7O9M: Mitochondrial ribosome-associated GTPase 1

Name: PDB 7O9M: Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1 and the MALSU module
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 and the MALSU module. Determined by electron microscopy at 2.6 Å resolution. Released 30 Jun 2021.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 66
Atoms: 110,342
Mol. weight: 2078.39 kDa
Ligands: PNS, SAM, ZN, GDP
Released: 30 Jun 2021

Explore 7O9M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7O9M contains 519 α-helices and 408 β-strands across 64 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	156-159	4	2
β-strand	173-176	4	2
α-helix	180-182	3

Chain 1: 1 helix, 4 β-strands

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

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: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	108-113	6
β-strand	115-116	2	20
β-strand	122-125	4	20
α-helix	126	1
α-helix	133-135	3
α-helix	138-144	7
β-strand	147-149	3	20
α-helix	152-160	9
α-helix	164-167	4
β-strand	172	1	65
α-helix	179-181	3

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	68-69	2	25
β-strand	80-84	5	25
β-strand	87-91	5	25
α-helix	96-98	3
β-strand	100-102	3	25

Chain 5: 18 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	40-47	8
β-strand	59	1	31
β-strand	71	1	31
α-helix	72-78	7
α-helix	85-87	3
α-helix	90-92	3
α-helix	93-95	3
β-strand	99-107	9	32
α-helix	117-124	8
β-strand	126-130	5	33
α-helix	134-141	8
α-helix	150-159	10
α-helix	160-164	5
α-helix	173-189	17
α-helix	190-192	3
α-helix	196-200	5
β-strand	201-204	4	33
β-strand	207-215	9	32
β-strand	218-226	9	32
β-strand	229-232	4	33
α-helix	235-238	4
α-helix	242-247	6
α-helix	253-255	3
β-strand	259	1	18
β-strand	266-270	5	32
β-strand	276	1	32
β-strand	279	1	34
β-strand	287-294	8	33
α-helix	304-305	2
α-helix	306-329	24
β-strand	335-347	13	33
β-strand	351-361	11	33
β-strand	372-381	10	33
β-strand	385-387	3	35
β-strand	391-393	3	36
β-strand	396-399	4	36
β-strand	402-404	3	35
α-helix	409-419	11

Chain 6: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	111
α-helix	54-66	13
α-helix	74-78	5
α-helix	100-115	16
α-helix	118-125	8
α-helix	132-142	11
α-helix	144-154	11
α-helix	157-161	5
β-strand	174-179	6	40
β-strand	183-187	5	40
β-strand	191-192	2	41
α-helix	201-202	2
β-strand	203-205	3	40
β-strand	214-220	7	41
β-strand	231-240	10	41
β-strand	249-252	4	41
α-helix	259-260	2
β-strand	261	1	42
β-strand	266-275	10	41
α-helix	293-296	4
β-strand	297-298	2	41
α-helix	300-306	7
β-strand	311-321	11	41
α-helix	325-329	5
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-345	6	42
α-helix	346-350	5
α-helix	352-355	4
β-strand	362	1	20
α-helix	363-368	6

Chain 7: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	37-57	21
β-strand	64-69	6	44
β-strand	77-82	6	44
α-helix	88-95	8
α-helix	97-102	6
β-strand	105-108	4	44
β-strand	111-113	3	44
α-helix	118-119	2
β-strand	123-128	6	44
α-helix	136-157	22
β-strand	164-168	5	45
α-helix	174-176	3
β-strand	179-185	7	45
α-helix	187-189	3
α-helix	196-212	17
β-strand	215	1	46
β-strand	217-222	6	47
α-helix	223-229	7
α-helix	234-246	13
β-strand	251-256	6	47
β-strand	261-263	3	47
β-strand	271	1	46
α-helix	272-274	3
β-strand	275-285	11	45
β-strand	294-303	10	45
α-helix	307-309	3
α-helix	310-320	11

54 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	69	Homo sapiens
Mitochondrial ribosome-associated GTPase 1	C	protein	333	Homo sapiens	Q9BT17 (AlphaFold model)
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
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

49 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>7O9M_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

>7O9M_2 MT-TRNAVAL (chains B)
CAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUGA
CCGCUCUGA

Sequence of entity 3 (C), FASTA

>7O9M_3 Mitochondrial ribosome-associated GTPase 1 (chains C)
MRLTPRALCSAAQAAWRENFPLCGRDVARWFPGHMAKGLKKMQSSLKLVDCIIEVHDARI
PLSGRNPLFQETLGLKPHLLVLNKMDLADLTEQQKIMQHLEGEGLKNVIFTNCVKDENVK
QIIPMVTELIGRSHRYHRKENLEYCIMVIGVPNVGKSSLINSLRRQHLRKGKATRVGGEP
GITRAVMSKIQVSERPLMFLLDTPGVLAPRIESVETGLKLALCGTVLDHLVGEETMADYL
LYTLNKHQRFGYVQHYGLGSACDNVERVLKSVAVKLGKTQKVKVLTGTGNVNIIQPNYPA
AARDFLQTFRRGLLGSVMLDLDVLRGHPPAETL

Sequence of entity 4 (D), FASTA

>7O9M_4 39S ribosomal protein L2, mitochondrial (chains D)
MALCALTRALRSLNLAPPTVAAPAPSLFPAAQMMNNGLLQQPSALMLLPCRPVLTSVALN
ANFVSWKSRTKYTITPVKMRKSGGRDHTGRIRVHGIGGGHKQRYRMIDFLRFRPEETKSG
PFEEKVIQVRYDPCRSADIALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGD
AHPLGALPVGTLINNVESEPGRGAQYIRAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETC
VATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSGRWHRKGGWAGRKIRPLPPMKSYVKLPS
ASAQS

Sequence of entity 5 (E), FASTA

>7O9M_5 39S ribosomal protein L3, mitochondrial (chains E)
MPGWRLLTQVGAQVLGRLGDGLGAALGPGNRTHIWLFVRGLHGKSGTWWDEHLSEENVPF
IKQLVSDEDKAQLASKLCPLKDEPWPIHPWEPGSFRVGLIALKLGMMPLWTKDGQKHVVT
LLQVQDCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEFYRELGLPPKQTVKIFN
ITDNAAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRP
GAVATGDIGRVWPGTKMPGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGHKNCLVKVK
DSKLPAYKDLGKNLPFPTYFPDGDEEELPEDLYDENVCQPGAPSITFA

Sequence of entity 6 (F), FASTA

>7O9M_6 39S ribosomal protein L4, mitochondrial (chains F)
MLQFVRAGARAWLRPTGSQGLSSLAEEAARATENPEQVASEGLPEPVLRKVELPVPTHRR
PVQAWVESLRGFEQERVGLADLHPDVFATAPRLDILHQVAMWQKNFKRISYAKTKTRAEV
RGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRALGLKVALTV
KLAQDDLHIMDSLELPTGDPQYLTELAHYRRWGDSVLLVDLTHEEMPQSIVEATSRLKTF
NLIPAVGLNVHSMLKHQTLVLTLPTVAFLEDKLLWQDSRYRPLYPFSLPYSDFPRPLPHA
TQGPAATPYHC

Sequence of entity 7 (H), FASTA

>7O9M_7 39S ribosomal protein L9, mitochondrial (chains H)
MAAPVVTAPGRALLRAGAGRLLRGGVQELLRPRHEGNAPDLACNFSLSQNRGTVIVERWW
KVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGR
NRLLPQGLAVYASPENKKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNV
KWELNPEIVARHFFKNLGVVVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNF
EKPKTKRYKYWLAQQAAKAMAPTSPQI

Sequence of entity 8 (I), FASTA

>7O9M_8 39S ribosomal protein L10, mitochondrial (chains I)
MAAAVAGMLRGGLLPQAGRLPTLQTVRYGSKAVTRHRRVMHFQRQKLMAVTEYIPPKPAI
HPSCLPSPPSPPQEEIGLIRLLRREIAAVFQDNRMIAVCQNVALSAEDKLLMRHQLRKHK
ILMKVFPNQVLKPFLEDSKYQNLLPLFVGHNMLLVSEEPKVKEMVRILRTVPFLPLLGGC
IDDTILSRQGFINYSKLPSLPLVQGELVGGLTCLTAQTHSLLQHQPLQLTTLLDQYIREQ
REKDSVMSANGKPDPDTVPDS

Sequence of entity 9 (J), FASTA

>7O9M_9 39S ribosomal protein L11, mitochondrial (chains J)
MSKLGRAARGLRKPEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDI
KEGIPLPTKILVKPDRTFEIKIGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEI
ARIKAQDEAFALQDVPLSSVVRSIIGSARSLGIRVVKDLSSEELAAFQKERAIFLAAQKE
ADLAAQEEAAKK

Sequence of entity 10 (K), FASTA

>7O9M_10 39S ribosomal protein L13, mitochondrial (chains K)
MSSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIM
NTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRT
MMERLHLFPDEYIPEDILKNLVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDYRL

Sequence of entity 11 (L), FASTA

>7O9M_11 39S ribosomal protein L14, mitochondrial (chains L)
MAFFTGLWGPFTCVSRVLSHHCFSTTGSLSAIQKMTRVRVVDNSALGNSPYHRAPRCIHV
YKKNGVGKVGDQILLAIKGQKKKALIVGHCMPGPRMTPRFDSNNVVLIEDNGNPVGTRIK
TPIPTSLRKREGEYSKVLAIAQNFV

Sequence of entity 12 (M), FASTA

>7O9M_12 39S ribosomal protein L15, mitochondrial (chains M)
MAGPLQGGGARALDLLRGLPRVSLANLKPNPGSKKPERRPRGRRRGRKCGRGHKGERQRG
TRPRLGFEGGQTPFYIRIPKYGFNEGHSFRRQYKPLSLNRLQYLIDLGRVDPSQPIDLTQ
LVNGRGVTIQPLKRDYGVQLVEEGADTFTAKVNIEVQLASELAIAAIEKNGGVVTTAFYD
PRSLDIVCKPVPFFLRGQPIPKRMLPPEELVPYYTDAKNRGYLADPAKFPEARLELARKY
GYILPDITKDELFKMLCTRKDPRQIFFGLAPGWVVNMADKKILKPTDENLLKYYTS

Ligands and cofactors

ID	Name	Formula	Copies
PNS	4'-phosphopantetheine	C11 H23 N2 O7 P S	1
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
ZN	Zinc ion	Zn	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	104

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 Q9BT17 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QSJ 3.0 Å, Human mitoribosomal large subunit assembly intermediate 2 with GTPBP7
8PK0 3.03 Å, human mitoribosomal large subunit assembly intermediate 1 with GTPBP10-GTPBP7
7O9K 3.1 Å, Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4,…
7PD3 3.4 Å, Structure of the human mitoribosomal large subunit in complex with NSUN4.MTERF4.GTPBP7…

Browse structure collections

About this viewer

MolViewer shows 7O9M directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.