6ZSD: Human mitochondrial ribosome

Name: PDB 6ZSD: Human mitochondrial ribosome in complex with mRNA, P-site tRNA and E-site tRNA
Published: 2020-09-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Human mitochondrial ribosome in complex with mRNA, P-site tRNA and E-site tRNA. Determined by electron microscopy at 3.7 Å resolution. Released 16 Sept 2020.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Homo sapiens, synthetic construct
Chains: 93
Atoms: 170,662
Mol. weight: 3066.24 kDa
Ligands: ZN, MG, DOL, GTP
Released: 16 Sept 2020

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

Secondary structure: helices and β-sheets

6ZSD contains 694 α-helices and 513 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	87-95	9
α-helix	97-99	3
β-strand	107-109	3	1
β-strand	116-118	3	1
α-helix	124-145	22
β-strand	156-160	5	2
β-strand	173-177	5	2
α-helix	180-182	3

Chain 1: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	9
β-strand	29-35	7	9
β-strand	42-47	6	9
β-strand	52-64	13	9

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	57-63	7
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	114-117	4	18
β-strand	121-125	5	18
α-helix	126	1
α-helix	138-145	8
β-strand	147-149	3	18
α-helix	152-161	10
α-helix	164-167	4
β-strand	172	1	19
α-helix	178-181	4

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	68	1	30
β-strand	80-84	5	30
β-strand	87-91	5	30
α-helix	96-98	3
β-strand	100-101	2	30

Chain 5: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	40-47	8
β-strand	59	1	33
β-strand	71	1	33
α-helix	75-78	4
α-helix	85-87	3
β-strand	104-107	4	34
α-helix	117-124	8
β-strand	126-129	4	35
α-helix	134-140	7
α-helix	143-145	3
α-helix	147	1
α-helix	150-162	13
α-helix	173-189	17
α-helix	190-192	3
α-helix	196-199	4
β-strand	202-204	3	35
β-strand	210-214	5	34
β-strand	219-223	5	34
β-strand	228-232	5	35
α-helix	236-238	3
α-helix	242-247	6
α-helix	248-250	3
β-strand	259	1	36
β-strand	266-268	3	34
β-strand	276	1	34
β-strand	279	1	37
β-strand	287-294	8	35
α-helix	306-329	24
β-strand	340-347	8	35
β-strand	352-359	8	35
β-strand	372-377	6	35
β-strand	386-387	2	38
β-strand	391-392	2	39
β-strand	397-399	3	39
β-strand	402-403	2	38
α-helix	408-419	12

Chain 6: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	50	1	43
α-helix	54-66	13
α-helix	86-88	3
α-helix	92-95	4
α-helix	99-115	17
α-helix	119-125	7
α-helix	132-142	11
α-helix	144-155	12
α-helix	157-161	5
β-strand	174-179	6	44
β-strand	183-186	4	44
β-strand	192-193	2	45
α-helix	195-198	4
α-helix	201-202	2
β-strand	203-205	3	44
β-strand	215-220	6	45
β-strand	231	1	46
β-strand	232-238	7	45
β-strand	249	1	45
α-helix	259-260	2
β-strand	261	1	14
β-strand	266-273	8	45
α-helix	293-296	4
β-strand	298	1	46
α-helix	300-307	8
β-strand	313-321	9	45
α-helix	325-329	5
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-345	6	14
α-helix	346-350	5
α-helix	352-354	3
α-helix	363-365	3

Chain 7: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	37-58	22
β-strand	65-69	5	49
β-strand	78-81	4	49
α-helix	88-95	8
α-helix	97-102	6
β-strand	105-108	4	49
β-strand	114	1	49
α-helix	118-119	2
β-strand	124-128	5	49
α-helix	136-157	22
β-strand	168	1	50
α-helix	174-176	3
β-strand	179-183	5	50
α-helix	196-212	17
β-strand	215	1	51
β-strand	217-221	5	52
α-helix	223-229	7
α-helix	234-246	13
β-strand	252-257	6	52
β-strand	260-263	4	52
β-strand	271	1	51
α-helix	272-274	3
β-strand	275-284	10	50
β-strand	295-303	9	50
α-helix	310-320	11

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
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 mitochondrial rRNA	XA	RNA	1559	Homo sapiens
28S ribosomal protein S34, mitochondrial	A0	protein	218	Homo sapiens	P82930

76 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>6ZSD_1 39S ribosomal protein L32, mitochondrial (chains 0)
MALAMLVLVVSPWSAARGVLRNYWERLLRKLPQSRPGFPSPPWGPALAVQGPAMFTEPAN
DTSGSKENSSLLDSIFWMAAPKNRRTIEVNRCRRRNPQKLIKVKNNIDVCPECGHLKQKH
VLCAYCYEKVCKETAEIRRQIGKQEGGPFKAPTIETVVLYTGETPSEQDQGKRIIERDRK
RPSWFTQN

Sequence of entity 2 (1), FASTA

>6ZSD_2 39S ribosomal protein L33, mitochondrial (chains 1)
MFLSAVFFAKSKSKNILVRMVSEAGTGFCFNTKRNRLREKLTLLHYDPVVKQRVLFVEKK
KIRSL

Sequence of entity 3 (2), FASTA

>6ZSD_3 39S ribosomal protein L34, mitochondrial (chains 2)
MAVLAGSLLGPTSRSAALLGGRWLQPRAWLGFPDAWGLPTPQQARGKARGNEYQPSNIKR
KNKHGWVRRLSTPAGVQVILRRMLKGRKSLSH

Sequence of entity 4 (3), FASTA

>6ZSD_4 39S ribosomal protein L35, mitochondrial (chains 3)
MAASAFAGAVRAASGILRPLNILASSTYRNCVKNASLISALSTGRFSHIQTPVVSSTPRL
TTSERNLTCGHTSVILNRMAPVLPSVLKLPVRSLTYFSARKGKRKTVKAVIDRFLRLHCG
LWVRRKAGYKKKLWKKTPARKKRLREFVFCNKTQSKLLDKMTTSFWKRRNWYVDDPYQKY
HDRTNLKV

Sequence of entity 5 (4), FASTA

>6ZSD_5 39S ribosomal protein L36, mitochondrial (chains 4)
MANLFIRKMVNPLLYLSRHTVKPRALSTFLFGSIRGAAPVAVEPGAAVRSLLSPGLLPHL
LPALGFKNKTVLKKRCKDCYLVKRRGRWYVYCKTHPRHKQRQM

Sequence of entity 6 (5), FASTA

>6ZSD_6 39S ribosomal protein L37, mitochondrial (chains 5)
MALASGPARRALAGSGQLGLGGFGAPRRGAYEWGVRSTRKSEPPPLDRVYEIPGLEPITF
AGKMHFVPWLARPIFPPWDRGYKDPRFYRSPPLHEHPLYKDQACYIFHHRCRLLEGVKQA
LWLTKTKLIEGLPEKVLSLVDDPRNHIENQDECVLNVISHARLWQTTEEIPKRETYCPVI
VDNLIQLCKSQILKHPSLARRICVQNSTFSATWNRESLLLQVRGSGGARLSTKDPLPTIA
SREEIEATKNHVLETFYPISPIIDLHECNIYDVKNDTGFQEGYPYPYPHTLYLLDKANLR
PHRLQPDQLRAKMILFAFGSALAQARLLYGNDAKVLEQPVVVQSVGTDGRVFHFLVFQLN
TTDLDCNEGVKNLAWVDSDQLLYQHFWCLPVIKKRVVVEPVGPVGFKPETFRKFLALYLH
GAA

Sequence of entity 7 (6), FASTA

>6ZSD_7 39S ribosomal protein L38, mitochondrial (chains 6)
MAAPWWRAALCECRRWRGFSTSAVLGRRTPPLGPMPNSDIDLSNLERLEKYRSFDRYRRR
AEQEAQAPHWWRTYREYFGEKTDPKEKIDIGLPPPKVSRTQQLLERKQAIQELRANVEEE
RAARLRTASVPLDAVRAEWERTCGPYHKQRLAEYYGLYRDLFHGATFVPRVPLHVAYAVG
EDDLMPVYCGNEVTPTEAAQAPEVTYEAEEGSLWTLLLTSLDGHLLEPDAEYLHWLLTNI
PGNRVAEGQVTCPYLPPFPARGSGIHRLAFLLFKQDQPIDFSEDARPSPCYQLAQRTFRT
FDFYKKHQETMTPAGLSFFQCRWDDSVTYIFHQLLDMREPVFEFVRPPPYHPKQKRFPHR
QPLRYLDRYRDSHEPTYGIY

Sequence of entity 8 (7), FASTA

>6ZSD_8 39S ribosomal protein L39, mitochondrial (chains 7)
MEALAMGSRALRLWLVAPGGGIKWRFIATSSASQLSPTELTEMRNDLFNKEKARQLSLTP
RTEKIEVKHVGKTDPGTVFVMNKNISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLT
KSCEIKFLTFKDCDPGEVNKAYWRSCAMMMGCVIERAFKDEYMVNLVRAPEVPVISGAFC
YDVVLDSKLDEWMPTKENLRSFTKDAHALIYKDLPFETLEVEAKVALEIFQHSKYKVDFI
EEKASQNPERIVKLHRIGDFIDVSEGPLIPRTSICFQYEVSAVHNLQPTQPSLIRRFQGV
SLPVHLRAHFTIWDKLLERSRKMVTEDQSKATEECTST

Sequence of entity 9 (8), FASTA

>6ZSD_9 39S ribosomal protein L40, mitochondrial (chains 8)
MTASVLRSISLALRPTSGLLGTWQTQLRETHQRASLLSFWELIPMRSEPLRKKKKVDPKK
DQEAKERLKRKIRKLEKATQELIPIEDFITPLKFLDKARERPQVELTFEETERRALLLKK
WSLYKQQERKMERDTIRAMLEAQQEALEELQLESPKLHAEAIKRDPNLFPFEKEGPHYTP
PIPNYQPPEGRYNDITKVYTQVEFKR

Sequence of entity 10 (9), FASTA

>6ZSD_10 39S ribosomal protein L41, mitochondrial (chains 9)
MGVLAAAARCLVRGADRMSKWTSKRGPRSFRGRKGRGAKGIGFLTSGWRFVQIKEMVPEF
VVPDLTGFKLKPYVSYLAPESEETPLTAAQLFSEAVAPAIEKDFKDGTFDPDNLEKYGFE
PTQEGKLFQLYPRNFLR

Sequence of entity 11 (XA), FASTA

>6ZSD_11 16S mitochondrial rRNA (chains XA)
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
CCGUAAAUGAUAUCAUCUCAACUUAGUAUAAUACCCACACCCACCCAAGAACAGGGUUU

Sequence of entity 12 (A0), FASTA

>6ZSD_12 28S ribosomal protein S34, mitochondrial (chains A0)
MARKKVRPRLIAELARRVRALREQLNRPRDSQLYAVDYETLTRPFSGRRLPVRAWADVRR
ESRLLQLLGRLPLFGLGRLVTRKSWLWQHDEPCYWRLTRVRPDYTAQNLDHGKAWGILTF
KGKTESEAREIEHVMYHDWRLVPKHEEEAFTAFTPAPEDSLASVPYPPLLRAMIIAERQK
NGDTSTEEPMLNVQRIRMEPWDYPAKQEDKGRAKGTPV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7
MG	Magnesium ion	Mg	195
DOL	5-(2-diethylamino-ethanesulfonyl)-21-hydroxy-10-isopropyl-11,19-dimethyl-9,26-D…	C34 H50 N4 O9 S	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Primary citation

Structural basis of mitochondrial translation. Aibara, S., Singh, V., Modelska, A. et al. Elife (2020) 9. DOI 10.7554/eLife.58362 · 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…
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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