7L20: Human 39S mitoribosomal subunit

Name: PDB 7L20: Cryo-EM structure of the human 39S mitoribosomal subunit in complex with RRFmt and EF-G2mt.
Published: 2021-05-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of the human 39S mitoribosomal subunit in complex with RRFmt and EF-G2mt. Determined by electron microscopy at 3.15 Å resolution. Released 12 May 2021.

Method: Electron microscopy
Resolution: 3.15 Å
Organism: Homo sapiens
Chains: 58
Atoms: 110,234
Mol. weight: 1906.44 kDa
Ligands: MG, ZN, GCP
Released: 12 May 2021

Explore 7L20 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7L20 contains 439 α-helices and 434 β-strands across 56 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	87-93	7
α-helix	101-103	3
β-strand	107-108	2	107
β-strand	117-118	2	107
α-helix	124-144	21
β-strand	156-159	4	108
α-helix	164-166	3
β-strand	173-176	4	108
α-helix	180-182	3

Chain 1: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	110
β-strand	29-35	7	110
α-helix	39-41	3
β-strand	42-47	6	110
β-strand	52-59	8	110

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: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	108-113	6
β-strand	115-116	2	113
β-strand	122-125	4	113
α-helix	133-135	3
α-helix	138-144	7
β-strand	147-149	3	113
α-helix	152-161	10
β-strand	172	1	47

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	68-69	2	118
β-strand	80-84	5	118
β-strand	87-91	5	118
α-helix	96-98	3
β-strand	100-102	3	118

Chain 5: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	3
α-helix	40-47	8
α-helix	48-50	3
α-helix	60-62	3
α-helix	74-76	3
α-helix	84-86	3
α-helix	89-91	3
α-helix	92-94	3
β-strand	98-106	9	83
α-helix	115-123	9
β-strand	125-128	4	84
α-helix	133-140	8
α-helix	142-144	3
α-helix	149-158	10
α-helix	159-163	5
α-helix	172-174	3
α-helix	176-188	13
α-helix	189-191	3
α-helix	197-199	3
β-strand	200-204	5	84
β-strand	210-214	5	83
β-strand	217-221	5	83
β-strand	227-231	5	84
α-helix	234-237	4
α-helix	241-246	6
α-helix	247-249	3
β-strand	258	1	7
β-strand	265-269	5	83
β-strand	287-292	6	84
α-helix	299-301	3
α-helix	303-304	2
α-helix	305-327	23
β-strand	334-346	13	84
β-strand	350-360	11	84
β-strand	371-380	10	84
β-strand	382-386	5	85
β-strand	390-392	3	86
β-strand	395-398	4	86
β-strand	401-405	5	85
α-helix	407-417	11

Chain 6: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	49	1
β-strand	50	1	81
α-helix	55-64	10
α-helix	74-77	4
β-strand	89	1	92
α-helix	92-96	5
α-helix	99-115	17
α-helix	118-124	7
α-helix	132-141	10
α-helix	144-154	11
α-helix	157-161	5
β-strand	166	1	92
β-strand	174-177	4	93
β-strand	185-187	3	93
β-strand	189-192	4	94
β-strand	203-205	3	93
β-strand	213-220	8	94
β-strand	231-241	11	94
β-strand	249-252	4	94
β-strand	266-275	10	94
β-strand	297-298	2	94
α-helix	300-306	7
β-strand	311-321	11	94
α-helix	327-329	3
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-345	6	82
α-helix	347-350	4
α-helix	353-355	3
β-strand	362	1	113
α-helix	363-368	6

Chain 7: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	37-58	22
β-strand	64-65	2	97
β-strand	68-69	2	98
β-strand	78-80	3	98
β-strand	81-82	2	97
α-helix	89-95	7
α-helix	98-101	4
β-strand	105-108	4	99
β-strand	111-114	4	99
β-strand	124-125	2	98
β-strand	127-128	2	99
α-helix	136-154	19
β-strand	165-168	4	100
β-strand	179-184	6	100
α-helix	187-189	3
α-helix	196-211	16
β-strand	215	1	101
β-strand	217-222	6	102
α-helix	223-230	8
α-helix	234-245	12
β-strand	251-257	7	102
β-strand	260-263	4	102
β-strand	271	1	101
β-strand	275-285	11	100
β-strand	294-303	10	100
α-helix	310-319	10
α-helix	323-324	2

48 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 mitochondrial	A	RNA	1559	Homo sapiens
tRNAval	B	RNA	73	Homo sapiens
39S ribosomal protein L2, mitochondrial	D	protein	305	Homo sapiens	Q5T653 (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 L13, mitochondrial	K	protein	178	Homo sapiens	Q9BYD1 (AlphaFold model)
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 L17, mitochondrial	O	protein	175	Homo sapiens	Q9NRX2
39S ribosomal protein L20, mitochondrial	R	protein	149	Homo sapiens	Q9BYC9
39S ribosomal protein L21, mitochondrial	S	protein	205	Homo sapiens	Q7Z2W9
39S ribosomal protein L22, mitochondrial	T	protein	212	Homo sapiens	E7ESL0

44 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>7L20_1 16S rRNA mitochondrial (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

>7L20_2 tRNAval (chains B)
CCAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUG
ACCGCUCUGACCA

Sequence of entity 3 (D), FASTA

>7L20_3 39S ribosomal protein L2, mitochondrial (chains D)
MALCALTRALRSLNLAPPTVAAPAPSLFPAAQMMNNGLLQQPSALMLLPCRPVLTSVALN
ANFVSWKSRTKYTITPVKMRKSGGRDHTGRIRVHGIGGGHKQRYRMIDFLRFRPEETKSG
PFEEKVIQVRYDPCRSADIALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGD
AHPLGALPVGTLINNVESEPGRGAQYIRAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETC
VATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSGRWHRKGGWAGRKIRPLPPMKSYVKLPS
ASAQS

Sequence of entity 4 (F), FASTA

>7L20_4 39S ribosomal protein L4, mitochondrial (chains F)
MLQFVRAGARAWLRPTGSQGLSSLAEEAARATENPEQVASEGLPEPVLRKVELPVPTHRR
PVQAWVESLRGFEQERVGLADLHPDVFATAPRLDILHQVAMWQKNFKRISYAKTKTRAEV
RGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRALGLKVALTV
KLAQDDLHIMDSLELPTGDPQYLTELAHYRRWGDSVLLVDLTHEEMPQSIVEATSRLKTF
NLIPAVGLNVHSMLKHQTLVLTLPTVAFLEDKLLWQDSRYRPLYPFSLPYSDFPRPLPHA
TQGPAATPYHC

Sequence of entity 5 (H), FASTA

>7L20_5 39S ribosomal protein L9, mitochondrial (chains H)
MAAPVVTAPGRALLRAGAGRLLRGGVQELLRPRHEGNAPDLACNFSLSQNRGTVIVERWW
KVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGR
NRLLPQGLAVYASPENKKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNV
KWELNPEIVARHFFKNLGVVVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNF
EKPKTKRYKYWLAQQAAKAMAPTSPQI

Sequence of entity 6 (K), FASTA

>7L20_6 39S ribosomal protein L13, mitochondrial (chains K)
MSSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIM
NTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRT
MMERLHLFPDEYIPEDILKNLVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDYRL

Sequence of entity 7 (L), FASTA

>7L20_7 39S ribosomal protein L14, mitochondrial (chains L)
MAFFTGLWGPFTCVSRVLSHHCFSTTGSLSAIQKMTRVRVVDNSALGNSPYHRAPRCIHV
YKKNGVGKVGDQILLAIKGQKKKALIVGHCMPGPRMTPRFDSNNVVLIEDNGNPVGTRIK
TPIPTSLRKREGEYSKVLAIAQNFV

Sequence of entity 8 (M), FASTA

>7L20_8 39S ribosomal protein L15, mitochondrial (chains M)
MAGPLQGGGARALDLLRGLPRVSLANLKPNPGSKKPERRPRGRRRGRKCGRGHKGERQRG
TRPRLGFEGGQTPFYIRIPKYGFNEGHSFRRQYKPLSLNRLQYLIDLGRVDPSQPIDLTQ
LVNGRGVTIQPLKRDYGVQLVEEGADTFTAKVNIEVQLASELAIAAIEKNGGVVTTAFYD
PRSLDIVCKPVPFFLRGQPIPKRMLPPEELVPYYTDAKNRGYLADPAKFPEARLELARKY
GYILPDITKDELFKMLCTRKDPRQIFFGLAPGWVVNMADKKILKPTDENLLKYYTS

Sequence of entity 9 (O), FASTA

>7L20_9 39S ribosomal protein L17, mitochondrial (chains O)
MRLSVAAAISHGRVFRRMGLGPESRIHLLRNLLTGLVRHERIEAPWARVDEMRGYAEKLI
DYGKLGDTNERAMRMADFWLTEKDLIPKLFQVLAPRYKDQTGGYTRMLQIPNRSLDRAKM
AVIEYKGNCLPPLPLPRRDSHLTLLNQLLQGLRQDLRQSQEASNHSSHTAQTPGI

Sequence of entity 10 (R), FASTA

>7L20_10 39S ribosomal protein L20, mitochondrial (chains R)
MVFLTAQLWLRNRVTDRYFRIQEVLKHARHFRGRKNRCYRLAVRTVIRAFVKCTKARYLK
KKNMRTLWINRITAASQEHGLKYPALIGNLVKCQVELNRKVLADLAIYEPKTFKSLAALA
SRRRHEGFAAALGDGKEPEGIFSRVVQYH

Sequence of entity 11 (S), FASTA

>7L20_11 39S ribosomal protein L21, mitochondrial (chains S)
MAASSLTVTLGRLASACSHSILRPSGPGAASLWSASRRFNSQSTSYLPGYVPKTSLSSPP
WPEVVLPDPVEETRHHAEVVKKVNEMIVTGQYGRLFAVVHFASRQWKVTSEDLILIGNEL
DLACGERIRLEKVLLVGADNFTLLGKPLLGKDLVRVEATVIEKTESWPRIIMRFRKRKNF
KKKRIVTTPQTVLRINSIEIAPCLL

Sequence of entity 12 (T), FASTA

>7L20_12 39S ribosomal protein L22, mitochondrial (chains T)
MAAAVLGQLGALWIHNLRSRGKLALGLLSFHSVLPQSYIHTSASLDISRKWEKKNKIVYP
PQLPGEPRRPAEIYHCRRQIKYSKDKMWYLAKLIRGMSIDQALAQLEFNDKKGAKIIKEV
LLEAQDMAVRDHNVEFRSNLYIAESTSGRGQCLKRIRYHGRGRFGIMEKVYCHYFVKLVE
GPPPPPEPPKTAVAHAKEYIQQLRSRTIVHTL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	102
ZN	Zinc ion	Zn	3
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1

Primary citation

Distinct mechanisms of the human mitoribosome recycling and antibiotic resistance. Koripella, R.K., Deep, A., Agrawal, E.K. et al. Nat Commun (2021) 12:3607-3607. DOI 10.1038/s41467-021-23726-4 · 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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