7L08: Human 55S mitoribosome-RRFmt complex

Name: PDB 7L08: Cryo-EM structure of the human 55S mitoribosome-RRFmt complex.
Published: 2021-05-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of the human 55S mitoribosome-RRFmt complex. Determined by electron microscopy at 3.49 Å resolution. Released 12 May 2021.

Method: Electron microscopy
Resolution: 3.49 Å
Organism: Homo sapiens
Chains: 87
Atoms: 168,922
Mol. weight: 2950.3 kDa
Ligands: MG, ZN, GDP
Released: 12 May 2021

Explore 7L08 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7L08 contains 695 α-helices and 558 β-strands across 84 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	167
β-strand	117-118	2	167
α-helix	124-144	21
β-strand	156-159	4	168
α-helix	164-166	3
β-strand	173-176	4	168
α-helix	180-182	3

Chain 1: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	170
β-strand	29-35	7	170
β-strand	42-47	6	170
β-strand	52-59	8	170

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	57-63	7
α-helix	66-70	5
α-helix	73-85	13

Chain 3: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	108-113	6
β-strand	115-116	2	174
β-strand	122-125	4	174
α-helix	126	1
α-helix	138-144	7
β-strand	147-149	3	174
α-helix	152-160	9
α-helix	164-167	4
β-strand	172	1	92

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	181
β-strand	80-84	5	181
β-strand	87-91	5	181
α-helix	96-98	3
β-strand	100-102	3	181

Chain 5: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	56
α-helix	36-38	3
α-helix	40-47	8
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	142
α-helix	115-123	9
β-strand	125-128	4	143
α-helix	133-139	7
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	143
β-strand	210-214	5	142
β-strand	217-221	5	142
β-strand	227-231	5	143
α-helix	234-237	4
α-helix	241-246	6
α-helix	247-249	3
α-helix	250-253	4
β-strand	258	1	60
β-strand	265-269	5	142
β-strand	286-292	7	143
α-helix	303-304	2
α-helix	305-327	23
β-strand	334-346	13	143
β-strand	350-360	11	143
β-strand	371-380	10	143
β-strand	382-386	5	144
β-strand	391-392	2	145
β-strand	395-396	2	145
β-strand	401-405	5	144
α-helix	407-418	12

Chain 6: 15 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	140
α-helix	55-64	10
α-helix	74-77	4
β-strand	89	1	150
α-helix	92-95	4
α-helix	99-113	15
α-helix	118-124	7
α-helix	132-142	11
α-helix	144-154	11
α-helix	157-161	5
β-strand	166	1	150
β-strand	174-177	4	151
β-strand	185-187	3	151
β-strand	191-192	2	152
β-strand	203-205	3	151
β-strand	213-220	8	152
β-strand	231	1	153
β-strand	232-238	7	152
β-strand	240-241	2	152
β-strand	249-252	4	152
β-strand	266-275	10	152
β-strand	298	1	153
α-helix	300-306	7
β-strand	311-321	11	152
α-helix	326-329	4
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-345	6	141
α-helix	346-350	5
α-helix	352-355	4
β-strand	362	1	174
α-helix	363-367	5

Chain 7: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	37-58	22
β-strand	64-65	2	156
β-strand	68-69	2	157
β-strand	78-80	3	157
β-strand	81-82	2	156
α-helix	88-92	5
α-helix	97-102	6
β-strand	105-108	4	158
β-strand	111-114	4	158
β-strand	124-125	2	157
β-strand	127-128	2	158
α-helix	136-154	19
β-strand	165-168	4	159
β-strand	179-184	6	159
α-helix	187-189	3
α-helix	196-211	16
β-strand	215	1	160
β-strand	217-222	6	161
α-helix	223-230	8
α-helix	234-246	13
β-strand	251-257	7	161
β-strand	260-263	4	161
β-strand	271	1	160
α-helix	272-274	3
β-strand	275-285	11	159
β-strand	294-303	10	159
α-helix	310-319	10
α-helix	323-324	2

76 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
12S rRNA	AA	RNA	954	Homo sapiens
28S ribosomal protein S2, mitochondrial	AB	protein	296	Homo sapiens	Q9Y399 (AlphaFold model)
28S ribosomal protein S24, mitochondrial	AC	protein	167	Homo sapiens	Q96EL2 (AlphaFold model)
28S ribosomal protein S6, mitochondrial	AE	protein	125	Homo sapiens	P82932 (AlphaFold model)
28S ribosomal protein S11, mitochondrial	AI	protein	194	Homo sapiens	P82912 (AlphaFold model)
28S ribosomal protein S12, mitochondrial	AJ	protein	138	Homo sapiens	O15235
28S ribosomal protein S14, mitochondrial	AK	protein	128	Homo sapiens	O60783
28S ribosomal protein S16, mitochondrial	AM	protein	137	Homo sapiens	Q9Y3D3
28S ribosomal protein S17, mitochondrial	AN	protein	130	Homo sapiens	Q9Y2R5
28S ribosomal protein S18b, mitochondrial	AO	protein	258	Homo sapiens	Q9Y676
28S ribosomal protein S18c, mitochondrial	AP	protein	142	Homo sapiens	Q9Y3D5
28S ribosomal protein S21, mitochondrial	AQ	protein	87	Homo sapiens	P82921

74 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>7L08_1 12S rRNA (chains AA)
AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCC
CGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGAACAAGCAUCAAGCACGC
AGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAA
CCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCG
UGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUU
UUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUG
ACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACACAAUAGCUAAGACCCA
AACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAA
CUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAU
AUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUG
CUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAG
UACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACA
UUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUA
GCAGUAAACUAAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCC
CGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAU
AGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAAC

Sequence of entity 2 (AB), FASTA

>7L08_2 28S ribosomal protein S2, mitochondrial (chains AB)
MATSSAALPRILGAGARAPSRWLGFLGKATPRPARPSRRTLGSATALMIRESEDSTDFND
KILNEPLKHSDFFNVKELFSVRSLFDARVHLGHKAGCRHRFMEPYIFGSRLDHDIIDLEQ
TATHLQLALNFTAHMAYRKGIILFISRNRQFSYLIENMARDCGEYAHTRYFRGGMLTNAR
LLFGPTVRLPDLIIFLHTLNNIFEPHVAVRDAAKMNIPTVGIVDTNCNPCLITYPVPGND
DSPLAVHLYCRLFQTAITRAKEKRQQVEALYRLQGQKEPGDQGPAHPPGADMSHSL

Sequence of entity 3 (AC), FASTA

>7L08_3 28S ribosomal protein S24, mitochondrial (chains AC)
MAASVCSGLLGPRVLSWSRELPCAWRALHTSPVCAKNRAARVRVSKGDKPVTYEEAHAPH
YIAHRKGWLSLHTGNLDGEDHAAERTVEDVFLRKFMWGTFPGCLADQLVLKRRGNQLEIC
AVVLRQLSPHKYYFLVGYSETLLSYFYKCPVRLHLQTVPSKVVYKYL

Sequence of entity 4 (AE), FASTA

>7L08_4 28S ribosomal protein S6, mitochondrial (chains AE)
MPRYELALILKAMQRPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNR
GGYFLVDFYAPTAAVESMVEHLSRDIDVIRGNIVKHPLTQELKECEGIVPVPLAEKLYST
KKRKK

Sequence of entity 5 (AI), FASTA

>7L08_5 28S ribosomal protein S11, mitochondrial (chains AI)
MQAVRNAGSRFLRSWTWPQTAGRVVARTPAGTICTGARQLQDAAAKQKVEQNAAPSHTKF
SIYPPIPGEESSLRWAGKKFEEIPIAHIKASHNNTQIQVVSASNEPLAFASCGTEGFRNA
KKGTGIAAQTAGIAAAARAKQKGVIHIRVVVKGLGPGRLSAMHGLIMGGLEVISITDNTP
IPHNGCRPRKARKL

Sequence of entity 6 (AJ), FASTA

>7L08_6 28S ribosomal protein S12, mitochondrial (chains AJ)
MSWSGLLHGLNTSLTCGPALVPRLWATCSMATLNQMHRLGPPKRPPRKLGPTEGRPQLKG
VVLCTFTRKPKKPNSANRKCCRVRLSTGREAVCFIPGEGHTLQEHQIVLVEGGRTQDLPG
VKLTVVRGKYDCGHVQKK

Sequence of entity 7 (AK), FASTA

>7L08_7 28S ribosomal protein S14, mitochondrial (chains AK)
MAAFMLGSLLRTFKQMVPSSASGQVRSHYVDWRMWRDVKRRKMAYEYADERLRINSLRKN
TILPKILQDVADEEIAALPRDSCPVRIRNRCVMTSRPRGVKRRWRLSRIVFRHLADHGQL
SGIQRATW

Sequence of entity 8 (AM), FASTA

>7L08_8 28S ribosomal protein S16, mitochondrial (chains AM)
MVHLTTLLCKAYRGGHLTIRLALGGCTNRPFYRIVAAHNKCPRDGRFVEQLGSYDPLPNS
HGEKLVALNLDRIRHWIGCGAHLSKPMEKLLGLAGFFPLHPMMITNAERLRRKRAREVLL
ASQKTDAEATDTEATET

Sequence of entity 9 (AN), FASTA

>7L08_9 28S ribosomal protein S17, mitochondrial (chains AN)
MSVVRSSVHARWIVGKVIGTKMQKTAKVRVTRLVLDPYLLKYFNKRKTYFAHDALQQCTV
GDIVLLRALPVPRAKHVKHELAEIVFKVGKVIDPVTGKPCAGTTYLESPLSSETTQLSKN
LEELNISSAQ

Sequence of entity 10 (AO), FASTA

>7L08_10 28S ribosomal protein S18b, mitochondrial (chains AO)
MAASVLNTVLRRLPMLSLFRGSHRVQVPLQTLCTKAPSEEDSLSSVPISPYKDEPWKYLE
SEEYQERYGSRPVWADYRRNHKGGVPPQRTRKTCIRRNKVVGNPCPICRDHKLHVDFRNV
KLLEQFVCAHTGIIFYAPYTGVCVKQHKRLTQAIQKARDHGLLIYHIPQVEPRDLDFSTS
HGAVSATPPAPTLVSGDPWYPWYNWKQPPERELSRLRRLYQGHLQEESGPPPESMPKMPP
RTPAEASSTGQTGPQSAL

Sequence of entity 11 (AP), FASTA

>7L08_11 28S ribosomal protein S18c, mitochondrial (chains AP)
MAAVVAVCGGLGRKKLTHLVTAAVSLTHPGTHTVLWRRGCSQQVSSNEDLPISMENPYKE
PLKKCILCGKHVDYKNVQLLSQFVSPFTGCIYGRHITGLCGKKQKEITKAIKRAQIMGFM
PVTYKDPAYLKDPKVCNIRYRE

Sequence of entity 12 (AQ), FASTA

>7L08_12 28S ribosomal protein S21, mitochondrial (chains AQ)
MAKHLKFIARTVMVQEGNVESAYRTLNRILTMDGLIEDIKHRRYYEKPCRRRQRESYERC
RRIYNMEMARKINFLMRKNRADPWQGC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	127
ZN	Zinc ion	Zn	7
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	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 Q9Y399 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7QI4 2.21 Å, Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA)
8CSS 2.36 Å, Human mitochondrial small subunit assembly intermediate (State D)
7P2E 2.4 Å, Human mitochondrial ribosome small subunit in complex with IF3, GMPPMP and streptomycin
8RRI 2.4 Å, Human mitochondrial ribosome in complex with antibiotic tigecycline
9OLF 2.46 Å, Membrane-associated human mitoribosome in complex with TACO1
9OJM 2.5 Å, Human mitochondrial 28S PIC with tRNA and mtIF2
8CSQ 2.54 Å, Human mitochondrial small subunit assembly intermediate (State B)
8CSR 2.54 Å, Human mitochondrial small subunit assembly intermediate (State C)
6ZM6 2.59 Å, Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA
7QI5 2.63 Å, Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A…
9RU6 2.64 Å, Human mitoribosome bound to TACO1 (Translational activator of COX1), mRNA, A/A-, P/P-…
8CSP 2.66 Å, Human mitochondrial small subunit assembly intermediate (State A)

Browse structure collections

About this viewer

MolViewer shows 7L08 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.