7O9K: 39S ribosomal protein L32, mitochondrial

Name: PDB 7O9K: Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1, the MALSU module, GTPBP5 and mtEF-Tu
Published: 2021-06-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1, the MALSU module, GTPBP5 and mtEF-Tu. Determined by electron microscopy at 3.1 Å resolution. Released 30 Jun 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 69
Atoms: 115,679
Mol. weight: 2196.28 kDa
Ligands: ZN, MG, SAM, GDP
Released: 30 Jun 2021

Explore 7O9K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7O9K contains 545 α-helices and 455 β-strands across 67 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	1
β-strand	116-118	3	1
α-helix	124-145	22
β-strand	156-158	3	2
β-strand	173-175	3	2
α-helix	180-182	3

Chain 1: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	17
β-strand	29-35	7	17
α-helix	39-41	3
β-strand	42-47	6	17
β-strand	52-64	13	17

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: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	108-111	4
β-strand	115-116	2	23
β-strand	122-124	3	23
α-helix	125-126	2
α-helix	138-145	8
β-strand	148-149	2	23
α-helix	152-160	9
α-helix	164-167	4
β-strand	172	1	5
α-helix	179-181	3

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	31
β-strand	80-84	5	31
β-strand	87-91	5	31
α-helix	96-98	3
β-strand	100-102	3	31

Chain 5: 19 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	40-47	8
α-helix	48-51	4
β-strand	59	1	36
β-strand	71	1	36
α-helix	72-78	7
α-helix	90-92	3
β-strand	99-107	9	37
α-helix	117-124	8
β-strand	126-130	5	38
α-helix	134-137	4
α-helix	138-140	3
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	196-200	5
β-strand	201-204	4	38
β-strand	209-215	7	37
β-strand	218-224	7	37
β-strand	229-232	4	38
α-helix	235-238	4
α-helix	242-247	6
α-helix	248-250	3
β-strand	259	1	39
β-strand	266-270	5	37
β-strand	276	1	37
β-strand	279	1	40
β-strand	287-294	8	38
α-helix	304-305	2
α-helix	306-329	24
β-strand	335-347	13	38
β-strand	351-361	11	38
β-strand	372-381	10	38
β-strand	385-387	3	41
β-strand	391-393	3	42
β-strand	396-399	4	42
β-strand	402-404	3	41
α-helix	409-419	11

Chain 6: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
α-helix	49	1
β-strand	50	1	52
α-helix	54-66	13
α-helix	74-77	4
α-helix	100-113	14
α-helix	117-124	8
α-helix	132-142	11
α-helix	144-154	11
α-helix	157-161	5
β-strand	174-179	6	53
β-strand	183-187	5	53
β-strand	191-192	2	54
α-helix	201-202	2
β-strand	203-205	3	53
β-strand	214-220	7	54
β-strand	231-233	3	54
β-strand	237-240	4	54
β-strand	249-250	2	54
α-helix	259-260	2
β-strand	261	1	20
β-strand	266-275	10	54
α-helix	293-295	3
β-strand	297-298	2	54
α-helix	300-306	7
β-strand	311-321	11	54
α-helix	325-329	5
α-helix	330-335	6
α-helix	338-339	2
β-strand	340-345	6	20
α-helix	347-350	4
α-helix	352-354	3
β-strand	362	1	23
α-helix	365-368	4

Chain 7: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	37-57	21
β-strand	64-69	6	57
β-strand	78-82	5	57
α-helix	88-95	8
α-helix	97-101	5
β-strand	105-108	4	57
β-strand	111-113	3	57
β-strand	123-128	6	57
α-helix	136-155	20
β-strand	164-168	5	58
β-strand	179-185	7	58
α-helix	187-189	3
α-helix	196-212	17
β-strand	215	1	59
β-strand	216-222	7	60
α-helix	223-229	7
α-helix	234-246	13
β-strand	251-257	7	60
β-strand	260-264	5	60
β-strand	271	1	59
α-helix	272-274	3
β-strand	275-285	11	58
β-strand	295-303	9	58
α-helix	307-309	3
α-helix	310-320	11

57 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 L42, mitochondrial	a	protein	142	Homo sapiens	Q9Y6G3 (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
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	1559	Homo sapiens

51 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>7O9K_1 39S ribosomal protein L32, mitochondrial (chains 0)
MALAMLVLVVSPWSAARGVLRNYWERLLRKLPQSRPGFPSPPWGPALAVQGPAMFTEPAN
DTSGSKENSSLLDSIFWMAAPKNRRTIEVNRCRRRNPQKLIKVKNNIDVCPECGHLKQKH
VLCAYCYEKVCKETAEIRRQIGKQEGGPFKAPTIETVVLYTGETPSEQDQGKRIIERDRK
RPSWFTQN

Sequence of entity 2 (a), FASTA

>7O9K_2 39S ribosomal protein L42, mitochondrial (chains a)
MAVAAVKWVMSKRTILKHLFPVQNGALYCVCHKSTYSPLPDDYNCNVELALTSDGRTIVC
YHPSVDIPYEHTKPIPRPDPVHNNEETHDQVLKTRLEEKVEHLEEGPMIEQLSKMFFTTK
HRWYPHGRYHRCRKNLNPPKDR

Sequence of entity 3 (1), FASTA

>7O9K_3 39S ribosomal protein L33, mitochondrial (chains 1)
MFLSAVFFAKSKSKNILVRMVSEAGTGFCFNTKRNRLREKLTLLHYDPVVKQRVLFVEKK
KIRSL

Sequence of entity 4 (2), FASTA

>7O9K_4 39S ribosomal protein L34, mitochondrial (chains 2)
MAVLAGSLLGPTSRSAALLGGRWLQPRAWLGFPDAWGLPTPQQARGKARGNEYQPSNIKR
KNKHGWVRRLSTPAGVQVILRRMLKGRKSLSH

Sequence of entity 5 (3), FASTA

>7O9K_5 39S ribosomal protein L35, mitochondrial (chains 3)
MAASAFAGAVRAASGILRPLNILASSTYRNCVKNASLISALSTGRFSHIQTPVVSSTPRL
TTSERNLTCGHTSVILNRMAPVLPSVLKLPVRSLTYFSARKGKRKTVKAVIDRFLRLHCG
LWVRRKAGYKKKLWKKTPARKKRLREFVFCNKTQSKLLDKMTTSFWKRRNWYVDDPYQKY
HDRTNLKV

Sequence of entity 6 (4), FASTA

>7O9K_6 39S ribosomal protein L36, mitochondrial (chains 4)
MANLFIRKMVNPLLYLSRHTVKPRALSTFLFGSIRGAAPVAVEPGAAVRSLLSPGLLPHL
LPALGFKNKTVLKKRCKDCYLVKRRGRWYVYCKTHPRHKQRQM

Sequence of entity 7 (5), FASTA

>7O9K_7 39S ribosomal protein L37, mitochondrial (chains 5)
MALASGPARRALAGSGQLGLGGFGAPRRGAYEWGVRSTRKSEPPPLDRVYEIPGLEPITF
AGKMHFVPWLARPIFPPWDRGYKDPRFYRSPPLHEHPLYKDQACYIFHHRCRLLEGVKQA
LWLTKTKLIEGLPEKVLSLVDDPRNHIENQDECVLNVISHARLWQTTEEIPKRETYCPVI
VDNLIQLCKSQILKHPSLARRICVQNSTFSATWNRESLLLQVRGSGGARLSTKDPLPTIA
SREEIEATKNHVLETFYPISPIIDLHECNIYDVKNDTGFQEGYPYPYPHTLYLLDKANLR
PHRLQPDQLRAKMILFAFGSALAQARLLYGNDAKVLEQPVVVQSVGTDGRVFHFLVFQLN
TTDLDCNEGVKNLAWVDSDQLLYQHFWCLPVIKKRVVVEPVGPVGFKPETFRKFLALYLH
GAA

Sequence of entity 8 (6), FASTA

>7O9K_8 39S ribosomal protein L38, mitochondrial (chains 6)
MAAPWWRAALCECRRWRGFSTSAVLGRRTPPLGPMPNSDIDLSNLERLEKYRSFDRYRRR
AEQEAQAPHWWRTYREYFGEKTDPKEKIDIGLPPPKVSRTQQLLERKQAIQELRANVEEE
RAARLRTASVPLDAVRAEWERTCGPYHKQRLAEYYGLYRDLFHGATFVPRVPLHVAYAVG
EDDLMPVYCGNEVTPTEAAQAPEVTYEAEEGSLWTLLLTSLDGHLLEPDAEYLHWLLTNI
PGNRVAEGQVTCPYLPPFPARGSGIHRLAFLLFKQDQPIDFSEDARPSPCYQLAQRTFRT
FDFYKKHQETMTPAGLSFFQCRWDDSVTYIFHQLLDMREPVFEFVRPPPYHPKQKRFPHR
QPLRYLDRYRDSHEPTYGIY

Sequence of entity 9 (7), FASTA

>7O9K_9 39S ribosomal protein L39, mitochondrial (chains 7)
MEALAMGSRALRLWLVAPGGGIKWRFIATSSASQLSPTELTEMRNDLFNKEKARQLSLTP
RTEKIEVKHVGKTDPGTVFVMNKNISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLT
KSCEIKFLTFKDCDPGEVNKAYWRSCAMMMGCVIERAFKDEYMVNLVRAPEVPVISGAFC
YDVVLDSKLDEWMPTKENLRSFTKDAHALIYKDLPFETLEVEAKVALEIFQHSKYKVDFI
EEKASQNPERIVKLHRIGDFIDVSEGPLIPRTSICFQYEVSAVHNLQPTQPSLIRRFQGV
SLPVHLRAHFTIWDKLLERSRKMVTEDQSKATEECTST

Sequence of entity 10 (8), FASTA

>7O9K_10 39S ribosomal protein L40, mitochondrial (chains 8)
MTASVLRSISLALRPTSGLLGTWQTQLRETHQRASLLSFWELIPMRSEPLRKKKKVDPKK
DQEAKERLKRKIRKLEKATQELIPIEDFITPLKFLDKARERPQVELTFEETERRALLLKK
WSLYKQQERKMERDTIRAMLEAQQEALEELQLESPKLHAEAIKRDPNLFPFEKEGPHYTP
PIPNYQPPEGRYNDITKVYTQVEFKR

Sequence of entity 11 (9), FASTA

>7O9K_11 39S ribosomal protein L41, mitochondrial (chains 9)
MGVLAAAARCLVRGADRMSKWTSKRGPRSFRGRKGRGAKGIGFLTSGWRFVQIKEMVPEF
VVPDLTGFKLKPYVSYLAPESEETPLTAAQLFSEAVAPAIEKDFKDGTFDPDNLEKYGFE
PTQEGKLFQLYPRNFLR

Sequence of entity 12 (A), FASTA

>7O9K_12 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

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	93
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1
PNS	4'-phosphopantetheine	C11 H23 N2 O7 P S	1

Primary citation

Structural basis for late maturation steps of the human mitoribosomal large subunit. Cipullo, M., Gese, G.V., Khawaja, A. et al. Nat Commun (2021) 12:3673-3673. DOI 10.1038/s41467-021-23617-8 · 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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