3J9M: Human mitochondrial ribosome

Name: PDB 3J9M: Structure of the human mitochondrial ribosome (class 1)
Published: 2015-04-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the human mitochondrial ribosome (class 1). Determined by electron microscopy at 3.5 Å resolution. Released 15 Apr 2015.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 85
Atoms: 158,384
Mol. weight: 2865.04 kDa
Ligands: GDP, ZN, MG
Released: 15 Apr 2015

Explore 3J9M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J9M contains 622 α-helices and 561 β-strands across 81 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	101-103	3
β-strand	107-108	2	173
β-strand	117-118	2	173
α-helix	124-144	21
β-strand	157-159	3	174
α-helix	164-166	3
β-strand	174-176	3	174
α-helix	180-182	3

Chain 1: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	177
β-strand	29-35	7	177
α-helix	39-41	3
β-strand	42-47	6	177
β-strand	52-64	13	177

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	57-64	8
α-helix	66-71	6
α-helix	73-85	13

Chain 3: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	108-113	6
β-strand	114-116	3	1
β-strand	122-125	4	1
α-helix	126	1
α-helix	138-144	7
β-strand	147-149	3	1
α-helix	150	1
α-helix	152-161	10
β-strand	172	1	90
α-helix	178-180	3

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	68	1	8
β-strand	80-84	5	8
β-strand	87-91	5	8
α-helix	96-98	3
β-strand	100-101	2	8

Chain 5: 18 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	36-38	3
α-helix	40-47	8
β-strand	59	1	19
β-strand	71	1	19
α-helix	72-73	2
α-helix	85-87	3
α-helix	90-92	3
α-helix	103	1
β-strand	104-107	4	20
α-helix	117-124	8
β-strand	126-129	4	21
α-helix	134-138	5
α-helix	151-159	9
α-helix	160-164	5
α-helix	173-189	17
α-helix	196-199	4
β-strand	201-204	4	21
β-strand	209-214	6	20
β-strand	219-223	5	20
β-strand	228-232	5	21
α-helix	235-238	4
α-helix	242-246	5
α-helix	247-250	4
α-helix	252-255	4
β-strand	259	1	5
β-strand	266-268	3	20
β-strand	276-277	2	20
β-strand	279	1	22
β-strand	287-292	6	21
α-helix	306-328	23
β-strand	335-345	11	21
β-strand	354-361	8	21
β-strand	372-377	6	21
β-strand	385-386	2	23
β-strand	391	1	24
β-strand	399	1	24
β-strand	403-404	2	23
α-helix	409-419	11

Chain 6: 20 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	29-31	3
α-helix	34-35	2
α-helix	55-66	12
α-helix	74-77	4
α-helix	100-117	18
α-helix	132-141	10
α-helix	144-155	12
α-helix	157-160	4
β-strand	174-178	5	32
β-strand	184-187	4	32
β-strand	191-192	2	33
α-helix	201-202	2
β-strand	203-205	3	32
β-strand	214	1	33
β-strand	217-220	4	33
β-strand	232-238	7	33
β-strand	240	1	33
β-strand	249-252	4	33
α-helix	254-257	4
α-helix	259-260	2
β-strand	261	1	34
β-strand	266-275	10	33
α-helix	293-296	4
β-strand	297	1	33
α-helix	300-305	6
β-strand	311-321	11	33
α-helix	325-329	5
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-342	3	160
β-strand	345	1	159
α-helix	346-349	4
α-helix	353-355	3
β-strand	362	1	1
α-helix	363-369	7
α-helix	375-376	2

Chain 7: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	37-58	22
β-strand	64-69	6	43
β-strand	78-82	5	43
α-helix	88-95	8
α-helix	97-102	6
β-strand	105-107	3	44
β-strand	112-114	3	44
β-strand	124-125	2	43
β-strand	126-128	3	44
α-helix	136-157	22
β-strand	166	1	45
β-strand	179-183	5	45
α-helix	196-212	17
β-strand	215	1	46
β-strand	217-221	5	47
α-helix	223-229	7
α-helix	234-246	13
β-strand	252-257	6	47
β-strand	260-263	4	47
β-strand	271	1	46
α-helix	272-274	3
β-strand	275-279	5	48
β-strand	283-284	2	45
β-strand	295-299	5	45
β-strand	300-303	4	48
α-helix	310-321	12

73 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 rRNA	A	RNA	1559	Homo sapiens
mt-tRNAVal	B	RNA	73	Homo sapiens
uL2m	D	protein	305	Homo sapiens	Q5T653 (AlphaFold model)
uL3m	E	protein	348	Homo sapiens	P09001 (AlphaFold model)
uL4m	F	protein	311	Homo sapiens	Q9BYD3 (AlphaFold model)
bL9m	H	protein	267	Homo sapiens	Q9BYD2 (AlphaFold model)
uL10m	I	protein	261	Homo sapiens	Q7Z7H8
uL11m	J	protein	192	Homo sapiens	Q9Y3B7
uL13m	K	protein	178	Homo sapiens	Q9BYD1
uL14m	L	protein	145	Homo sapiens	Q6P1L8
uL15m	M	protein	296	Homo sapiens	Q9P015
uL16m	N	protein	251	Homo sapiens	Q9NX20

73 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>3J9M_1 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 2 (B), FASTA

>3J9M_2 mt-tRNAVal (chains B)
CCAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUG
ACCGCUCUGACCA

Sequence of entity 3 (D), FASTA

>3J9M_3 uL2m (chains D)
MALCALTRALRSLNLAPPTVAAPAPSLFPAAQMMNNGLLQQPSALMLLPCRPVLTSVALN
ANFVSWKSRTKYTITPVKMRKSGGRDHTGRIRVHGIGGGHKQRYRMIDFLRFRPEETKSG
PFEEKVIQVRYDPCRSADIALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGD
AHPLGALPVGTLINNVESEPGRGAQYIRAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETC
VATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSGRWHRKGGWAGRKIRPLPPMKSYVKLPS
ASAQS

Sequence of entity 4 (E), FASTA

>3J9M_4 uL3m (chains E)
MPGWRLLTQVGAQVLGRLGDGLGAALGPGNRTHIWLFVRGLHGKSGTWWDEHLSEENVPF
IKQLVSDEDKAQLASKLCPLKDEPWPIHPWEPGSFRVGLIALKLGMMPLWTKDGQKHVVT
LLQVQDCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEFYRELGLPPKQTVKIFN
ITDNAAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRP
GAVATGDIGRVWPGTKMPGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGHKNCLVKVK
DSKLPAYKDLGKNLPFPTYFPDGDEEELPEDLYDENVCQPGAPSITFA

Sequence of entity 5 (F), FASTA

>3J9M_5 uL4m (chains F)
MLQFVRAGARAWLRPTGSQGLSSLAEEAARATENPEQVASEGLPEPVLRKVELPVPTHRR
PVQAWVESLRGFEQERVGLADLHPDVFATAPRLDILHQVAMWQKNFKRISYAKTKTRAEV
RGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRALGLKVALTV
KLAQDDLHIMDSLELPTGDPQYLTELAHYRRWGDSVLLVDLTHEEMPQSIVEATSRLKTF
NLIPAVGLNVHSMLKHQTLVLTLPTVAFLEDKLLWQDSRYRPLYPFSLPYSDFPRPLPHA
TQGPAATPYHC

Sequence of entity 6 (H), FASTA

>3J9M_6 bL9m (chains H)
MAAPVVTAPGRALLRAGAGRLLRGGVQELLRPRHEGNAPDLACNFSLSQNRGTVIVERWW
KVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGR
NRLLPQGLAVYASPENKKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNV
KWELNPEIVARHFFKNLGVVVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNF
EKPKTKRYKYWLAQQAAKAMAPTSPQI

Sequence of entity 7 (I), FASTA

>3J9M_7 uL10m (chains I)
MAAAVAGMLRGGLLPQAGRLPTLQTVRYGSKAVTRHRRVMHFQRQKLMAVTEYIPPKPAI
HPSCLPSPPSPPQEEIGLIRLLRREIAAVFQDNRMIAVCQNVALSAEDKLLMRHQLRKHK
ILMKVFPNQVLKPFLEDSKYQNLLPLFVGHNMLLVSEEPKVKEMVRILRTVPFLPLLGGC
IDDTILSRQGFINYSKLPSLPLVQGELVGGLTCLTAQTHSLLQHQPLQLTTLLDQYIREQ
REKDSVMSANGKPDPDTVPDS

Sequence of entity 8 (J), FASTA

>3J9M_8 uL11m (chains J)
MSKLGRAARGLRKPEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDI
KEGIPLPTKILVKPDRTFEIKIGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEI
ARIKAQDEAFALQDVPLSSVVRSIIGSARSLGIRVVKDLSSEELAAFQKERAIFLAAQKE
ADLAAQEEAAKK

Sequence of entity 9 (K), FASTA

>3J9M_9 uL13m (chains K)
MSSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIM
NTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRT
MMERLHLFPDEYIPEDILKNLVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDYRL

Sequence of entity 10 (L), FASTA

>3J9M_10 uL14m (chains L)
MAFFTGLWGPFTCVSRVLSHHCFSTTGSLSAIQKMTRVRVVDNSALGNSPYHRAPRCIHV
YKKNGVGKVGDQILLAIKGQKKKALIVGHCMPGPRMTPRFDSNNVVLIEDNGNPVGTRIK
TPIPTSLRKREGEYSKVLAIAQNFV

Sequence of entity 11 (M), FASTA

>3J9M_11 uL15m (chains M)
MAGPLQGGGARALDLLRGLPRVSLANLKPNPGSKKPERRPRGRRRGRKCGRGHKGERQRG
TRPRLGFEGGQTPFYIRIPKYGFNEGHSFRRQYKPLSLNRLQYLIDLGRVDPSQPIDLTQ
LVNGRGVTIQPLKRDYGVQLVEEGADTFTAKVNIEVQLASELAIAAIEKNGGVVTTAFYD
PRSLDIVCKPVPFFLRGQPIPKRMLPPEELVPYYTDAKNRGYLADPAKFPEARLELARKY
GYILPDITKDELFKMLCTRKDPRQIFFGLAPGWVVNMADKKILKPTDENLLKYYTS

Sequence of entity 12 (N), FASTA

>3J9M_12 uL16m (chains N)
MWRLLARASAPLLRVPLSDSWALLPASAGVKTLLPVPSFEDVSIPEKPKLRFIERAPLVP
KVRREPKNLSDIRGPSTEATEFTEGNFAILALGGGYLHWGHFEMMRLTINRSMDPKNMFA
IWRVPAPFKPITRKSVGHRMGGGKGAIDHYVTPVKAGRLVVEMGGRCEFEEVQGFLDQVA
HKLPFAAKAVSRGTLEKMRKDQEERERNNQNPWTFERIATANMLGIRKVLSPYDLTHKGK
YWGKFYMPKRV

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
ZN	Zinc ion	Zn	7
MG	Magnesium ion	Mg	127

Primary citation

Ribosome. The structure of the human mitochondrial ribosome. Amunts, A., Brown, A., Toots, J. et al. Science (2015) 348:95-98. DOI 10.1126/science.aaa1193 · 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…
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…

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3J9M is part of these collections:

The ribosome and protein synthesis

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