6VLZ: Human mitochondrial ribosome-EF-G1 complex

Name: PDB 6VLZ: Structure of the human mitochondrial ribosome-EF-G1 complex (ClassI)
Published: 2020-08-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the human mitochondrial ribosome-EF-G1 complex (ClassI). Determined by electron microscopy at 2.97 Å resolution. Released 5 Aug 2020.

Method: Electron microscopy
Resolution: 2.97 Å
Organism: Homo sapiens
Chains: 90
Atoms: 174,849
Mol. weight: 3057.18 kDa
Ligands: MG, ZN, GDP, GCP
Released: 5 Aug 2020

Explore 6VLZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VLZ contains 639 α-helices and 619 β-strands across 85 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: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	87-94	8
α-helix	101-102	2
β-strand	107-108	2	196
β-strand	117-118	2	196
β-strand	121	1	196
α-helix	124-145	22
β-strand	156-159	4	197
β-strand	173-176	4	197
α-helix	180-182	3

Chain 1: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	200
β-strand	29-35	7	200
β-strand	44-47	4	201
β-strand	52-55	4	201
β-strand	56-58	3	200

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	207
β-strand	122-125	4	207
α-helix	138-144	7
β-strand	147-149	3	207
α-helix	152-160	9
α-helix	165-167	3
β-strand	172	1	118
α-helix	178-180	3

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	67-68	2	216
β-strand	80-84	5	216
β-strand	87-91	5	216
α-helix	96-98	3
β-strand	100-101	2	216

Chain 5: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	40-46	7
α-helix	75-77	3
α-helix	85-87	3
α-helix	90-92	3
α-helix	93-95	3
β-strand	99-107	9	174
α-helix	116-124	9
β-strand	126-129	4	175
α-helix	132-133	2
α-helix	134-140	7
α-helix	150-162	13
α-helix	173-189	17
α-helix	190-192	3
α-helix	198-200	3
β-strand	201-205	5	175
β-strand	211-214	4	174
β-strand	219-222	4	174
β-strand	228-232	5	175
α-helix	235-238	4
α-helix	242-247	6
α-helix	248-250	3
β-strand	259	1	60
β-strand	266-270	5	174
β-strand	287-294	8	175
α-helix	304-305	2
α-helix	306-328	23
β-strand	335-347	13	175
β-strand	351-361	11	175
β-strand	372-381	10	175
β-strand	383-387	5	176
β-strand	392	1	177
β-strand	397	1	177
β-strand	402-406	5	176
α-helix	408-419	12

Chain 6: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	29-31	3
α-helix	49	1
β-strand	50	1	172
α-helix	55-64	10
α-helix	68-69	2
α-helix	74-77	4
β-strand	89	1	181
α-helix	92-95	4
α-helix	99-114	16
α-helix	118-124	7
α-helix	132-141	10
α-helix	144-154	11
α-helix	157-160	4
β-strand	166	1	181
β-strand	174-177	4	182
β-strand	185-187	3	182
β-strand	189-192	4	183
α-helix	195-197	3
β-strand	203-205	3	182
β-strand	213-220	8	183
β-strand	231	1	184
β-strand	232-237	6	183
β-strand	240-241	2	183
α-helix	249	1
β-strand	250-252	3	183
β-strand	266-275	10	183
β-strand	298	1	184
α-helix	300-306	7
β-strand	311-321	11	183
α-helix	326-333	8
α-helix	338-339	2
β-strand	340-345	6	173
α-helix	347-350	4
α-helix	363-368	6

Chain 7: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	39-57	19
β-strand	64-69	6	186
β-strand	77-82	6	186
α-helix	88-93	6
α-helix	98-101	4
β-strand	105-108	4	186
β-strand	111-114	4	186
β-strand	124-127	4	186
α-helix	137-154	18
β-strand	165-166	2	187
β-strand	179-184	6	187
α-helix	196-211	16
β-strand	217-219	3	188
β-strand	222	1	189
α-helix	223-230	8
α-helix	234-244	11
β-strand	251	1	189
β-strand	254-256	3	188
β-strand	261-263	3	188
β-strand	275-279	5	190
β-strand	283-286	4	187
β-strand	294-299	6	187
β-strand	300-303	4	190
α-helix	310-319	10

77 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

76 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>6VLZ_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

>6VLZ_2 28S ribosomal protein S2, mitochondrial (chains AB)
MATSSAALPRILGAGARAPSRWLGFLGKATPRPARPSRRTLGSATALMIRESEDSTDFND
KILNEPLKHSDFFNVKELFSVRSLFDARVHLGHKAGCRHRFMEPYIFGSRLDHDIIDLEQ
TATHLQLALNFTAHMAYRKGIILFISRNRQFSYLIENMARDCGEYAHTRYFRGGMLTNAR
LLFGPTVRLPDLIIFLHTLNNIFEPHVAVRDAAKMNIPTVGIVDTNCNPCLITYPVPGND
DSPLAVHLYCRLFQTAITRAKEKRQQVEALYRLQGQKEPGDQGPAHPPGADMSHSL

Sequence of entity 3 (AC), FASTA

>6VLZ_3 28S ribosomal protein S24, mitochondrial (chains AC)
MAASVCSGLLGPRVLSWSRELPCAWRALHTSPVCAKNRAARVRVSKGDKPVTYEEAHAPH
YIAHRKGWLSLHTGNLDGEDHAAERTVEDVFLRKFMWGTFPGCLADQLVLKRRGNQLEIC
AVVLRQLSPHKYYFLVGYSETLLSYFYKCPVRLHLQTVPSKVVYKYL

Sequence of entity 4 (AE), FASTA

>6VLZ_4 28S ribosomal protein S6, mitochondrial (chains AE)
MPRYELALILKAMQRPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNR
GGYFLVDFYAPTAAVESMVEHLSRDIDVIRGNIVKHPLTQELKECEGIVPVPLAEKLYST
KKRKK

Sequence of entity 5 (AI), FASTA

>6VLZ_5 28S ribosomal protein S11, mitochondrial (chains AI)
MQAVRNAGSRFLRSWTWPQTAGRVVARTPAGTICTGARQLQDAAAKQKVEQNAAPSHTKF
SIYPPIPGEESSLRWAGKKFEEIPIAHIKASHNNTQIQVVSASNEPLAFASCGTEGFRNA
KKGTGIAAQTAGIAAAARAKQKGVIHIRVVVKGLGPGRLSAMHGLIMGGLEVISITDNTP
IPHNGCRPRKARKL

Sequence of entity 6 (AJ), FASTA

>6VLZ_6 28S ribosomal protein S12, mitochondrial (chains AJ)
MSWSGLLHGLNTSLTCGPALVPRLWATCSMATLNQMHRLGPPKRPPRKLGPTEGRPQLKG
VVLCTFTRKPKKPNSANRKCCRVRLSTGREAVCFIPGEGHTLQEHQIVLVEGGRTQDLPG
VKLTVVRGKYDCGHVQKK

Sequence of entity 7 (AK), FASTA

>6VLZ_7 28S ribosomal protein S14, mitochondrial (chains AK)
MAAFMLGSLLRTFKQMVPSSASGQVRSHYVDWRMWRDVKRRKMAYEYADERLRINSLRKN
TILPKILQDVADEEIAALPRDSCPVRIRNRCVMTSRPRGVKRRWRLSRIVFRHLADHGQL
SGIQRATW

Sequence of entity 8 (AM), FASTA

>6VLZ_8 28S ribosomal protein S16, mitochondrial (chains AM)
MVHLTTLLCKAYRGGHLTIRLALGGCTNRPFYRIVAAHNKCPRDGRFVEQLGSYDPLPNS
HGEKLVALNLDRIRHWIGCGAHLSKPMEKLLGLAGFFPLHPMMITNAERLRRKRAREVLL
ASQKTDAEATDTEATET

Sequence of entity 9 (AN), FASTA

>6VLZ_9 28S ribosomal protein S17, mitochondrial (chains AN)
MSVVRSSVHARWIVGKVIGTKMQKTAKVRVTRLVLDPYLLKYFNKRKTYFAHDALQQCTV
GDIVLLRALPVPRAKHVKHELAEIVFKVGKVIDPVTGKPCAGTTYLESPLSSETTQLSKN
LEELNISSAQ

Sequence of entity 10 (AO), FASTA

>6VLZ_10 28S ribosomal protein S18b, mitochondrial (chains AO)
MAASVLNTVLRRLPMLSLFRGSHRVQVPLQTLCTKAPSEEDSLSSVPISPYKDEPWKYLE
SEEYQERYGSRPVWADYRRNHKGGVPPQRTRKTCIRRNKVVGNPCPICRDHKLHVDFRNV
KLLEQFVCAHTGIIFYAPYTGVCVKQHKRLTQAIQKARDHGLLIYHIPQVEPRDLDFSTS
HGAVSATPPAPTLVSGDPWYPWYNWKQPPERELSRLRRLYQGHLQEESGPPPESMPKMPP
RTPAEASSTGQTGPQSAL

Sequence of entity 11 (AP), FASTA

>6VLZ_11 28S ribosomal protein S18c, mitochondrial (chains AP)
MAAVVAVCGGLGRKKLTHLVTAAVSLTHPGTHTVLWRRGCSQQVSSNEDLPISMENPYKE
PLKKCILCGKHVDYKNVQLLSQFVSPFTGCIYGRHITGLCGKKQKEITKAIKRAQIMGFM
PVTYKDPAYLKDPKVCNIRYRE

Sequence of entity 12 (AQ), FASTA

>6VLZ_12 28S ribosomal protein S21, mitochondrial (chains AQ)
MAKHLKFIARTVMVQEGNVESAYRTLNRILTMDGLIEDIKHRRYYEKPCRRRQRESYERC
RRIYNMEMARKINFLMRKNRADPWQGC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	130
ZN	Zinc ion	Zn	7
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1

Primary citation

Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation. Koripella, R.K., Sharma, M.R., Bhargava, K. et al. Nat Commun (2020) 11:3830-3830. DOI 10.1038/s41467-020-17715-2 · 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)

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