8PW5: CS respirasome from murine liver

CS respirasome from murine liver. Determined by electron microscopy at 3.6 Å resolution. Released 24 Apr 2024.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Mus musculus
Chains: 92
Atoms: 130,610
Mol. weight: 2128.78 kDa
Ligands: DGT, ZMP, NDP, FMN
Released: 24 Apr 2024

Explore 8PW5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PW5 contains 848 α-helices and 365 β-strands across 92 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: 23 helices, 17 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	69
β-strand	74	1	69
α-helix	75-80	6
β-strand	92-97	6	70
α-helix	106-113	8
α-helix	115-129	15
β-strand	133-138	6	70
α-helix	143-159	17
α-helix	166-168	3
β-strand	174-179	6	70
α-helix	189-197	9
α-helix	203-205	3
α-helix	209	1
α-helix	215-217	3
β-strand	220-224	5	70
α-helix	225-237	13
α-helix	239-244	6
β-strand	246-247	2	71
β-strand	250-251	2	71
β-strand	253-260	8	72
β-strand	262	1	73
β-strand	266-271	6	72
β-strand	275	1	74
α-helix	276-283	8
β-strand	287	1	73
β-strand	294-298	5	72
α-helix	305-306	2
β-strand	307-308	2	72
α-helix	309-312	4
β-strand	316	1	74
α-helix	319-324	6
β-strand	333-338	6	72
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	63
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	64
α-helix	106-110	5
α-helix	114-124	11
β-strand	130-131	2	64
β-strand	137-142	6	64
β-strand	154-156	3	64
β-strand	159-162	4	64
α-helix	166-178	13
β-strand	185-186	2	64
α-helix	195	1
α-helix	205-206	2
α-helix	213-214	2

Chain 3: 33 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	77
β-strand	16-20	5	77
β-strand	25	1	78
α-helix	26-33	8
β-strand	56-57	2	79
β-strand	58-59	2	77
β-strand	66-67	2	79
α-helix	71	1
β-strand	72	1	78
α-helix	73	1
β-strand	78-80	3	77
α-helix	84-100	17
α-helix	115-123	9
α-helix	133-135	3
β-strand	146-148	3	80
α-helix	158-162	5
α-helix	163-167	5
β-strand	173-175	3	81
α-helix	178-180	3
β-strand	182-184	3	81
α-helix	198-202	5
β-strand	208-210	3	80
α-helix	222	1
β-strand	223-228	6	82
β-strand	237-242	6	82
β-strand	247-252	6	82
β-strand	255	1	83
β-strand	260	1	83
α-helix	265-269	5
α-helix	271-275	5
β-strand	278	1	84
β-strand	283-285	3	85
β-strand	291-293	3	85
α-helix	296-309	14
β-strand	315-319	5	85
α-helix	325-337	13
β-strand	343-345	3	85
β-strand	358	1	86
α-helix	359-362	4
α-helix	367-373	7
β-strand	376-380	5	87
α-helix	384-387	4
α-helix	389-401	13
β-strand	405-409	5	87
β-strand	420-423	4	87
α-helix	427-434	8
α-helix	438-445	8
β-strand	449-454	6	87
α-helix	455-459	5
α-helix	463-481	19
β-strand	490-493	4	87
α-helix	497-505	9
α-helix	507	1
β-strand	508	1	85
α-helix	512-516	5
β-strand	521-525	5	85
β-strand	542-547	6	85
β-strand	549	1	84
β-strand	559-562	4	85
β-strand	571-574	4	88
β-strand	580-583	4	88
α-helix	588-589	2
α-helix	596-607	12
α-helix	616-626	11
β-strand	633	1	88
α-helix	642-651	10
α-helix	668-672	5
α-helix	676-680	5
α-helix	682-692	11

Chain 6: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	36-53	18
β-strand	57	1	47
β-strand	58	1	48
α-helix	64-73	10
α-helix	79-82	4
β-strand	87	1	48
α-helix	90-92	3
β-strand	95-99	5	47
β-strand	103	1	49
α-helix	107-115	9
β-strand	122-126	5	47
α-helix	127-132	6
α-helix	134-136	3
β-strand	142	1	49
α-helix	146-148	3
β-strand	154-156	3	47
α-helix	161-162	2
α-helix	163-179	17
α-helix	182-188	7

Chain 7: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	108
α-helix	9	1
β-strand	10	1	108
α-helix	11-12	2
α-helix	23-25	3
α-helix	40-45	6
α-helix	48-49	2
β-strand	50-52	3	109
β-strand	56-59	4	110
α-helix	64-66	3
β-strand	71-74	4	110
β-strand	82-83	2	109
β-strand	90-93	4	109

Chain 9: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	58
α-helix	7-8	2
α-helix	16-28	13
α-helix	30-43	14
β-strand	67-69	3	93
β-strand	71	1	94
β-strand	77	1	94
α-helix	84-88	5
β-strand	94-100	7	95
β-strand	106-114	9	95
α-helix	123-127	5
β-strand	133-135	3	93
β-strand	143	1	47
α-helix	147-149	3
β-strand	150-151	2	95
α-helix	153-162	10
α-helix	164-174	11

Chain a: 26 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2	1
α-helix	3-7	5
α-helix	12-40	29
α-helix	52-67	16
α-helix	70-77	8
α-helix	78-87	10
α-helix	95-117	23
α-helix	142-170	29
α-helix	183-213	31
α-helix	222-224	3
α-helix	228-261	34
α-helix	270-283	14
α-helix	284-291	8
α-helix	299-327	29
α-helix	336-359	24
α-helix	361-366	6
β-strand	370	1	12
α-helix	371-379	9
α-helix	380-385	6
α-helix	386-395	10
α-helix	397-401	5
β-strand	403	1	13
α-helix	407-434	28
β-strand	437	1	12
α-helix	445-447	3
α-helix	448-478	31
α-helix	480	1
β-strand	481	1	13
β-strand	482-484	3	5
α-helix	492-494	3
α-helix	508-509	2
β-strand	510-511	2	14

Chain A: 22 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
α-helix	12-13	2
β-strand	14-18	5	8
β-strand	24-29	6	8
β-strand	34-42	9	8
α-helix	55-63	9
β-strand	67	1	9
α-helix	74-82	9
β-strand	85-90	6	8
β-strand	94-102	9	8
α-helix	103-105	3
α-helix	106-118	13
β-strand	120	1	9
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	8
α-helix	205-211	7
α-helix	212-216	5
β-strand	239-244	6	10
β-strand	251-258	8	10
α-helix	266-277	12
β-strand	279-281	3	10
α-helix	287-289	3
α-helix	293-301	9
β-strand	304-314	11	10
β-strand	317-326	10	10
α-helix	331-348	18
α-helix	351-369	19
α-helix	372-385	14
α-helix	392-401	10
α-helix	404-414	11
β-strand	421-426	6	10
α-helix	434-441	8

82 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 6A1, mitochondrial	g, t	protein	111	Mus musculus	P43023 (AlphaFold model)
Cytochrome c oxidase subunit 8A, mitochondrial	m, z	protein	69	Mus musculus	P48772 (AlphaFold model)
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
Cytochrome c1, heme protein, mitochondrial	D, O	protein	325	Mus musculus	Q9D0M3
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

56 more molecules are not listed.

Sequence of entity 1 (g, t), FASTA

>8PW5_1 Cytochrome c oxidase subunit 6A1, mitochondrial (chains g, t)
MASAVLSASRVSRPLGRALPGLRRPMSSGAHGEEGSARMWKALTYFVALPGVGVSMLNVF
LKSRHEEHERPPFVAYPHLRIRTKPFPWGDGNHTLFHNPHVNPLPTGYEDE

Sequence of entity 2 (m, z), FASTA

>8PW5_2 Cytochrome c oxidase subunit 8A, mitochondrial (chains m, z)
MSVLTPLLLRSLTGSARRLMVPRAQVHSKPAREQLGVLDITIGLTSCFVCCLLPAGWVLS
HLESYKKRE

Sequence of entity 3 (A, L), FASTA

>8PW5_3 Cytochrome b-c1 complex subunit 1, mitochondrial (chains A, L)
MAASAVCRAACSGTQVLLRTRRSPALLRLPALRGTATFAQALQSVPETQVSILDNGLRVA
SEQSSHATCTVGVWIDAGSRYETEKNNGAGYFLEHLAFKGTKNRPGNALEKEVESIGAHL
NAYSTREHTAYLIKALSKDLPKVVELLADIVQNSSLEDSQIEKERDVILREMQENDASMQ
NVVFDYLHATAFQGTPLAQAVEGPSENVRRLSRTDLTDYLNRHYKAPRMVLAAAGGVEHQ
QLLDLAQKHLSSVSRVYEEDAVPGLTPCRFTGSEIRHRDDALPLAHVAIAVEGPGWANPD
NVTLQVANAIIGHYDCTYGGGVHLSSPLASVAVANKLCQSFQTFNISYSDTGLLGAHFVC
DAMSIDDMVFFLQGQWMRLCTSATESEVTRGKNILRNALVSHLDGTTPVCEDIGRSLLTY
GRRIPLAEWESRIQEVDAQMLRDICSKYFYDQCPAVAGYGPIEQLPDYNRIRSGMFWLRF

Sequence of entity 4 (B, M), FASTA

>8PW5_4 Cytochrome b-c1 complex subunit 2, mitochondrial (chains B, M)
MKLLSRAGSFSRFYSLKVAPKVKTSAAPGGVPLQPQDLEFTKLPNGLVIASLENYAPLSR
IGLFVKAGSRYEDSNNLGTSHLLRLASSLTTKGASSFKITRGIEAVGGKLSVTATRENMA
YTVEGIRSDIEILMEFLLNVTTAPEFRRWEVAALRSQLKIDKAVAFQNSQTRIIENLHDV
AYKNALANPLYCPDYRMGKITSEELHYFVQNHFTSARMALVGLGVSHSVLKQVAEQFLNM
RGGLGLAGAKAKYRGGEIREQNGDNLVHAAIVAESAAIGNAEANAFSVLQHLLGAGPHIK
RGNNTTSLLSQSVAKGSHQPFDVSAFNASYSDSGLFGIYTISQAAAAGEVINAAYNQVKA
VAQGNLSSADVQAAKNKLKAGYLMSVETSEGFLSEIGSQALAAGSYMPPSTVLQQIDSVA
DADVVKAAKKFVSGKKSMAASGNLGHTPFLDEL

Sequence of entity 5 (C, N), FASTA

>8PW5_5 Cytochrome b (chains C, N)
MTNMRKTHPLFKIINHSFIDLPAPSNISSWWNFGSLLGVCLMVQIITGLFLAMHYTSDTM
TAFSSVTHICRDVNYGWLIRYMHANGASMFFICLFLHVGRGLYYGSYTFMETWNIGVLLL
FAVMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTTLVEWIWGGFSVDKATLTRFFA
FHFILPFIIAALAIVHLLFLHETGSNNPTGLNSDADKIPFHPYYTIKDILGILIMFLILM
TLVLFFPDMLGDPDNYMPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALILSILI
LALMPFLHTSKQRSLMFRPITQILYWILVANLLILTWIGGQPVEHPFIIIGQLASISYFS
IILILMPISGIIEDKMLKLYP

Sequence of entity 6 (D, O), FASTA

>8PW5_6 Cytochrome c1, heme protein, mitochondrial (chains D, O)
MAAAAASLRRTVLGPRGVGLPGASAPGLLGGARSRQLPLRTPQAVSLSSKSGPSRGRKVM
LSALGMLAAGGAGLAVALHSAVSASDLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQV
CSSCHSMDYVAYRHLVGVCYTEEEAKALAEEVEVQDGPNDDGEMFMRPGKLSDYFPKPYP
NPEAARAANNGALPPDLSYIVRARHGGEDYVFSLLTGYCEPPTGVSLREGLYFNPYFPGQ
AIGMAPPIYTEVLEYDDGTPATMSQVAKDVATFLRWASEPEHDHRKRMGLKMLLMMGLLL
PLTYAMKRHKWSVLKSRKLAYRPPK

Sequence of entity 7 (E, P, T), FASTA

>8PW5_7 Cytochrome b-c1 complex subunit Rieske, mitochondrial (chains E, P, T)
MLSVAARSGPFAPVLSATSRGVAGALRPLLQGAVPAASEPPVLDVKRPFLCRESLSGQAA
ARPLVATVGLNVPASVRFSHTDVKVPDFSDYRRAEVLDSTKSSKESSEARKGFSYLVTAT
TTVGVAYAAKNVVSQFVSSMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRT
KKEIDQEAAVEVSQLRDPQHDLDRVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHG
SHYDASGRIRKGPAPLNLEVPAYEFTSDDVVVVG

Sequence of entity 8 (F, Q), FASTA

>8PW5_8 Cytochrome b-c1 complex subunit 7 (chains F, Q)
MAGRSAVSASSKWLDGFRKWYYNAAGFNKLGLMRDDTLHETEDVKEAIRRLPEDLYNDRM
FRIKRALDLTMRHQILPKDQWTKYEEDKFYLEPYLKEVIRERKEREEWAKK

Sequence of entity 9 (G, R), FASTA

>8PW5_9 Cytochrome b-c1 complex subunit 8 (chains G, R)
MGREFGNLARIRHVISYSLSPFEQRAFPSYFSKGIPNVLRRTRERILRVAPPFVVVYLIY
TWGNQEFEQSKRKNPAMYENDK

Sequence of entity 10 (H, S), FASTA

>8PW5_10 Cytochrome b-c1 complex subunit 6, mitochondrial (chains H, S)
MGLEDERKMLTGSGDPKEEEEEELVDPLTTVREHCEQLEKCVKARERLELCDNRVSSRSQ
TEEDCTEELFDFLHARDHCVAHKLFKNLK

Sequence of entity 11 (J, U), FASTA

>8PW5_11 Cytochrome b-c1 complex subunit 9 (chains J, U)
MSSPTIPSRLYSLLFRRTSTFALTIAVGALFFERAFDQGADAIYEHINEGKLWKHIKHKY
ENKE

Sequence of entity 12 (K, V), FASTA

>8PW5_12 Cytochrome b-c1 complex subunit 10 (chains K, V)
MLSRFLGPRYRELARNWIPTAGMWGTVGAVGLVWATDWRLILDWVPYINGKFKKDD

Ligands and cofactors

ID	Name	Formula	Copies
DGT	2'-deoxyguanosine-5'-triphosphate	C10 H16 N5 O13 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
NDP	NADPH dihydro-nicotinamide-adenine-dinucleotide phosphate	C21 H30 N7 O17 P3	1
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	1
SF4	Iron/sulfur cluster	Fe4 S4	6
TGL	Tristearoylglycerol	C57 H110 O6	2
ZN	Zinc ion	Zn	3
CUA	Dinuclear copper ion	Cu2	2
MG	Magnesium ion	Mg	3
HEA	Heme-a	C49 H56 Fe N4 O6	4
CU	Copper (II) ion	Cu	2
FES	FE2/S2 (inorganic) cluster	Fe2 S2	4
HEC	Heme C	C34 H36 Fe N4 O4	2
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	4
CDL	Cardiolipin	C81 H156 O17 P2	18
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	13
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	C41 H82 N O8 P	41

Water and common crystallization additives (K, NA) 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 P43023 (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
8PW7 3.5 Å, A respirasome from murine liver
7O3E 3.6 Å, Murine supercomplex CIII2CIV in the intermediate locked conformation

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