8PW6: C respirasome from murine liver

C respirasome from murine liver. Determined by electron microscopy at 3.3 Å resolution. Released 24 Apr 2024.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Mus musculus
Chains: 79
Atoms: 115,652
Mol. weight: 1886.75 kDa
Ligands: 3PE, CDL, HEM, HEC
Released: 24 Apr 2024

Explore 8PW6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PW6 contains 760 α-helices and 340 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: 25 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	33-39	7
α-helix	45-51	7
α-helix	53-63	11
α-helix	65	1
β-strand	66	1	57
α-helix	67	1
β-strand	74	1	57
α-helix	75-80	6
β-strand	92-97	6	58
α-helix	106-113	8
α-helix	115-129	15
β-strand	133-138	6	58
α-helix	143-159	17
β-strand	174-179	6	58
α-helix	189-197	9
α-helix	203-205	3
α-helix	209	1
α-helix	215-217	3
β-strand	220-224	5	58
α-helix	225-237	13
α-helix	239-244	6
β-strand	246-247	2	59
β-strand	250-251	2	59
β-strand	253-260	8	60
β-strand	262	1	61
β-strand	266-271	6	60
β-strand	275	1	62
α-helix	276-279	4
α-helix	280-284	5
β-strand	287	1	61
β-strand	294-298	5	60
α-helix	305-306	2
β-strand	307-308	2	60
α-helix	309-312	4
β-strand	316	1	62
α-helix	319-324	6
β-strand	333-338	6	60
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	53
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	54
α-helix	106-110	5
α-helix	114-124	11
β-strand	130-131	2	54
β-strand	137-142	6	54
β-strand	154-156	3	54
β-strand	159-162	4	54
α-helix	166-178	13
β-strand	185-186	2	54
α-helix	195	1
α-helix	205-206	2
α-helix	213-214	2

Chain 3: 34 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	67
β-strand	16-20	5	67
β-strand	25	1	68
α-helix	26-33	8
β-strand	56-57	2	69
β-strand	58-59	2	67
β-strand	66-67	2	69
α-helix	71	1
β-strand	72	1	68
α-helix	73	1
β-strand	78-80	3	67
α-helix	84-100	17
α-helix	105-107	3
α-helix	115-123	9
α-helix	133-135	3
β-strand	146-148	3	70
α-helix	150-152	3
α-helix	158-162	5
α-helix	163-167	5
β-strand	173-175	3	71
α-helix	178-180	3
β-strand	182-184	3	71
α-helix	198-202	5
β-strand	208-210	3	70
β-strand	223-228	6	72
β-strand	237-242	6	72
β-strand	247-252	6	72
β-strand	255	1	73
β-strand	260	1	73
α-helix	265-269	5
α-helix	270-275	6
β-strand	278	1	74
β-strand	283-285	3	75
β-strand	291-293	3	75
α-helix	296-309	14
β-strand	315-319	5	75
α-helix	325-337	13
β-strand	343-345	3	75
β-strand	358	1	76
α-helix	359-362	4
β-strand	364	1	77
α-helix	367-373	7
β-strand	376-380	5	77
α-helix	384-387	4
α-helix	389-401	13
β-strand	405-409	5	77
β-strand	420-423	4	77
α-helix	427-434	8
α-helix	438-445	8
β-strand	449-454	6	77
α-helix	455-458	4
α-helix	463-481	19
β-strand	490-493	4	77
α-helix	497-505	9
α-helix	507	1
β-strand	508-509	2	75
α-helix	512-516	5
β-strand	521-525	5	75
β-strand	542-547	6	75
β-strand	549	1	74
β-strand	559-562	4	75
β-strand	571-574	4	78
β-strand	580-583	4	78
α-helix	584-585	2
α-helix	596-607	12
α-helix	616-626	11
β-strand	633	1	78
α-helix	642-651	10
α-helix	660-661	2
α-helix	676-680	5
α-helix	682-692	11

Chain 6: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	35-53	19
β-strand	57	1	33
β-strand	58	1	34
α-helix	64-73	10
α-helix	79-82	4
β-strand	87	1	34
α-helix	90-92	3
β-strand	95-99	5	33
β-strand	103	1	35
α-helix	107-115	9
β-strand	122-126	5	33
α-helix	127-132	6
α-helix	134-136	3
β-strand	142	1	35
α-helix	146-148	3
β-strand	154-156	3	33
α-helix	161-162	2
α-helix	163-179	17
α-helix	182-188	7

Chain 7: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	94
β-strand	10-11	2	94
α-helix	23-25	3
α-helix	40-45	6
α-helix	48-49	2
β-strand	50-52	3	95
β-strand	56-59	4	96
α-helix	64-66	3
β-strand	71-74	4	96
β-strand	82-83	2	95
β-strand	90-93	4	95

Chain 9: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	82
β-strand	3-4	2	47
α-helix	16-28	13
α-helix	30-43	14
β-strand	67-69	3	83
β-strand	71	1	84
β-strand	77	1	84
α-helix	84-88	5
β-strand	94-100	7	85
β-strand	106-114	9	85
α-helix	123-127	5
β-strand	133-135	3	83
β-strand	143	1	33
α-helix	147-149	3
β-strand	150-151	2	85
α-helix	153-162	10
α-helix	164-174	11

Chain A: 22 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
α-helix	12-14	3
β-strand	15-18	4	1
β-strand	24-29	6	1
β-strand	34-41	8	1
α-helix	55-62	8
β-strand	67	1	2
α-helix	74-82	9
β-strand	85-90	6	1
β-strand	95-102	8	1
α-helix	103-105	3
α-helix	106-118	13
β-strand	120	1	2
α-helix	124-143	20
α-helix	146-157	12
α-helix	171-176	6
α-helix	179-189	11
α-helix	192-194	3
β-strand	195-201	7	1
α-helix	205-215	11
α-helix	228-230	3
β-strand	239-244	6	3
β-strand	251-258	8	3
α-helix	267-277	11
β-strand	279-281	3	3
α-helix	287-289	3
α-helix	293-301	9
β-strand	304-314	11	3
β-strand	317-326	10	3
α-helix	331-348	18
α-helix	351-368	18
α-helix	372-385	14
α-helix	392-401	10
α-helix	404-414	11
β-strand	421-426	6	3
α-helix	434-440	7

Chain a1: 5 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
α-helix	66-68	3

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 b-c1 complex subunit 1, mitochondrial	A, L	protein	480	Mus musculus	Q9CZ13 (AlphaFold model)
Cytochrome b-c1 complex subunit 2, mitochondrial	B, M	protein	453	Mus musculus	Q9DB77 (AlphaFold model)
Cytochrome b	C, N	protein	381	Mus musculus	P00158 (AlphaFold model)
Cytochrome c1, heme protein, mitochondrial	D, O	protein	325	Mus musculus	Q9D0M3 (AlphaFold model)
Cytochrome b-c1 complex subunit Rieske, mitochondrial	E, P, T	protein	274	Mus musculus	Q9CR68
Cytochrome b-c1 complex subunit 7	F, Q	protein	111	Mus musculus	Q9D855
Cytochrome b-c1 complex subunit 8	G, R	protein	82	Mus musculus	Q9CQ69
Cytochrome b-c1 complex subunit 6, mitochondrial	H, S	protein	89	Mus musculus	P99028
Cytochrome b-c1 complex subunit 9	J, U	protein	64	Mus musculus	Q8R1I1
Cytochrome b-c1 complex subunit 10	K, V	protein	56	Mus musculus	Q9CPX8
Cytochrome c oxidase subunit 1	n	protein	514	Mus musculus	P00397
Cytochrome c oxidase subunit 2	o	protein	227	Mus musculus	P00405

55 more molecules are not listed.

Sequence of entity 1 (A, L), FASTA

>8PW6_1 Cytochrome b-c1 complex subunit 1, mitochondrial (chains A, L)
MAASAVCRAACSGTQVLLRTRRSPALLRLPALRGTATFAQALQSVPETQVSILDNGLRVA
SEQSSHATCTVGVWIDAGSRYETEKNNGAGYFLEHLAFKGTKNRPGNALEKEVESIGAHL
NAYSTREHTAYLIKALSKDLPKVVELLADIVQNSSLEDSQIEKERDVILREMQENDASMQ
NVVFDYLHATAFQGTPLAQAVEGPSENVRRLSRTDLTDYLNRHYKAPRMVLAAAGGVEHQ
QLLDLAQKHLSSVSRVYEEDAVPGLTPCRFTGSEIRHRDDALPLAHVAIAVEGPGWANPD
NVTLQVANAIIGHYDCTYGGGVHLSSPLASVAVANKLCQSFQTFNISYSDTGLLGAHFVC
DAMSIDDMVFFLQGQWMRLCTSATESEVTRGKNILRNALVSHLDGTTPVCEDIGRSLLTY
GRRIPLAEWESRIQEVDAQMLRDICSKYFYDQCPAVAGYGPIEQLPDYNRIRSGMFWLRF

Sequence of entity 2 (B, M), FASTA

>8PW6_2 Cytochrome b-c1 complex subunit 2, mitochondrial (chains B, M)
MKLLSRAGSFSRFYSLKVAPKVKTSAAPGGVPLQPQDLEFTKLPNGLVIASLENYAPLSR
IGLFVKAGSRYEDSNNLGTSHLLRLASSLTTKGASSFKITRGIEAVGGKLSVTATRENMA
YTVEGIRSDIEILMEFLLNVTTAPEFRRWEVAALRSQLKIDKAVAFQNSQTRIIENLHDV
AYKNALANPLYCPDYRMGKITSEELHYFVQNHFTSARMALVGLGVSHSVLKQVAEQFLNM
RGGLGLAGAKAKYRGGEIREQNGDNLVHAAIVAESAAIGNAEANAFSVLQHLLGAGPHIK
RGNNTTSLLSQSVAKGSHQPFDVSAFNASYSDSGLFGIYTISQAAAAGEVINAAYNQVKA
VAQGNLSSADVQAAKNKLKAGYLMSVETSEGFLSEIGSQALAAGSYMPPSTVLQQIDSVA
DADVVKAAKKFVSGKKSMAASGNLGHTPFLDEL

Sequence of entity 3 (C, N), FASTA

>8PW6_3 Cytochrome b (chains C, N)
MTNMRKTHPLFKIINHSFIDLPAPSNISSWWNFGSLLGVCLMVQIITGLFLAMHYTSDTM
TAFSSVTHICRDVNYGWLIRYMHANGASMFFICLFLHVGRGLYYGSYTFMETWNIGVLLL
FAVMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTTLVEWIWGGFSVDKATLTRFFA
FHFILPFIIAALAIVHLLFLHETGSNNPTGLNSDADKIPFHPYYTIKDILGILIMFLILM
TLVLFFPDMLGDPDNYMPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALILSILI
LALMPFLHTSKQRSLMFRPITQILYWILVANLLILTWIGGQPVEHPFIIIGQLASISYFS
IILILMPISGIIEDKMLKLYP

Sequence of entity 4 (D, O), FASTA

>8PW6_4 Cytochrome c1, heme protein, mitochondrial (chains D, O)
MAAAAASLRRTVLGPRGVGLPGASAPGLLGGARSRQLPLRTPQAVSLSSKSGPSRGRKVM
LSALGMLAAGGAGLAVALHSAVSASDLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQV
CSSCHSMDYVAYRHLVGVCYTEEEAKALAEEVEVQDGPNDDGEMFMRPGKLSDYFPKPYP
NPEAARAANNGALPPDLSYIVRARHGGEDYVFSLLTGYCEPPTGVSLREGLYFNPYFPGQ
AIGMAPPIYTEVLEYDDGTPATMSQVAKDVATFLRWASEPEHDHRKRMGLKMLLMMGLLL
PLTYAMKRHKWSVLKSRKLAYRPPK

Sequence of entity 5 (E, P, T), FASTA

>8PW6_5 Cytochrome b-c1 complex subunit Rieske, mitochondrial (chains E, P, T)
MLSVAARSGPFAPVLSATSRGVAGALRPLLQGAVPAASEPPVLDVKRPFLCRESLSGQAA
ARPLVATVGLNVPASVRFSHTDVKVPDFSDYRRAEVLDSTKSSKESSEARKGFSYLVTAT
TTVGVAYAAKNVVSQFVSSMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRT
KKEIDQEAAVEVSQLRDPQHDLDRVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHG
SHYDASGRIRKGPAPLNLEVPAYEFTSDDVVVVG

Sequence of entity 6 (F, Q), FASTA

>8PW6_6 Cytochrome b-c1 complex subunit 7 (chains F, Q)
MAGRSAVSASSKWLDGFRKWYYNAAGFNKLGLMRDDTLHETEDVKEAIRRLPEDLYNDRM
FRIKRALDLTMRHQILPKDQWTKYEEDKFYLEPYLKEVIRERKEREEWAKK

Sequence of entity 7 (G, R), FASTA

>8PW6_7 Cytochrome b-c1 complex subunit 8 (chains G, R)
MGREFGNLARIRHVISYSLSPFEQRAFPSYFSKGIPNVLRRTRERILRVAPPFVVVYLIY
TWGNQEFEQSKRKNPAMYENDK

Sequence of entity 8 (H, S), FASTA

>8PW6_8 Cytochrome b-c1 complex subunit 6, mitochondrial (chains H, S)
MGLEDERKMLTGSGDPKEEEEEELVDPLTTVREHCEQLEKCVKARERLELCDNRVSSRSQ
TEEDCTEELFDFLHARDHCVAHKLFKNLK

Sequence of entity 9 (J, U), FASTA

>8PW6_9 Cytochrome b-c1 complex subunit 9 (chains J, U)
MSSPTIPSRLYSLLFRRTSTFALTIAVGALFFERAFDQGADAIYEHINEGKLWKHIKHKY
ENKE

Sequence of entity 10 (K, V), FASTA

>8PW6_10 Cytochrome b-c1 complex subunit 10 (chains K, V)
MLSRFLGPRYRELARNWIPTAGMWGTVGAVGLVWATDWRLILDWVPYINGKFKKDD

Sequence of entity 11 (n), FASTA

>8PW6_11 Cytochrome c oxidase subunit 1 (chains n)
MFINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSILIRAELGQPGALLGDDQIYNVIVTA
HAFVMIFFMVMPMMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEA
GAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMTQYQ
TPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGH
PEVYILILPGFGIISHVVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGLDVD
TRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMLWALGFIFLFTVGGLTGIVLSN
SSLDIVLHDTYYVVAHFHYVLSMGAVFAIMAGFVHWFPLFSGFTLDDTWAKAHFAIMFVG
VNMTFFPQHFLGLSGMPRRYSDYPDAYTTWNTVSSMGSFISLTAVLIMIFMIWEAFASKR
EVMSVSYASTNLEWLHGCPPPYHTFEEPTYVKVK

Sequence of entity 12 (o), FASTA

>8PW6_12 Cytochrome c oxidase subunit 2 (chains o)
MAYPFQLGLQDATSPIMEELMNFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE
VETIWTILPAVILIMIALPSLRILYMMDEINNPVLTVKTMGHQWYWSYEYTDYEDLCFDS
YMIPTNDLKPGELRLLEVDNRVVLPMELPIRMLISSEDVLHSWAVPSLGLKTDAIPGRLN
QATVTSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKYFENWSASMI

Ligands and cofactors

ID	Name	Formula	Copies
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	C41 H82 N O8 P	33
CDL	Cardiolipin	C81 H156 O17 P2	16
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	12
CU	Copper (II) ion	Cu	1
HEA	Heme-a	C49 H56 Fe N4 O6	2
MG	Magnesium ion	Mg	2
CUA	Dinuclear copper ion	Cu2	1
ZN	Zinc ion	Zn	2
TGL	Tristearoylglycerol	C57 H110 O6	1
SF4	Iron/sulfur cluster	Fe4 S4	6
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	1
NDP	NADPH dihydro-nicotinamide-adenine-dinucleotide phosphate	C21 H30 N7 O17 P3	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

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 Q9CZ13 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7O3H 2.6 Å, Murine CIII2 focus-refined from supercomplex CICIII2
7O37 3.2 Å, Murine supercomplex CIII2CIV in the assembled locked conformation
7O3C 3.3 Å, Murine supercomplex CIII2CIV in the mature unlocked conformation
8IAR 3.4 Å, Respiratory complex CIII2, focus-refined of type I, Wild type mouse under thermoneutral…
8IB7 3.4 Å, Respiratory complex CIII2, focus-refined of type IA, Wild type mouse under cold…
8PW7 3.5 Å, A respirasome from murine liver
7O3E 3.6 Å, Murine supercomplex CIII2CIV in the intermediate locked conformation
8IBC 3.6 Å, Respiratory complex CIII2, focus-refined of type IB, Wild type mouse under cold…
8PW5 3.6 Å, CS respirasome from murine liver
8UCA 3.7 Å, Formation of I2+III2 supercomplex rescues respiratory chain defects
8IBG 3.8 Å, Respiratory complex CIII2, focus-refined of type II, Wild type mouse under cold…
8IC5 4.1 Å, Respiratory complex CIII2, focus-refined of type I, PERK -/- mouse under cold temperature

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