9QEF

Respiratory supercomplex from Mycobacterium smegmatis with decylubiquinone

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, M (O, C)	Cytochrome bc1 complex cytochrome c subunit	polymer	278	29109.9	2	UniProt (A0R050) Pfam (PF00034) Pfam (PF13442)	Mycolicibacterium smegmatis
2	B, N (M, G)	Cytochrome bc1 complex cytochrome c subunit	polymer	408	44869.4	2	UniProt (A0R051) Pfam (PF19297) Pfam (PF00355)	Mycolicibacterium smegmatis
3	C, O (N, H)	Cytochrome bc1 complex cytochrome b subunit	polymer	556	61514.3	2	UniProt (A0R052) Pfam (PF13631)	Mycolicibacterium smegmatis	Cytochrome bc1 reductase complex subunit QcrB
4	D, P (P, I)	Transmembrane protein	polymer	100	11329.9	2	UniProt (A0QVH4) Pfam (PF10939)	Mycolicibacterium smegmatis
5	E, Q (S, J)	Probable cytochrome c oxidase subunit 3	polymer	203	22196.9	2	UniProt (A0R049) Pfam (PF00510)	Mycolicibacterium smegmatis	Cytochrome aa3 subunit 3
6	F, R (T, K)	Cytochrome c oxidase polypeptide 4	polymer	139	15177.4	2	UniProt (A0R056) Pfam (PF12270)	Mycolicibacterium smegmatis	Cytochrome aa3 subunit 4,Cytochrome c oxidase polypeptide IV
7	G, S (R, L)	Cytochrome c oxidase subunit 1	polymer	575	64163.0	2	UniProt (A0A2U9PNL2)	Mycolicibacterium smegmatis
8	H, T (Q, X)	cytochrome-c oxidase	polymer	341	38077.5	2	UniProt (A0R057) Pfam (PF00116)	Mycolicibacterium smegmatis	Cytochrome aa3 subunit 2
9	I, U (U, Z)	Cytochrome c oxidase subunit	polymer	79	8365.5	2	UniProt (A0R1B6)	Mycolicibacterium smegmatis
10	J, V (V, a)	Uncharacterized protein MSMEG_4692/MSMEI_4575	polymer	157	15911.0	2	UniProt (A0R1B5) Pfam (PF17174)	Mycolicibacterium smegmatis
11	K, W (W, b)	LpqE protein	polymer	186	19119.0	2	UniProt (A0R562) Pfam (PF04314)	Mycolicibacterium smegmatis
12	L, X (Y, c)	Superoxide dismutase [Cu-Zn]	polymer	236	23232.4	2	UniProt (A0QQQ1) Pfam (PF00080)	Mycolicibacterium smegmatis
13	AA, Y (E, A)	Co-purified transmembrane protein	polymer	123	13027.8	2	UniProt (A0A653FDI6)	Mycolicibacterium smegmatis
14	BA, Z (F, B)	Co-purified peptide	polymer	65	7075.9	2	UniProt (I7FT03)	Mycolicibacterium smegmatis
15	CA, DA, RB, SB (O, C)	HEME C	non-polymer		618.5	4	Chemie (HEC)
16	EA, HC, OA, QA, TB... (O, H, N, C, T)	MENAQUINONE-9	non-polymer		785.2	7	Chemie (MQ9)
17	FA, MC, UA, UB (O, I, P, C)	acyl-phosphatidyl-myo-inositol dimannoside (AcPIM2)	non-polymer		1415.8	4	Chemie (WUO)
18	GA, WB (M, G)	FE2/S2 (INORGANIC) CLUSTER	non-polymer		175.8	2	Chemie (FES)
19	HA, XB (M, G)	[(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{R})-10-methyldodecanoate	non-polymer		1677.8	2	Chemie (IZL)
20	ED, IA, OB, YB (b, M, W, G)	(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate	non-polymer		853.1	4	Chemie (9YF)
21	AC, CC, JA, WA, ZB (G, H, M, S)	(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate	non-polymer		564.7	5	Chemie (7PH)
22	DC, IC, KA, PA (H, N)	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	4	Chemie (HEM)
23	AB, BC, CB, EC, FC... (T, G, R, H, I...)	CARDIOLIPIN	non-polymer		1464.0	17	Chemie (CDL)
24	AD, GD, QB, RA (L, c, W, N)	PALMITIC ACID	non-polymer		256.4	4	Chemie (PLM)
25	FD, HD, PB, SA (b, c, W, N)	(2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate	non-polymer		595.0	4	Chemie (9XX)
26	BB, DD, JB, KB, NB... (T, X, R, Q, J...)	TRIDECANE	non-polymer		184.4	10	Chemie (TRD)
27	OC, YA (J, S)	1,2-Distearoyl-sn-glycerophosphoethanolamine	non-polymer		748.1	2	Chemie (3PE)
28	DB, EB, SC, TC (R, L)	HEME-A	non-polymer		852.8	4	Chemie (HEA)
29	BD, CD, FB, LB, MB... (X, R, Q, L)	COPPER (II) ION	non-polymer		63.5	6	Chemie (CU)
30	HB, VC (R, L)	MAGNESIUM ION	non-polymer		24.3	2	Chemie (MG)
31	IB, WC (R, L)	CALCIUM ION	non-polymer		40.1	2	Chemie (CA)
32	JC (H)	2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione	non-polymer		322.4	1	Chemie (DCQ)
33	AE, BE, CE, DE, EE... (a, b, c, F, B...)	water	water		18.0	606	Chemie (HOH)

Sequence modifications

O, C: 27 - 294 (UniProt: A0R050)

PDB	External Database	Details
Met 17	-	initiating methionine
His 18	-	expression tag
His 19	-	expression tag
His 20	-	expression tag
His 21	-	expression tag
His 22	-	expression tag
His 23	-	expression tag
Met 24	-	expression tag
Gly 25	-	expression tag
Ser 26	-	expression tag

N, H: 1 - 546 (UniProt: A0R052)

PDB	External Database	Details
Lys 547	-	expression tag
Leu 548	-	expression tag
Asp 549	-	expression tag
Tyr 550	-	expression tag
Lys 551	-	expression tag
Asp 552	-	expression tag
Asp 553	-	expression tag
Asp 554	-	expression tag
Asp 555	-	expression tag
Lys 556	-	expression tag

P, I: 18 - 100 (UniProt: A0QVH4)

PDB	External Database	Details
Met 1	-	initiating methionine
Ser 2	-	expression tag
Ser 3	-	expression tag
Thr 4	-	expression tag
Gln 5	-	expression tag
Asp 6	-	expression tag
Arg 7	-	expression tag
Ser 8	-	expression tag
Gln 9	-	expression tag
Leu 10	-	expression tag
Asp 11	-	expression tag
Pro 12	-	expression tag
Glu 13	-	expression tag
Glu 14	-	expression tag
Gln 15	-	expression tag
Pro 16	-	expression tag
Val 17	-	expression tag

R, L: 21 - 575 (UniProt: A0A2U9PNL2)

PDB	External Database	Details
Met 1	-	initiating methionine
Val 2	-	expression tag
Ala 3	-	expression tag
Glu 4	-	expression tag
Ala 5	-	expression tag
Pro 6	-	expression tag
Pro 7	-	expression tag
Ile 8	-	expression tag
Gly 9	-	expression tag
Glu 10	-	expression tag
Leu 11	-	expression tag
Glu 12	-	expression tag
Ala 13	-	expression tag
Arg 14	-	expression tag
Arg 15	-	expression tag
Pro 16	-	expression tag
Phe 17	-	expression tag
Pro 18	-	expression tag
Glu 19	-	expression tag
Arg 20	-	expression tag

E, A: 1 - 133 (UniProt: A0A653FDI6)

PDB	External Database	Details
Ala 126	Val 116	conflict

Contents of the asymmetric unit

Polymers	Number of chains	28
	Total formula weight	746339.8
Non-Polymers*	Number of molecules	84
	Total formula weight	61921.1
All*	Total formula weight	808260.9

*Water molecules are not included.