8QU1: 39S ribosomal protein L2, mitochondrial

Name: PDB 8QU1: mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 1
Published: 2024-06-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 1. Determined by electron microscopy at 2.74 Å resolution. Released 26 Jun 2024.

Method: Electron microscopy
Resolution: 2.74 Å
Organism: Homo sapiens
Chains: 30
Atoms: 57,235
Mol. weight: 1237.16 kDa
Released: 26 Jun 2024

Explore 8QU1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QU1 contains 215 α-helices and 225 β-strands across 28 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	101-103	3
β-strand	107-109	3	74
β-strand	116-118	3	74
α-helix	124-145	22
β-strand	156-159	4	75
β-strand	173-176	4	75
α-helix	180-182	3

Chain 1: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	76
β-strand	29-35	7	76
β-strand	42-47	6	76
β-strand	52-60	9	76

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	108-113	6
β-strand	115-116	2	1
β-strand	122-125	4	1
α-helix	126	1
α-helix	138-144	7
β-strand	147-149	3	1
α-helix	152-160	9
α-helix	164-167	4
β-strand	172	1	36
α-helix	178-180	3

Chain 5: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	48-51	4
α-helix	55-58	4
β-strand	59	1	6
β-strand	71	1	6
α-helix	72-74	3
α-helix	85-87	3
α-helix	90-92	3
β-strand	104-107	4	7
α-helix	117-124	8
β-strand	126-130	5	8
α-helix	134-137	4
α-helix	138-140	3
α-helix	150-162	13
α-helix	173-189	17
α-helix	196-200	5
β-strand	201-204	4	8
β-strand	207-215	9	7
β-strand	218-226	9	7
β-strand	229-232	4	8
α-helix	235-238	4
α-helix	242-247	6
α-helix	248-250	3
β-strand	266-268	3	7
β-strand	276	1	7
β-strand	287-294	8	8
α-helix	304-305	2
α-helix	306-329	24
β-strand	335-347	13	8
β-strand	351-361	11	8
β-strand	372-381	10	8
β-strand	385-387	3	9
β-strand	391	1	10
β-strand	399	1	10
β-strand	402-404	3	9
α-helix	409-419	11

Chain 6: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	50	1	66
α-helix	54-59	6

Chain D: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	77-78	2	2
β-strand	103-104	2	2
α-helix	105-106	2
β-strand	107	1	3
β-strand	122-130	9	3
β-strand	139-144	6	3
β-strand	147-152	6	3
α-helix	153	1
β-strand	154	1	4
β-strand	162-165	4	3
β-strand	181-183	3	3
α-helix	184-186	3
β-strand	192-194	3	3
β-strand	196	1	5
β-strand	206	1	5
β-strand	214-220	7	3
β-strand	223-227	5	3
β-strand	233-237	5	3
β-strand	241-244	4	3
β-strand	247	1	4

Chain E: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	57-75	19
α-helix	84-87	4
β-strand	99-110	12	11
β-strand	111	1	12
β-strand	116-124	9	11
β-strand	128-133	6	13
α-helix	135-138	4
β-strand	143-151	9	13
α-helix	154-156	3
α-helix	159-168	10
α-helix	171-172	2
β-strand	173-181	9	13
α-helix	187-188	2
β-strand	192	1	13
α-helix	195-197	3
β-strand	203-209	7	11
α-helix	210-212	3
β-strand	215-216	2	14
α-helix	218-221	4
β-strand	259-260	2	14
β-strand	265-277	13	11
β-strand	282-286	5	11
β-strand	296-301	6	11
α-helix	305-307	3
α-helix	321-323	3
β-strand	331-333	3	11
β-strand	337	1	12

20 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 ribosomal RNA	A	RNA	1559	Homo sapiens
mitochondrial tRNAVal	B	RNA	69	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	178	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

18 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8QU1_1 16S ribosomal RNA (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

>8QU1_2 mitochondrial tRNAVal (chains B)
CAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUGA
CCGCUCUGA

Sequence of entity 3 (D), FASTA

>8QU1_3 39S ribosomal protein L2, mitochondrial (chains D)
MALCALTRALRSLNLAPPTVAAPAPSLFPAAQMMNNGLLQQPSALMLLPCRPVLTSVALN
ANFVSWKSRTKYTITPVKMRKSGGRDHTGRIRVHGIGGGHKQRYRMIDFLRFRPEETKSG
PFEEKVIQVRYDPCRSADIALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGD
AHPLGALPVGTLINNVESEPGRGAQYIRAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETC
VATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSGRWHRKGGWAGRKIRPLPPMKSYVKLPS
ASAQS

Sequence of entity 4 (E), FASTA

>8QU1_4 39S ribosomal protein L3, mitochondrial (chains E)
MPGWRLLTQVGAQVLGRLGDGLGAALGPGNRTHIWLFVRGLHGKSGTWWDEHLSEENVPF
IKQLVSDEDKAQLASKLCPLKDEPWPIHPWEPGSFRVGLIALKLGMMPLWTKDGQKHVVT
LLQVQDCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEFYRELGLPPKQTVKIFN
ITDNAAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRP
GAVATGDIGRVWPGTKMPGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGHKNCLVKVK
DSKLPAYKDLGKNLPFPTYFPDGDEEELPEDLYDENVCQPGAPSITFA

Sequence of entity 5 (F), FASTA

>8QU1_5 39S ribosomal protein L4, mitochondrial (chains F)
MLQFVRAGARAWLRPTGSQGLSSLAEEAARATENPEQVASEGLPEPVLRKVELPVPTHRR
PVQAWVESLRGFEQERVGLADLHPDVFATAPRLDILHQVAMWQKNFKRISYAKTKTRAEV
RGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRALGLKVALTV
KLAQDDLHIMDSLELPTGDPQYLTELAHYRRWGDSVLLVDLTHEEMPQSIVEATSRLKTF
NLIPAVGLNVHSMLKHQTLVLTLPTVAFLEDKLLWQDSRYRPLYPFSLPYSDFPRPLPHA
TQGPAATPYHC

Sequence of entity 6 (H), FASTA

>8QU1_6 39S ribosomal protein L9, mitochondrial (chains H)
MAAPVVTAPGRALLRAGAGRLLRGGVQELLRPRHEGNAPDLACNFSLSQNRGTVIVERWW
KVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGR
NRLLPQGLAVYASPENKKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNV
KWELNPEIVARHFFKNLGVVVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNF
EKPKTKRYKYWLAQQAAKAMAPTSPQI

Sequence of entity 7 (I), FASTA

>8QU1_7 39S ribosomal protein L10, mitochondrial (chains I)
MAAAVAGMLRGGLLPQAGRLPTLQTVRYGSKAVTRHRRVMHFQRQKLMAVTEYIPPKPAI
HPSCLPSPPSPPQEEIGLIRLLRREIAAVFQDNRMIAVCQNVALSAEDKLLMRHQLRKHK
ILMKVFPNQVLKPFLEDSKYQNLLPLFVGHNMLLVSEEPKVKEMVRILRTVPFLPLLGGC
IDDTILSRQGFINYSKLPSLPLVQGELVGGLTCLTAQTHSLLQHQPLQLTTLLDQYIREQ
REKDSVMSANGKPDPDTVPDS

Sequence of entity 8 (J), FASTA

>8QU1_8 39S ribosomal protein L11, mitochondrial (chains J)
MSKLGRAARGLRKPEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDI
KEGIPLPTKILVKPDRTFEIKIGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEI
ARIKAQDEAFALQDVPLSSVVRSIIGSARSLGIRVVKDLSSEELAAFQKERAIFLAAQKE
ADLAAQEEAAKK

Sequence of entity 9 (K), FASTA

>8QU1_9 39S ribosomal protein L13, mitochondrial (chains K)
MSSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIM
NTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRT
MMERLHLFPDEYIPEDILKNLVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDYRL

Sequence of entity 10 (L), FASTA

>8QU1_10 39S ribosomal protein L14, mitochondrial (chains L)
MAFFTGLWGPFTCVSRVLSHHCFSTTGSLSAIQKMTRVRVVDNSALGNSPYHRAPRCIHV
YKKNGVGKVGDQILLAIKGQKKKALIVGHCMPGPRMTPRFDSNNVVLIEDNGNPVGTRIK
TPIPTSLRKREGEYSKVLAIAQNFV

Sequence of entity 11 (M), FASTA

>8QU1_11 39S ribosomal protein L15, mitochondrial (chains M)
MAGPLQGGGARALDLLRGLPRVSLANLKPNPGSKKPERRPRGRRRGRKCGRGHKGERQRG
TRPRLGFEGGQTPFYIRIPKYGFNEGHSFRRQYKPLSLNRLQYLIDLGRVDPSQPIDLTQ
LVNGRGVTIQPLKRDYGVQLVEEGADTFTAKVNIEVQLASELAIAAIEKNGGVVTTAFYD
PRSLDIVCKPVPFFLRGQPIPKRMLPPEELVPYYTDAKNRGYLADPAKFPEARLELARKY
GYILPDITKDELFKMLCTRKDPRQIFFGLAPGWVVNMADKKILKPTDENLLKYYTS

Sequence of entity 12 (N), FASTA

>8QU1_12 39S ribosomal protein L16, mitochondrial (chains N)
MWRLLARASAPLLRVPLSDSWALLPASAGVKTLLPVPSFEDVSIPEKPKLRFIERAPLVP
KVRREPKNLSDIRGPSTEATEFTEGNFAILALGGGYLHWGHFEMMRLTINRSMDPKNMFA
IWRVPAPFKPITRKSVGHRMGGGKGAIDHYVTPVKAGRLVVEMGGRCEFEEVQGFLDQVA
HKLPFAAKAVSRGTLEKMRKDQEERERNNQNPWTFERIATANMLGIRKVLSPYDLTHKGK
YWGKFYMPKRV

Primary citation

GTPBP8 plays a role in mitoribosome formation in human mitochondria. Cipullo, M., Valentin Gese, G., Gopalakrishna, S. et al. Nat Commun (2024) 15:5664-5664. DOI 10.1038/s41467-024-50011-x · 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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