7OIC: Large ribosomal subunit protein uL2m

Name: PDB 7OIC: Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 4
Published: 2021-09-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 4. Determined by electron microscopy at 3.1 Å resolution. Released 15 Sept 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 58
Atoms: 100,859
Mol. weight: 1882.69 kDa
Ligands: MG, ZN, PNS, SAM
Released: 15 Sept 2021

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

Secondary structure: helices and β-sheets

7OIC contains 398 α-helices and 365 β-strands across 55 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: 6 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	107-108	2	103
β-strand	117-118	2	103
α-helix	124-145	22
β-strand	156-159	4	104
α-helix	164-166	3
β-strand	173-176	4	104
α-helix	180-182	3

Chain 1: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	16-22	7	108
β-strand	29-34	6	108
β-strand	42-47	6	108
β-strand	52-59	8	108

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: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	108-113	6
β-strand	115-116	2	2
β-strand	122-124	3	2
α-helix	138-145	8
β-strand	148-149	2	2
α-helix	152-161	10
α-helix	164-166	3
β-strand	172	1	52

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	68	1	8
β-strand	80-84	5	8
β-strand	87-91	5	8
α-helix	96-98	3
β-strand	100-101	2	8

Chain 5: 16 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	40-47	8
α-helix	56-58	3
α-helix	85-87	3
α-helix	90-92	3
α-helix	103	1
β-strand	104-106	3	12
β-strand	107	1	13
α-helix	117-124	8
β-strand	126-129	4	14
α-helix	134-140	7
α-helix	151-162	12
α-helix	173-188	16
α-helix	191-193	3
α-helix	196-200	5
β-strand	201-204	4	14
β-strand	209-214	6	13
β-strand	219-223	5	13
β-strand	228-232	5	14
α-helix	235-238	4
α-helix	242-250	9
β-strand	259	1	6
β-strand	266-268	3	12
β-strand	276-277	2	13
β-strand	279	1	15
β-strand	287-292	6	14
α-helix	304-305	2
α-helix	306-328	23
β-strand	335-345	11	14
β-strand	354-361	8	14
β-strand	372-377	6	14
β-strand	385-387	3	16
β-strand	391	1	17
β-strand	399	1	17
β-strand	402-404	3	16
α-helix	409-419	11

Chain 6: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	55-66	12
α-helix	74-77	4
α-helix	100-117	18
α-helix	132-142	11
α-helix	144-155	12
α-helix	157-160	4
β-strand	174-178	5	25
β-strand	184-187	4	25
β-strand	191-193	3	26
β-strand	203-205	3	25
β-strand	214-220	7	26
β-strand	231-240	10	26
β-strand	250	1	26
α-helix	255-257	3
α-helix	259-260	2
β-strand	261	1	27
β-strand	266-275	10	26
α-helix	293-296	4
β-strand	297-298	2	26
α-helix	300-305	6
β-strand	311-321	11	26
α-helix	325-329	5
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-342	3	27
β-strand	345	1	93
α-helix	347-350	4
α-helix	352-355	4
α-helix	364-368	5

Chain 7: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	37-58	22
β-strand	64-69	6	30
β-strand	77-82	6	30
α-helix	88-95	8
α-helix	97-102	6
β-strand	103-108	6	30
β-strand	111-113	3	30
β-strand	124-129	6	30
α-helix	136-157	22
β-strand	166-168	3	31
β-strand	179-183	5	31
α-helix	196-212	17
β-strand	215	1	32
β-strand	216-222	7	33
α-helix	223-229	7
α-helix	234-246	13
β-strand	251-257	7	33
β-strand	260-263	4	33
β-strand	271	1	32
α-helix	272-274	3
β-strand	275-284	10	31
β-strand	295-303	9	31
α-helix	310-321	12

47 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
mitochondrial Val tRNA	B	RNA	69	Homo sapiens
Large ribosomal subunit protein uL2m	D	protein	305	Homo sapiens	Q5T653 (AlphaFold model)
Large ribosomal subunit protein uL3m	E	protein	348	Homo sapiens	P09001 (AlphaFold model)
Large ribosomal subunit protein uL4m	F	protein	311	Homo sapiens	Q9BYD3 (AlphaFold model)
Large ribosomal subunit protein bL9m	H	protein	267	Homo sapiens	Q9BYD2 (AlphaFold model)
Large ribosomal subunit protein uL10m	I	protein	261	Homo sapiens	Q7Z7H8
Large ribosomal subunit protein uL11m	J	protein	192	Homo sapiens	Q9Y3B7
Large ribosomal subunit protein uL13m	K	protein	178	Homo sapiens	Q9BYD1
Large ribosomal subunit protein uL14m	L	protein	145	Homo sapiens	Q6P1L8
Large ribosomal subunit protein uL15m	M	protein	296	Homo sapiens	Q9P015
Large ribosomal subunit protein uL16m	N	protein	251	Homo sapiens	Q9NX20

46 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>7OIC_1 16S rRNA (chains A)
GCUAAACCUAGCCCCAAACCCACUCCACCUUACUACCAGACAACCUUAGCCAAACCAUUU
ACCAAAAUAAAGUAUAGGCGAUAGAAAUUGAAACCUGGCGCAAUAGAUAUAGUACCGCAA
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

>7OIC_2 mitochondrial Val tRNA (chains B)
CAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUGA
CCGCUCUGA

Sequence of entity 3 (D), FASTA

>7OIC_3 Large ribosomal subunit protein uL2m (chains D)
MALCALTRALRSLNLAPPTVAAPAPSLFPAAQMMNNGLLQQPSALMLLPCRPVLTSVALN
ANFVSWKSRTKYTITPVKMRKSGGRDHTGRIRVHGIGGGHKQRYRMIDFLRFRPEETKSG
PFEEKVIQVRYDPCRSADIALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGD
AHPLGALPVGTLINNVESEPGRGAQYIRAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETC
VATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSGRWHRKGGWAGRKIRPLPPMKSYVKLPS
ASAQS

Sequence of entity 4 (E), FASTA

>7OIC_4 Large ribosomal subunit protein uL3m (chains E)
MPGWRLLTQVGAQVLGRLGDGLGAALGPGNRTHIWLFVRGLHGKSGTWWDEHLSEENVPF
IKQLVSDEDKAQLASKLCPLKDEPWPIHPWEPGSFRVGLIALKLGMMPLWTKDGQKHVVT
LLQVQDCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEFYRELGLPPKQTVKIFN
ITDNAAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRP
GAVATGDIGRVWPGTKMPGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGHKNCLVKVK
DSKLPAYKDLGKNLPFPTYFPDGDEEELPEDLYDENVCQPGAPSITFA

Sequence of entity 5 (F), FASTA

>7OIC_5 Large ribosomal subunit protein uL4m (chains F)
MLQFVRAGARAWLRPTGSQGLSSLAEEAARATENPEQVASEGLPEPVLRKVELPVPTHRR
PVQAWVESLRGFEQERVGLADLHPDVFATAPRLDILHQVAMWQKNFKRISYAKTKTRAEV
RGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRALGLKVALTV
KLAQDDLHIMDSLELPTGDPQYLTELAHYRRWGDSVLLVDLTHEEMPQSIVEATSRLKTF
NLIPAVGLNVHSMLKHQTLVLTLPTVAFLEDKLLWQDSRYRPLYPFSLPYSDFPRPLPHA
TQGPAATPYHC

Sequence of entity 6 (H), FASTA

>7OIC_6 Large ribosomal subunit protein bL9m (chains H)
MAAPVVTAPGRALLRAGAGRLLRGGVQELLRPRHEGNAPDLACNFSLSQNRGTVIVERWW
KVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGR
NRLLPQGLAVYASPENKKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNV
KWELNPEIVARHFFKNLGVVVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNF
EKPKTKRYKYWLAQQAAKAMAPTSPQI

Sequence of entity 7 (I), FASTA

>7OIC_7 Large ribosomal subunit protein uL10m (chains I)
MAAAVAGMLRGGLLPQAGRLPTLQTVRYGSKAVTRHRRVMHFQRQKLMAVTEYIPPKPAI
HPSCLPSPPSPPQEEIGLIRLLRREIAAVFQDNRMIAVCQNVALSAEDKLLMRHQLRKHK
ILMKVFPNQVLKPFLEDSKYQNLLPLFVGHNMLLVSEEPKVKEMVRILRTVPFLPLLGGC
IDDTILSRQGFINYSKLPSLPLVQGELVGGLTCLTAQTHSLLQHQPLQLTTLLDQYIREQ
REKDSVMSANGKPDPDTVPDS

Sequence of entity 8 (J), FASTA

>7OIC_8 Large ribosomal subunit protein uL11m (chains J)
MSKLGRAARGLRKPEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDI
KEGIPLPTKILVKPDRTFEIKIGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEI
ARIKAQDEAFALQDVPLSSVVRSIIGSARSLGIRVVKDLSSEELAAFQKERAIFLAAQKE
ADLAAQEEAAKK

Sequence of entity 9 (K), FASTA

>7OIC_9 Large ribosomal subunit protein uL13m (chains K)
MSSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIM
NTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRT
MMERLHLFPDEYIPEDILKNLVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDYRL

Sequence of entity 10 (L), FASTA

>7OIC_10 Large ribosomal subunit protein uL14m (chains L)
MAFFTGLWGPFTCVSRVLSHHCFSTTGSLSAIQKMTRVRVVDNSALGNSPYHRAPRCIHV
YKKNGVGKVGDQILLAIKGQKKKALIVGHCMPGPRMTPRFDSNNVVLIEDNGNPVGTRIK
TPIPTSLRKREGEYSKVLAIAQNFV

Sequence of entity 11 (M), FASTA

>7OIC_11 Large ribosomal subunit protein uL15m (chains M)
MAGPLQGGGARALDLLRGLPRVSLANLKPNPGSKKPERRPRGRRRGRKCGRGHKGERQRG
TRPRLGFEGGQTPFYIRIPKYGFNEGHSFRRQYKPLSLNRLQYLIDLGRVDPSQPIDLTQ
LVNGRGVTIQPLKRDYGVQLVEEGADTFTAKVNIEVQLASELAIAAIEKNGGVVTTAFYD
PRSLDIVCKPVPFFLRGQPIPKRMLPPEELVPYYTDAKNRGYLADPAKFPEARLELARKY
GYILPDITKDELFKMLCTRKDPRQIFFGLAPGWVVNMADKKILKPTDENLLKYYTS

Sequence of entity 12 (N), FASTA

>7OIC_12 Large ribosomal subunit protein uL16m (chains N)
MWRLLARASAPLLRVPLSDSWALLPASAGVKTLLPVPSFEDVSIPEKPKLRFIERAPLVP
KVRREPKNLSDIRGPSTEATEFTEGNFAILALGGGYLHWGHFEMMRLTINRSMDPKNMFA
IWRVPAPFKPITRKSVGHRMGGGKGAIDHYVTPVKAGRLVVEMGGRCEFEEVQGFLDQVA
HKLPFAAKAVSRGTLEKMRKDQEERERNNQNPWTFERIATANMLGIRKVLSPYDLTHKGK
YWGKFYMPKRV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	76
ZN	Zinc ion	Zn	3
PNS	4'-phosphopantetheine	C11 H23 N2 O7 P S	1
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1

Primary citation

A distinct assembly pathway of the human 39S late pre-mitoribosome. Cheng, J., Berninghausen, O., Beckmann, R. Nat Commun (2021) 12:4544-4544. DOI 10.1038/s41467-021-24818-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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