8K2A: Human 55S mitoribosome with Tigecycline

Name: PDB 8K2A: Cryo-EM structure of the human 55S mitoribosome with Tigecycline
Published: 2024-07-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of the human 55S mitoribosome with Tigecycline. Determined by electron microscopy at 2.9 Å resolution. Released 10 Jul 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 83
Atoms: 165,285
Mol. weight: 2889.2 kDa
Ligands: GDP, ZN, T1C, MG
Released: 10 Jul 2024

Explore 8K2A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K2A contains 686 α-helices and 538 β-strands across 80 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 L3: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
β-strand	13-19	7	125
α-helix	28-37	10
α-helix	40-43	4
β-strand	50-53	4	125
β-strand	63-68	6	125
β-strand	73-77	5	125
α-helix	83-96	14

Chain L4: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	65-70	6
β-strand	71-72	2	137
β-strand	84-85	2	137
α-helix	86-87	2
α-helix	104-105	2
α-helix	115-132	18

Chain L5: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	52-57	6	142
β-strand	63-68	6	142
β-strand	74-75	2	142

Chain L6: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	29-48	20
α-helix	64-79	16
α-helix	83-85	3
β-strand	86	1	112
α-helix	88-92	5
α-helix	93-98	6

Chain L7: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	45-48	4
α-helix	50-52	3
β-strand	77-81	5	151
β-strand	98-104	7	151
α-helix	113-122	10
α-helix	124-126	3
β-strand	127	1	151
β-strand	132-137	6	151
α-helix	143-162	20
α-helix	175-186	12
β-strand	191-192	2	35

Chain L8: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	26	1	32
α-helix	27-31	5
α-helix	49-51	3
α-helix	54-63	10
α-helix	72-74	3
α-helix	77-78	2
α-helix	79-92	14
α-helix	96-151	56

Chain La: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	46-48	3
β-strand	52-53	2	139
β-strand	60-61	2	140
β-strand	66-69	4	139
β-strand	76-77	2	140
β-strand	79	1	103
β-strand	81-84	4	139
β-strand	88-91	4	139
β-strand	95-103	9	140
α-helix	111-117	7
β-strand	121	1	141
β-strand	127-135	9	140
β-strand	141-147	7	37

Chain Lb: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	144
α-helix	9-15	7
α-helix	20-23	4
α-helix	26-32	7
α-helix	36-40	5
β-strand	50-53	4	145
β-strand	58-61	4	145
α-helix	66-68	3
β-strand	70	1	146
α-helix	73-77	5
β-strand	79	1	147
β-strand	85	1	146
β-strand	86-91	6	41
β-strand	100-105	6	41
β-strand	110-116	7	147
β-strand	121-127	7	147
α-helix	129-136	8
α-helix	141-147	7
α-helix	150-153	4
α-helix	156-170	15
α-helix	181-190	10
α-helix	192-194	3
α-helix	198-201	4
α-helix	208-218	11
α-helix	222-225	4
α-helix	226-243	18

72 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	L1	RNA	1559	Homo sapiens
Val tRNA	L2	RNA	69	Homo sapiens
Large ribosomal subunit protein uL2m	LB	protein	305	Homo sapiens	Q5T653 (AlphaFold model)
Large ribosomal subunit protein uL3m	LC	protein	348	Homo sapiens	P09001 (AlphaFold model)
Large ribosomal subunit protein uL4m	LD	protein	311	Homo sapiens	Q9BYD3 (AlphaFold model)
Large ribosomal subunit protein bL9m	LI	protein	267	Homo sapiens	Q9BYD2 (AlphaFold model)
Large ribosomal subunit protein uL10m	LJ	protein	261	Homo sapiens	Q7Z7H8
Large ribosomal subunit protein uL11m	LK	protein	192	Homo sapiens	Q9Y3B7
Large ribosomal subunit protein uL13m	LM	protein	178	Homo sapiens	Q9BYD1
Large ribosomal subunit protein uL14m	LN	protein	145	Homo sapiens	Q6P1L8
Large ribosomal subunit protein uL15m	LO	protein	296	Homo sapiens	Q9P015
Large ribosomal subunit protein uL16m	LP	protein	251	Homo sapiens	Q9NX20

71 more molecules are not listed.

Sequence of entity 1 (L1), FASTA

>8K2A_1 16S rRNA (chains L1)
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 (L2), FASTA

>8K2A_2 Val tRNA (chains L2)
CAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUGA
CCGCUCUGA

Sequence of entity 3 (LB), FASTA

>8K2A_3 Large ribosomal subunit protein uL2m (chains LB)
MALCALTRALRSLNLAPPTVAAPAPSLFPAAQMMNNGLLQQPSALMLLPCRPVLTSVALN
ANFVSWKSRTKYTITPVKMRKSGGRDHTGRIRVHGIGGGHKQRYRMIDFLRFRPEETKSG
PFEEKVIQVRYDPCRSADIALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGD
AHPLGALPVGTLINNVESEPGRGAQYIRAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETC
VATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSGRWHRKGGWAGRKIRPLPPMKSYVKLPS
ASAQS

Sequence of entity 4 (LC), FASTA

>8K2A_4 Large ribosomal subunit protein uL3m (chains LC)
MPGWRLLTQVGAQVLGRLGDGLGAALGPGNRTHIWLFVRGLHGKSGTWWDEHLSEENVPF
IKQLVSDEDKAQLASKLCPLKDEPWPIHPWEPGSFRVGLIALKLGMMPLWTKDGQKHVVT
LLQVQDCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEFYRELGLPPKQTVKIFN
ITDNAAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRP
GAVATGDIGRVWPGTKMPGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGHKNCLVKVK
DSKLPAYKDLGKNLPFPTYFPDGDEEELPEDLYDENVCQPGAPSITFA

Sequence of entity 5 (LD), FASTA

>8K2A_5 Large ribosomal subunit protein uL4m (chains LD)
MLQFVRAGARAWLRPTGSQGLSSLAEEAARATENPEQVASEGLPEPVLRKVELPVPTHRR
PVQAWVESLRGFEQERVGLADLHPDVFATAPRLDILHQVAMWQKNFKRISYAKTKTRAEV
RGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRALGLKVALTV
KLAQDDLHIMDSLELPTGDPQYLTELAHYRRWGDSVLLVDLTHEEMPQSIVEATSRLKTF
NLIPAVGLNVHSMLKHQTLVLTLPTVAFLEDKLLWQDSRYRPLYPFSLPYSDFPRPLPHA
TQGPAATPYHC

Sequence of entity 6 (LI), FASTA

>8K2A_6 Large ribosomal subunit protein bL9m (chains LI)
MAAPVVTAPGRALLRAGAGRLLRGGVQELLRPRHEGNAPDLACNFSLSQNRGTVIVERWW
KVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGR
NRLLPQGLAVYASPENKKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNV
KWELNPEIVARHFFKNLGVVVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNF
EKPKTKRYKYWLAQQAAKAMAPTSPQI

Sequence of entity 7 (LJ), FASTA

>8K2A_7 Large ribosomal subunit protein uL10m (chains LJ)
MAAAVAGMLRGGLLPQAGRLPTLQTVRYGSKAVTRHRRVMHFQRQKLMAVTEYIPPKPAI
HPSCLPSPPSPPQEEIGLIRLLRREIAAVFQDNRMIAVCQNVALSAEDKLLMRHQLRKHK
ILMKVFPNQVLKPFLEDSKYQNLLPLFVGHNMLLVSEEPKVKEMVRILRTVPFLPLLGGC
IDDTILSRQGFINYSKLPSLPLVQGELVGGLTCLTAQTHSLLQHQPLQLTTLLDQYIREQ
REKDSVMSANGKPDPDTVPDS

Sequence of entity 8 (LK), FASTA

>8K2A_8 Large ribosomal subunit protein uL11m (chains LK)
MSKLGRAARGLRKPEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDI
KEGIPLPTKILVKPDRTFEIKIGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEI
ARIKAQDEAFALQDVPLSSVVRSIIGSARSLGIRVVKDLSSEELAAFQKERAIFLAAQKE
ADLAAQEEAAKK

Sequence of entity 9 (LM), FASTA

>8K2A_9 Large ribosomal subunit protein uL13m (chains LM)
MSSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIM
NTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRT
MMERLHLFPDEYIPEDILKNLVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDYRL

Sequence of entity 10 (LN), FASTA

>8K2A_10 Large ribosomal subunit protein uL14m (chains LN)
MAFFTGLWGPFTCVSRVLSHHCFSTTGSLSAIQKMTRVRVVDNSALGNSPYHRAPRCIHV
YKKNGVGKVGDQILLAIKGQKKKALIVGHCMPGPRMTPRFDSNNVVLIEDNGNPVGTRIK
TPIPTSLRKREGEYSKVLAIAQNFV

Sequence of entity 11 (LO), FASTA

>8K2A_11 Large ribosomal subunit protein uL15m (chains LO)
MAGPLQGGGARALDLLRGLPRVSLANLKPNPGSKKPERRPRGRRRGRKCGRGHKGERQRG
TRPRLGFEGGQTPFYIRIPKYGFNEGHSFRRQYKPLSLNRLQYLIDLGRVDPSQPIDLTQ
LVNGRGVTIQPLKRDYGVQLVEEGADTFTAKVNIEVQLASELAIAAIEKNGGVVTTAFYD
PRSLDIVCKPVPFFLRGQPIPKRMLPPEELVPYYTDAKNRGYLADPAKFPEARLELARKY
GYILPDITKDELFKMLCTRKDPRQIFFGLAPGWVVNMADKKILKPTDENLLKYYTS

Sequence of entity 12 (LP), FASTA

>8K2A_12 Large ribosomal subunit protein uL16m (chains LP)
MWRLLARASAPLLRVPLSDSWALLPASAGVKTLLPVPSFEDVSIPEKPKLRFIERAPLVP
KVRREPKNLSDIRGPSTEATEFTEGNFAILALGGGYLHWGHFEMMRLTINRSMDPKNMFA
IWRVPAPFKPITRKSVGHRMGGGKGAIDHYVTPVKAGRLVVEMGGRCEFEEVQGFLDQVA
HKLPFAAKAVSRGTLEKMRKDQEERERNNQNPWTFERIATANMLGIRKVLSPYDLTHKGK
YWGKFYMPKRV

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
ZN	Zinc ion	Zn	7
T1C	Tigecycline	C29 H41 N5 O8	4
MG	Magnesium ion	Mg	145

Primary citation

Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline. Li, X., Wang, M., Denk, T. et al. Nat Commun (2024) 15:5481-5481. DOI 10.1038/s41467-024-49797-7 · 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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