVVT
LLQVQDCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEFYRELGLPPKQTVKIFN
ITDNAAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRP
GAVATGDIGRVWPGTKMPGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGHKNCLVKVK
DSKLPAYKDLGKNLPFPTYFPDGDEEELPEDLYDENVCQPGAPSITFA

Sequence of entity 5 (F), FASTA

>6ZM6_5 39S ribosomal protein L4, mitochondrial (chains F)
MLQFVRAGARAWLRPTGSQGLSSLAEEAARATENPEQVASEGLPEPVLRKVELPVPTHRR
PVQAWVESLRGFEQERVGLADLHPDVFATAPRLDILHQVAMWQKNFKRISYAKTKTRAEV
RGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRALGLKVALTV
KLAQDDLHIMDSLELPTGDPQYLTELAHYRRWGDSVLLVDLTHEEMPQSIVEATSRLKTF
NLIPAVGLNVHSMLKHQTLVLTLPTVAFLEDKLLWQDSRYRPLYPFSLPYSDFPRPLPHA
TQGPAATPYHC

Sequence of entity 6 (H), FASTA

>6ZM6_6 39S ribosomal protein L9, mitochondrial (chains H)
MAAPVVTAPGRALLRAGAGRLLRGGVQELLRPRHEGNAPDLACNFSLSQNRGTVIVERWW
KVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGR
NRLLPQGLAVYASPENKKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNV
KWELNPEIVARHFFKNLGVVVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNF
EKPKTKRYKYWLAQQAAKAMAPTSPQI

Sequence of entity 7 (I), FASTA

>6ZM6_7 39S ribosomal protein L10, mitochondrial (chains I)
MAAAVAGMLRGGLLPQAGRLPTLQTVRYGSKAVTRHRRVMHFQRQKLMAVTEYIPPKPAI
HPSCLPSPPSPPQEEIGLIRLLRREIAAVFQDNRMIAVCQNVALSAEDKLLMRHQLRKHK
ILMKVFPNQVLKPFLEDSKYQNLLPLFVGHNMLLVSEEPKVKEMVRILRTVPFLPLLGGC
IDDTILSRQGFINYSKLPSLPLVQGELVGGLTCLTAQTHSLLQHQPLQLTTLLDQYIREQ
REKDSVMSANGKPDPDTVPDS

Sequence of entity 8 (J), FASTA

>6ZM6_8 39S ribosomal protein L11, mitochondrial (chains J)
MSKLGRAARGLRKPEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDI
KEGIPLPTKILVKPDRTFEIKIGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEI
ARIKAQDEAFALQDVPLSSVVRSIIGSARSLGIRVVKDLSSEELAAFQKERAIFLAAQKE
ADLAAQEEAAKK

Sequence of entity 9 (K), FASTA

>6ZM6_9 39S ribosomal protein L13, mitochondrial (chains K)
SSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMN
TRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRTM
MERLHLFPDEYIPEDILKNLVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDYRL

Sequence of entity 10 (L), FASTA

>6ZM6_10 39S ribosomal protein L14, mitochondrial (chains L)
MAFFTGLWGPFTCVSRVLSHHCFSTTGSLSAIQKMTRVRVVDNSALGNSPYHRAPRCIHV
YKKNGVGKVGDQILLAIKGQKKKALIVGHCMPGPRMTPRFDSNNVVLIEDNGNPVGTRIK
TPIPTSLRKREGEYSKVLAIAQNFV

Sequence of entity 11 (M), FASTA

>6ZM6_11 39S ribosomal protein L15, mitochondrial (chains M)
MAGPLQGGGARALDLLRGLPRVSLANLKPNPGSKKPERRPRGRRRGRKCGRGHKGERQRG
TRPRLGFEGGQTPFYIRIPKYGFNEGHSFRRQYKPLSLNRLQYLIDLGRVDPSQPIDLTQ
LVNGRGVTIQPLKRDYGVQLVEEGADTFTAKVNIEVQLASELAIAAIEKNGGVVTTAFYD
PRSLDIVCKPVPFFLRGQPIPKRMLPPEELVPYYTDAKNRGYLADPAKFPEARLELARKY
GYILPDITKDELFKMLCTRKDPRQIFFGLAPGWVVNMADKKILKPTDENLLKYYTS

Sequence of entity 12 (N), FASTA

>6ZM6_12 39S ribosomal protein L16, mitochondrial (chains N)
MWRLLARASAPLLRVPLSDSWALLPASAGVKTLLPVPSFEDVSIPEKPKLRFIERAPLVP
KVRREPKNLSDIRGPSTEATEFTEGNFAILALGGGYLHWGHFEMMRLTINRSMDPKNMFA
IWRVPAPFKPITRKSVGHRMGGGKGAIDHYVTPVKAGRLVVEMGGRCEFEEVQGFLDQVA
HKLPFAAKAVSRGTLEKMRKDQEERERNNQNPWTFERIATANMLGIRKVLSPYDLTHKGK
YWGKFYMPKRV

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
FES	FE2/S2 (inorganic) cluster	Fe2 S2	3
ZN	Zinc ion	Zn	3
MG	Magnesium ion	Mg	189

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

Primary citation

Mechanism of membrane-tethered mitochondrial protein synthesis. Itoh, Y., Andrell, J., Choi, A. et al. Science (2021) 371:846-849. DOI 10.1126/science.abe0763 · 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)
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…
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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