8PW7: A respirasome from murine liver

A respirasome from murine liver. Determined by electron microscopy at 3.5 Å resolution. Released 24 Apr 2024.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Mus musculus
Chains: 79
Atoms: 115,575
Mol. weight: 1884.38 kDa
Ligands: CU, HEA, 3PE, CUA
Released: 24 Apr 2024

Explore 8PW7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PW7 contains 760 α-helices and 336 β-strands across 79 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 1: 22 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	33-39	7
α-helix	45-51	7
α-helix	53-63	11
β-strand	66	1	42
β-strand	74	1	42
α-helix	75-80	6
β-strand	92-97	6	43
α-helix	106-113	8
α-helix	115-129	15
β-strand	133-138	6	43
α-helix	143-159	17
β-strand	174-179	6	43
α-helix	189-197	9
α-helix	202-205	4
α-helix	209	1
α-helix	215-217	3
β-strand	220-224	5	43
α-helix	225-237	13
α-helix	239-244	6
β-strand	246-247	2	44
β-strand	250-251	2	44
β-strand	253-260	8	45
β-strand	262	1	46
β-strand	266-271	6	45
α-helix	276-279	4
α-helix	280-284	5
β-strand	287	1	46
β-strand	294-298	5	45
β-strand	307-308	2	45
α-helix	309-312	4
α-helix	319-324	6
β-strand	333-338	6	45
α-helix	343-357	15
α-helix	363-381	19
α-helix	387-399	13
α-helix	407-421	15
α-helix	423-437	15

Chain 2: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	25-37	13
α-helix	39	1
β-strand	40	1	40
α-helix	43-46	4
α-helix	47-58	12
α-helix	63-73	11
α-helix	77-86	10
β-strand	98-103	6	41
α-helix	106-110	5
α-helix	114-124	11
β-strand	131	1	41
β-strand	137-142	6	41
β-strand	153-156	4	41
β-strand	159-162	4	41
α-helix	166-178	13
β-strand	185-186	2	41
α-helix	195	1
α-helix	205-206	2
α-helix	213-214	2

Chain 3: 36 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	50
β-strand	16-20	5	50
β-strand	25	1	51
α-helix	26-33	8
α-helix	36-38	3
α-helix	47-48	2
β-strand	56-57	2	52
β-strand	58-59	2	50
β-strand	66-67	2	52
α-helix	71	1
β-strand	72	1	51
α-helix	73	1
β-strand	78-80	3	50
α-helix	84-100	17
α-helix	105-107	3
α-helix	115-123	9
α-helix	133-135	3
α-helix	138-140	3
β-strand	146-148	3	53
α-helix	150-152	3
α-helix	158-165	8
β-strand	173-175	3	54
α-helix	178-180	3
β-strand	182-184	3	54
α-helix	198-202	5
β-strand	208-210	3	53
β-strand	223-228	6	55
β-strand	237-242	6	55
β-strand	247-252	6	55
β-strand	255	1	56
β-strand	260	1	56
α-helix	265-269	5
α-helix	271-275	5
β-strand	276-278	3	57
β-strand	283-285	3	58
β-strand	291-293	3	58
α-helix	296-309	14
β-strand	315-319	5	58
α-helix	325-337	13
β-strand	343-345	3	58
β-strand	358	1	59
α-helix	359-362	4
β-strand	364	1	60
α-helix	367-373	7
β-strand	376-380	5	60
α-helix	384-387	4
α-helix	389-401	13
β-strand	405-409	5	60
β-strand	420-423	4	60
α-helix	427-434	8
α-helix	438-445	8
β-strand	449-454	6	60
α-helix	455-458	4
α-helix	463-481	19
β-strand	490-493	4	60
α-helix	497-505	9
α-helix	507	1
β-strand	508-509	2	58
α-helix	512-516	5
β-strand	521-525	5	58
β-strand	542-547	6	58
β-strand	549	1	57
β-strand	559-562	4	58
β-strand	571-574	4	61
β-strand	580-583	4	61
α-helix	584-585	2
α-helix	596-607	12
α-helix	616-626	11
β-strand	633	1	61
α-helix	642-651	10
α-helix	668-672	5
α-helix	676-680	5
α-helix	682-692	11

Chain 6: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	35-53	19
α-helix	56	1
β-strand	57	1	26
β-strand	58	1	27
α-helix	64-73	10
α-helix	79-82	4
β-strand	87	1	27
α-helix	90-92	3
β-strand	95-99	5	26
β-strand	103	1	28
α-helix	107-115	9
β-strand	122-126	5	26
α-helix	127-132	6
α-helix	134-136	3
β-strand	142	1	28
α-helix	146-148	3
β-strand	154-156	3	26
α-helix	161-162	2
α-helix	163-178	16
α-helix	182-188	7

Chain 7: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	88
α-helix	9	1
β-strand	10	1	88
α-helix	11-12	2
α-helix	40-45	6
α-helix	48-49	2
β-strand	50-52	3	89
β-strand	56-59	4	90
α-helix	64-66	3
α-helix	68-70	3
β-strand	71-74	4	90
β-strand	82-83	2	89
β-strand	90-93	4	89

Chain 9: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	66
β-strand	3-4	2	38
α-helix	16-27	12
α-helix	30-44	15
α-helix	46-47	2
β-strand	66-69	4	67
β-strand	71	1	68
β-strand	77	1	68
α-helix	84-88	5
β-strand	94-100	7	69
β-strand	106-114	9	69
α-helix	123-127	5
β-strand	133-136	4	67
β-strand	143	1	26
α-helix	147-149	3
β-strand	150-151	2	69
α-helix	153-162	10
α-helix	164-174	11

Chain A: 24 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
α-helix	12-13	2
β-strand	15-18	4	47
β-strand	24-29	6	47
β-strand	34-41	8	47
α-helix	55-63	9
β-strand	67	1	48
α-helix	74-82	9
β-strand	85-90	6	47
β-strand	95-102	8	47
α-helix	103-105	3
α-helix	106-118	13
β-strand	120	1	48
α-helix	124-142	19
α-helix	146-157	12
α-helix	171-176	6
α-helix	179-189	11
β-strand	195-201	7	47
α-helix	205-215	11
α-helix	232-236	5
β-strand	239-244	6	49
β-strand	251-258	8	49
α-helix	266-277	12
β-strand	279-281	3	49
α-helix	287-289	3
α-helix	293-301	9
β-strand	304-314	11	49
β-strand	317-326	10	49
α-helix	331-347	17
α-helix	351-368	18
α-helix	372-385	14
α-helix	389-391	3
α-helix	392-401	10
α-helix	404-414	11
α-helix	418-420	3
β-strand	421-426	6	49
α-helix	432-433	2
α-helix	434-441	8

Chain a1: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	2-4	3
α-helix	6-30	25
α-helix	35-38	4
α-helix	42-55	14

71 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
Cytochrome c oxidase subunit 1	n	protein	514	Mus musculus	P00397 (AlphaFold model)
Cytochrome c oxidase subunit 2	o	protein	227	Mus musculus	P00405 (AlphaFold model)
Cytochrome c oxidase subunit 3	p	protein	261	Mus musculus	P00416 (AlphaFold model)
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial	q	protein	169	Mus musculus	P19783 (AlphaFold model)
Cytochrome c oxidase subunit 5A, mitochondrial	r	protein	146	Mus musculus	P12787
Cytochrome c oxidase subunit 5B, mitochondrial	s	protein	128	Mus musculus	P19536
Cytochrome c oxidase subunit 6A1, mitochondrial	t	protein	111	Mus musculus	P43023
Cytochrome c oxidase subunit 6B1	u	protein	86	Mus musculus	P56391
Cytochrome c oxidase subunit 6C	v	protein	76	Mus musculus	Q9CPQ1
Cytochrome c oxidase subunit 7B, mitochondrial	x	protein	80	Mus musculus	P56393
Cytochrome c oxidase subunit 7C, mitochondrial	y	protein	63	Mus musculus	P17665
Cytochrome c oxidase subunit 7A2, mitochondrial	w	protein	83	Mus musculus	P48771

55 more molecules are not listed.

Sequence of entity 1 (n), FASTA

>8PW7_1 Cytochrome c oxidase subunit 1 (chains n)
MFINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSILIRAELGQPGALLGDDQIYNVIVTA
HAFVMIFFMVMPMMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEA
GAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMTQYQ
TPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGH
PEVYILILPGFGIISHVVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGLDVD
TRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMLWALGFIFLFTVGGLTGIVLSN
SSLDIVLHDTYYVVAHFHYVLSMGAVFAIMAGFVHWFPLFSGFTLDDTWAKAHFAIMFVG
VNMTFFPQHFLGLSGMPRRYSDYPDAYTTWNTVSSMGSFISLTAVLIMIFMIWEAFASKR
EVMSVSYASTNLEWLHGCPPPYHTFEEPTYVKVK

Sequence of entity 2 (o), FASTA

>8PW7_2 Cytochrome c oxidase subunit 2 (chains o)
MAYPFQLGLQDATSPIMEELMNFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE
VETIWTILPAVILIMIALPSLRILYMMDEINNPVLTVKTMGHQWYWSYEYTDYEDLCFDS
YMIPTNDLKPGELRLLEVDNRVVLPMELPIRMLISSEDVLHSWAVPSLGLKTDAIPGRLN
QATVTSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKYFENWSASMI

Sequence of entity 3 (p), FASTA

>8PW7_3 Cytochrome c oxidase subunit 3 (chains p)
MTHQTHAYHMVNPSPWPLTGAFSALLLTSGLVMWFHYNSITLLTLGLLTNILTMYQWWRD
VIREGTYQGHHTPIVQKGLRYGMILFIVSEVFFFAGFFWAFYHSSLVPTHDLGGCWPPTG
ISPLNPLEVPLLNTSVLLASGVSITWAHHSLMEGKRNHMNQALLITIMLGLYFTILQASE
YFETSFSISDGIYGSTFFMATGFHGLHVIIGSTFLIVCLLRQLKFHFTSKHHFGFEAAAW
YWHFVDVVWLFLYVSIYWWGS

Sequence of entity 4 (q), FASTA

>8PW7_4 Cytochrome c oxidase subunit 4 isoform 1, mitochondrial (chains q)
MLASRALSLIGKRAISTSVCLRAHGSVVKSEDYAFPTYADRRDYPLPDVAHVTMLSASQK
ALKEKEKADWSSLSRDEKVQLYRIQFNESFAEMNRGTNEWKTVVGMAMFFIGFTALVLIW
EKSYVYGPIPHTFDRDWVAMQTKRMLDMKANPIQGFSAKWDYDKNEWKK

Sequence of entity 5 (r), FASTA

>8PW7_5 Cytochrome c oxidase subunit 5A, mitochondrial (chains r)
MLAAALRRCTAAAAARGLLHPASAPSPAAAVCSIRCYSHGSHETDEEFDARWVTYFNKPD
IDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYP
YVIQELRPTLNELGISTPEELGLDKV

Sequence of entity 6 (s), FASTA

>8PW7_6 Cytochrome c oxidase subunit 5B, mitochondrial (chains s)
MASRLLRGVGALAAQALRRTARGAAVTRSMASGGGVPTDEEQATGLEREIMIAAQKGLDP
YNMLPPKAASGTKEDPNLVPSISNKRIVGCICEEDNCTVIWFWLHKGESQRCPNCGTHYK
LVPHQMAH

Sequence of entity 7 (t), FASTA

>8PW7_7 Cytochrome c oxidase subunit 6A1, mitochondrial (chains t)
MASAVLSASRVSRPLGRALPGLRRPMSSGAHGEEGSARMWKALTYFVALPGVGVSMLNVF
LKSRHEEHERPPFVAYPHLRIRTKPFPWGDGNHTLFHNPHVNPLPTGYEDE

Sequence of entity 8 (u), FASTA

>8PW7_8 Cytochrome c oxidase subunit 6B1 (chains u)
MAEDIKTKIKNYKTAPFDSRFPNQNQTKNCWQNYLDFHRCEKAMTAKGGDVSVCEWYRRV
YKSLCPVSWVSAWDDRIAEGTFPGKI

Sequence of entity 9 (v), FASTA

>8PW7_9 Cytochrome c oxidase subunit 6C (chains v)
MSSGALLPKPQMRGLLAKRLRVHIAGAFIVALGVAAAYKFGVAEPRKKAYAEFYRNYDSM
KDFEEMRKAGIFQSAK

Sequence of entity 10 (x), FASTA

>8PW7_10 Cytochrome c oxidase subunit 7B, mitochondrial (chains x)
MLPLAKNALSRLQVRSIQQVVARQSHQKRAPSFHDKYGNAILAGGAIFCVSTWTYTATQI
GIEWNMSPVGRVTPKEWRDQ

Sequence of entity 11 (y), FASTA

>8PW7_11 Cytochrome c oxidase subunit 7C, mitochondrial (chains y)
MLGQSIRRFTTSVVRRSHYEEGPGKNLPFSVENKWRLLAMMTVYFGSGFAAPFFIVRHQL
LKK

Sequence of entity 12 (w), FASTA

>8PW7_12 Cytochrome c oxidase subunit 7A2, mitochondrial (chains w)
MLRNLLALRQIAQRTISTTSRRHFENKVPEKQKLFQEDNGMPVHLKGGASDALLYRATMA
LTLGGTAYAIYLLAMAAFPKKQN

Ligands and cofactors

ID	Name	Formula	Copies
CU	Copper (II) ion	Cu	1
HEA	Heme-a	C49 H56 Fe N4 O6	2
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	C41 H82 N O8 P	33
CUA	Dinuclear copper ion	Cu2	1
ZN	Zinc ion	Zn	2
TGL	Tristearoylglycerol	C57 H110 O6	1
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	4
HEC	Heme C	C34 H36 Fe N4 O4	2
FES	FE2/S2 (inorganic) cluster	Fe2 S2	4
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	9
SF4	Iron/sulfur cluster	Fe4 S4	6
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	1
ZMP	S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}ami…	C25 H49 N2 O8 P S	2
DGT	2'-deoxyguanosine-5'-triphosphate	C10 H16 N5 O13 P3	1
NDP	NADPH dihydro-nicotinamide-adenine-dinucleotide phosphate	C21 H30 N7 O17 P3	1
CDL	Cardiolipin	C81 H156 O17 P2	16
MG	Magnesium ion	Mg	2

Water and common crystallization additives (NA, K) are not listed.

Primary citation

SCAF1 drives the compositional diversity of mammalian respirasomes. Vercellino, I., Sazanov, L.A. Nat Struct Mol Biol (2024) 31:1061-1071. DOI 10.1038/s41594-024-01255-0 · PubMed

Other PDB entries of the same protein (UniProt P00397 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7O37 3.2 Å, Murine supercomplex CIII2CIV in the assembled locked conformation
7O3C 3.3 Å, Murine supercomplex CIII2CIV in the mature unlocked conformation
8PW6 3.3 Å, C respirasome from murine liver
7O3E 3.6 Å, Murine supercomplex CIII2CIV in the intermediate locked conformation
8PW5 3.6 Å, CS respirasome from murine liver

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