7PD3: Human mitoribosomal large subunit

Name: PDB 7PD3: Structure of the human mitoribosomal large subunit in complex with NSUN4.MTERF4.GTPBP7 and MALSU1.L0R8F8.mt-ACP
Published: 2021-11-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the human mitoribosomal large subunit in complex with NSUN4.MTERF4.GTPBP7 and MALSU1.L0R8F8.mt-ACP. Determined by electron microscopy at 3.4 Å resolution. Released 17 Nov 2021.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 60
Atoms: 108,075
Mol. weight: 2010.5 kDa
Ligands: GCP, SAM, PNS, MG
Released: 17 Nov 2021

Explore 7PD3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PD3 contains 439 α-helices and 425 β-strands across 58 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: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	87-93	7
α-helix	101-102	2
β-strand	107	1	1
β-strand	118	1	1
α-helix	124-145	22
β-strand	156-159	4	2
β-strand	173-176	4	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	42-46	5	9
β-strand	53-64	12	9

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: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	108-111	4
β-strand	115-116	2	16
β-strand	122-123	2	16
β-strand	124-125	2	17
α-helix	138-144	7
β-strand	147-148	2	17
β-strand	149	1	18
α-helix	152-160	9
α-helix	164-166	3
α-helix	178-180	3

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	68	1	21
β-strand	80-84	5	21
β-strand	87-91	5	21
α-helix	96-98	3
β-strand	100-101	2	21

Chain 5: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	36-38	3
α-helix	40-47	8
β-strand	59	1	28
β-strand	71	1	28
α-helix	72-76	5
α-helix	90-92	3
α-helix	103	1
β-strand	104-107	4	29
α-helix	117-122	6
β-strand	126-130	5	30
α-helix	134-137	4
α-helix	152-162	11
α-helix	173-189	17
α-helix	196-199	4
β-strand	201-202	2	31
β-strand	208-215	8	29
β-strand	218-225	8	29
β-strand	229-232	4	31
α-helix	235-238	4
α-helix	242-246	5
α-helix	251-255	5
β-strand	259	1	32
β-strand	266-268	3	29
β-strand	276	1	29
β-strand	287-291	5	31
β-strand	292-293	2	30
α-helix	306-325	20
β-strand	335-347	13	30
β-strand	351-361	11	30
β-strand	372-376	5	30
β-strand	380-381	2	30
β-strand	385-387	3	33
β-strand	393	1	34
β-strand	396	1	34
β-strand	402-404	3	33
α-helix	409-418	10

Chain 6: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	29-31	3
α-helix	34-35	2
β-strand	50	1	37
α-helix	55-66	12
α-helix	74-77	4
α-helix	100-113	14
α-helix	117-124	8
α-helix	133-142	10
α-helix	144-154	11
β-strand	174-176	3	38
β-strand	183	1	39
β-strand	186-187	2	38
β-strand	191-192	2	40
α-helix	195-197	3
α-helix	201-202	2
β-strand	203-205	3	38
β-strand	214-220	7	40
β-strand	231-232	2	41
β-strand	233	1	40
β-strand	236-240	5	40
β-strand	249-252	4	40
α-helix	259-260	2
β-strand	261	1	42
β-strand	266-274	9	40
α-helix	293-296	4
β-strand	297-298	2	41
α-helix	300-305	6
β-strand	312-321	10	40
α-helix	327-329	3
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-345	6	43
α-helix	346-350	5
α-helix	352-355	4
β-strand	359	1	18
β-strand	362	1	17
α-helix	363-367	5

Chain 7: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	37-56	20
β-strand	64-69	6	53
β-strand	78-82	5	53
α-helix	88-95	8
α-helix	98-101	4
β-strand	105-108	4	53
β-strand	112-113	2	53
α-helix	118-119	2
β-strand	124-128	5	53
α-helix	136-155	20
β-strand	164-168	5	54
α-helix	174-176	3
β-strand	179-185	7	54
α-helix	187-189	3
α-helix	196-210	15
β-strand	215	1	55
β-strand	217-222	6	56
α-helix	223-229	7
α-helix	234-246	13
β-strand	251-256	6	56
β-strand	261-263	3	56
β-strand	271	1	55
α-helix	272-274	3
β-strand	275-285	11	54
β-strand	294-303	10	54
α-helix	310-319	10

50 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 rRNA	A	RNA	1737	Homo sapiens
mt-tRNAVal	B	RNA	69	Homo sapiens

47 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>7PD3_1 39S ribosomal protein L32, mitochondrial (chains 0)
MALAMLVLVVSPWSAARGVLRNYWERLLRKLPQSRPGFPSPPWGPALAVQGPAMFTEPAN
DTSGSKENSSLLDSIFWMAAPKNRRTIEVNRCRRRNPQKLIKVKNNIDVCPECGHLKQKH
VLCAYCYEKVCKETAEIRRQIGKQEGGPFKAPTIETVVLYTGETPSEQDQGKRIIERDRK
RPSWFTQN

Sequence of entity 2 (1), FASTA

>7PD3_2 39S ribosomal protein L33, mitochondrial (chains 1)
MFLSAVFFAKSKSKNILVRMVSEAGTGFCFNTKRNRLREKLTLLHYDPVVKQRVLFVEKK
KIRSL

Sequence of entity 3 (2), FASTA

>7PD3_3 39S ribosomal protein L34, mitochondrial (chains 2)
MAVLAGSLLGPTSRSAALLGGRWLQPRAWLGFPDAWGLPTPQQARGKARGNEYQPSNIKR
KNKHGWVRRLSTPAGVQVILRRMLKGRKSLSH

Sequence of entity 4 (3), FASTA

>7PD3_4 39S ribosomal protein L35, mitochondrial (chains 3)
MAASAFAGAVRAASGILRPLNILASSTYRNCVKNASLISALSTGRFSHIQTPVVSSTPRL
TTSERNLTCGHTSVILNRMAPVLPSVLKLPVRSLTYFSARKGKRKTVKAVIDRFLRLHCG
LWVRRKAGYKKKLWKKTPARKKRLREFVFCNKTQSKLLDKMTTSFWKRRNWYVDDPYQKY
HDRTNLKV

Sequence of entity 5 (4), FASTA

>7PD3_5 39S ribosomal protein L36, mitochondrial (chains 4)
MANLFIRKMVNPLLYLSRHTVKPRALSTFLFGSIRGAAPVAVEPGAAVRSLLSPGLLPHL
LPALGFKNKTVLKKRCKDCYLVKRRGRWYVYCKTHPRHKQRQM

Sequence of entity 6 (5), FASTA

>7PD3_6 39S ribosomal protein L37, mitochondrial (chains 5)
MALASGPARRALAGSGQLGLGGFGAPRRGAYEWGVRSTRKSEPPPLDRVYEIPGLEPITF
AGKMHFVPWLARPIFPPWDRGYKDPRFYRSPPLHEHPLYKDQACYIFHHRCRLLEGVKQA
LWLTKTKLIEGLPEKVLSLVDDPRNHIENQDECVLNVISHARLWQTTEEIPKRETYCPVI
VDNLIQLCKSQILKHPSLARRICVQNSTFSATWNRESLLLQVRGSGGARLSTKDPLPTIA
SREEIEATKNHVLETFYPISPIIDLHECNIYDVKNDTGFQEGYPYPYPHTLYLLDKANLR
PHRLQPDQLRAKMILFAFGSALAQARLLYGNDAKVLEQPVVVQSVGTDGRVFHFLVFQLN
TTDLDCNEGVKNLAWVDSDQLLYQHFWCLPVIKKRVVVEPVGPVGFKPETFRKFLALYLH
GAA

Sequence of entity 7 (6), FASTA

>7PD3_7 39S ribosomal protein L38, mitochondrial (chains 6)
MAAPWWRAALCECRRWRGFSTSAVLGRRTPPLGPMPNSDIDLSNLERLEKYRSFDRYRRR
AEQEAQAPHWWRTYREYFGEKTDPKEKIDIGLPPPKVSRTQQLLERKQAIQELRANVEEE
RAARLRTASVPLDAVRAEWERTCGPYHKQRLAEYYGLYRDLFHGATFVPRVPLHVAYAVG
EDDLMPVYCGNEVTPTEAAQAPEVTYEAEEGSLWTLLLTSLDGHLLEPDAEYLHWLLTNI
PGNRVAEGQVTCPYLPPFPARGSGIHRLAFLLFKQDQPIDFSEDARPSPCYQLAQRTFRT
FDFYKKHQETMTPAGLSFFQCRWDDSVTYIFHQLLDMREPVFEFVRPPPYHPKQKRFPHR
QPLRYLDRYRDSHEPTYGIY

Sequence of entity 8 (7), FASTA

>7PD3_8 39S ribosomal protein L39, mitochondrial (chains 7)
MEALAMGSRALRLWLVAPGGGIKWRFIATSSASQLSPTELTEMRNDLFNKEKARQLSLTP
RTEKIEVKHVGKTDPGTVFVMNKNISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLT
KSCEIKFLTFKDCDPGEVNKAYWRSCAMMMGCVIERAFKDEYMVNLVRAPEVPVISGAFC
YDVVLDSKLDEWMPTKENLRSFTKDAHALIYKDLPFETLEVEAKVALEIFQHSKYKVDFI
EEKASQNPERIVKLHRIGDFIDVSEGPLIPRTSICFQYEVSAVHNLQPTQPSLIRRFQGV
SLPVHLRAHFTIWDKLLERSRKMVTEDQSKATEECTST

Sequence of entity 9 (8), FASTA

>7PD3_9 39S ribosomal protein L40, mitochondrial (chains 8)
MTASVLRSISLALRPTSGLLGTWQTQLRETHQRASLLSFWELIPMRSEPLRKKKKVDPKK
DQEAKERLKRKIRKLEKATQELIPIEDFITPLKFLDKARERPQVELTFEETERRALLLKK
WSLYKQQERKMERDTIRAMLEAQQEALEELQLESPKLHAEAIKRDPNLFPFEKEGPHYTP
PIPNYQPPEGRYNDITKVYTQVEFKR

Sequence of entity 10 (9), FASTA

>7PD3_10 39S ribosomal protein L41, mitochondrial (chains 9)
MGVLAAAARCLVRGADRMSKWTSKRGPRSFRGRKGRGAKGIGFLTSGWRFVQIKEMVPEF
VVPDLTGFKLKPYVSYLAPESEETPLTAAQLFSEAVAPAIEKDFKDGTFDPDNLEKYGFE
PTQEGKLFQLYPRNFLR

Sequence of entity 11 (A), FASTA

>7PD3_11 16S rRNA (chains A)
GCUAAACCUAGCCCCAAACCCACUCCACCUUACUACCAGACAACCUUAGCCAAACCAUUU
ACCCAAAUAAAGUAUAGGCGAUAGAAAUUGAAACCUGGCGCAAUAGAUAUAGUACCGCAA
GGGAAAGAUGAAAAAUUAUAACCAAGCAUAAUAUAGCAAGGACUAACCCCUAUACCUUCU
GCAUAAUGAAUUAACUAGAAAUAACUUUGCAAGGAGAGCCAAAGCUAAGACCCCCGAAAC
CAGACGAGCUACCUAAGAACAGCUAAAAGAGCACACCCGUCUAUGUAGCAAAAUAGUGGG
AAGAUUUAUAGGUAGAGGCGACAAACCUACCGAGCCUGGUGAUAGCUGGUUGUCCAAGAU
AGAAUCUUAGUUCAACUUUAAAUUUGCCCACAGAACCCUCUAAAUCCCCUUGUAAAUUUA
ACUGUUAGUCCAAAGAGGAACAGCUCUUUGGACACUAGGAAAAAACCUUGUAGAGAGAGU
AAAAAAUUUAACACCCAUAGUAGGCCUAAAAGCAGCCACCAAUUAAGAAAGCGUUCAAGC
UCAACACCCACUACCUAAAAAAUCCCAAACAUAUAACUGAACUCCUCACACCCAAUUGGA
CCAAUCUAUCACCCUAUAGAAGAACUAAUGUUAGUAUAAGUAACAUGAAAACAUUCUCCU
CCGCAUAAGCCUGCGUCAGAUUAAAACACUGAACUGACAAUUAACAGCCCAAUAUCUACA
AUCAACCAACAAGUCAUUAUUACCCUCACUGUCAACCCAACACAGGCAUGCUCAUAAGGA
AAGGUUAAAAAAAGUAAAAGGAACUCGGCAAAUCUUACCCCGCCUGUUUACCAAAAACAU
CACCUCUAGCAUCACCAGUAUUAGAGGCACCGCCUGCCCAGUGACACAUGUUUAACGGCC
GCGGUACCCUAACCGUGCAAAGGUAGCAUAAUCACUUGUUCCUUAAAUAGGGACCUGUAU
GAAUGGCACCACGAGGGUUCAGCUGUCUCUUACUUUUAACCAGUGAAAUUGACCUGCCCG
UGAAGAGGCGGGCAUAACACAGCAAGACGAGAAGACCCUAUGGAGCUUUAAUUUAUUAAU
GCAAACAGUACCUAACAAACCCACAGGUCCUAAACUACCAAACCUGCAUUAAAAAUUUCG
GUUGGGGCGACCUCGGAGCAGAACCCAACCUCCGAGCAGUACAUGCUAAGACUUCACCAG
UCAAAGCGAACUACUAUACUCAAUUGAUCCAAUAACUUGACCAACGGAACAAGUUACCCU
AGGGAUAACAGCGCAAUCCUAUUCUAGAGUCCAUAUCAACAAUAGGGUUUACGACCUCGA
UGUUGGAUCAGGACAUCCCGAUGGUGCAGCCGCUAUUAAAGGUUCGUUUGUUCAACGAUU
AAAGUCCUACGUGAUCUGAGUUCAGACCGGAGUAAUCCAGGUCGGUUUCUAUCUACUUUC
AAAUUCCUCCCUGUACGAAAGGACAAGAGAAAUAAGGCCUACUUCACAAAGCGCCUUCCC
CCGUAAAUGAUAUCAUCUCAACUUAGUAUUAUACCCACACCCACCCAAGAACAGGGUUUG
UUCAACGAUUAAAGUCCUACGUGAUCUGAGUUCAGACCGGAGUAAUCCAGGUCGGUUUCU
AUCUACUUUAUUCCUCCCUGUACGAAAGGACAAGAGAAAUAAGGCCUACUUCACAAAGCG
CCUUCCCCCGUAAAUGAUAUCAUCUCAACUUAGAUACCCACACCCAAGAACAGGGUU

Sequence of entity 12 (B), FASTA

>7PD3_12 mt-tRNAVal (chains B)
CAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUGA
CCGCUCUGA

Ligands and cofactors

ID	Name	Formula	Copies
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	2
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
PNS	4'-phosphopantetheine	C11 H23 N2 O7 P S	1
MG	Magnesium ion	Mg	91
ZN	Zinc ion	Zn	2

Primary citation

Visualizing formation of the active site in the mitochondrial ribosome. Chandrasekaran, V., Desai, N., Burton, N.O. et al. Elife (2021) 10. DOI 10.7554/eLife.68806 · 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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