5J7Y

Architecture of loose respirasome

PDB DOI: https://doi.org/10.2210/pdb5J7Y/pdb
EM Map EMD-8128: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Ovis aries
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2016-04-07 Released: 2016-09-21
Deposition Author(s): Letts, J.A., Fiedorczuk, F., Sazanov, L.A.
Funding Organization(s): Medical Research Council (United Kingdom)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The architecture of respiratory supercomplexes.

Letts, J.A., Fiedorczuk, K., Sazanov, L.A.

(2016) Nature 537: 644-648

PubMed: 27654913 Search on PubMed
DOI: https://doi.org/10.1038/nature19774
Primary Citation of Related Structures:
5J4Z, 5J7Y, 5J8K

PubMed Abstract:
Mitochondrial electron transport chain complexes are organized into supercomplexes responsible for carrying out cellular respiration. Here we present three architectures of mammalian (ovine) supercomplexes determined by cryo-electron microscopy. We identify two distinct arrangements of supercomplex CICIII ₂CIV (the respirasome)-a major 'tight' form and a minor 'loose' form (resolved at the resolution of 5.8 Å and 6.7 Å, respectively), which may represent different stages in supercomplex assembly or disassembly. We have also determined an architecture of supercomplex CICIII ₂ at 7.8 Å resolution. All observed density can be attributed to the known 80 subunits of the individual complexes, including 132 transmembrane helices. The individual complexes form tight interactions that vary between the architectures, with complex IV subunit COX7a switching contact from complex III to complex I. The arrangement of active sites within the supercomplex may help control reactive oxygen species production. To our knowledge, these are the first complete architectures of the dominant, physiologically relevant state of the electron transport chain.

Organizational Affiliation

Institute of Science and Technology Austria, Klosterneuburg 3400, Austria.

Macromolecule Content

Total Structure Weight: 1,284.76 kDa
Atom Count: 64,743
Modelled Residue Count: 12,936
Deposited Residue Count: 13,068
Unique protein chains: 74

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ND3	A	102	Ovis aries	Mutation(s): 0
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I PSST/NDUFS7	B	154	Ovis aries	Mutation(s): 0
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 30KDA/NDUFS3	C	194	Ovis aries	Mutation(s): 0
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 49KDA/NDUFS2	D	384	Ovis aries	Mutation(s): 0
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 24KDA/NDUFV2	E	189	Ovis aries	Mutation(s): 0
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 51KDA/NDUFV1	F	429	Ovis aries	Mutation(s): 0
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 75KDA/NDUFS1	G	652	Ovis aries	Mutation(s): 0
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ND1	H	297	Ovis aries	Mutation(s): 0
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I TYKY/NDUFS8	I	171	Ovis aries	Mutation(s): 0
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ND6	J	171	Ovis aries	Mutation(s): 0
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ND4L	K	93	Ovis aries	Mutation(s): 0
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ND5	L	575	Ovis aries	Mutation(s): 0
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ND4	M	455	Ovis aries	Mutation(s): 0
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ND2	N	345	Ovis aries	Mutation(s): 0
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 18KDA/NDUFS6	O	104	Ovis aries	Mutation(s): 0
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 13KDA/NDUFS6	P	85	Ovis aries	Mutation(s): 0
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 15KDA/NDUFS5	Q	66	Ovis aries	Mutation(s): 0
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I MWFE/NDUFA1	R	29	Ovis aries	Mutation(s): 0
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B8/NDUFA2	DA [auth d], S	80	Ovis aries	Mutation(s): 0
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B9/NDUFA3	T	53	Ovis aries	Mutation(s): 0
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B13/NDUFA5	U	96	Ovis aries	Mutation(s): 0
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B14/NDUFA6	V	112	Ovis aries	Mutation(s): 0
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I PGIV/NDUFA8	W	103	Ovis aries	Mutation(s): 0
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 39KDA/NDUFA9	X	309	Ovis aries	Mutation(s): 0
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 42KDA/NDUFA10	Y	322	Ovis aries	Mutation(s): 0
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B14.7/NDUFA11	Z	119	Ovis aries	Mutation(s): 0
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B17.2/NDUFA12	AA [auth a]	111	Ovis aries	Mutation(s): 0
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B16.6/NDUFA13	BA [auth b]	92	Ovis aries	Mutation(s): 0
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I SDAP/NDUFAB1	CA [auth c]	79	Ovis aries	Mutation(s): 0
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I SDAP/NDUFAB1	EA [auth e]	55	Ovis aries	Mutation(s): 0
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I SDAP/NDUFAB1	FA [auth f]	59	Ovis aries	Mutation(s): 0
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B15/NDUFB4	GA [auth g]	130	Ovis aries	Mutation(s): 0
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B18/NDUFB7	HA [auth h], UA [auth 9], VA [auth z]	63	Ovis aries	Mutation(s): 0
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B22/NDUFB9	IA [auth i]	70	Ovis aries	Mutation(s): 0
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I PDSW/NDUFB10	JA [auth j]	44	Ovis aries	Mutation(s): 0
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ESSS/NDUFB11	KA [auth k]	83	Ovis aries	Mutation(s): 0
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I KFYI/NDUFC1	LA [auth 0]	36	Ovis aries	Mutation(s): 0
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B14.5B/NDUFC2	MA [auth 1]	30	Ovis aries	Mutation(s): 0
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 1	NA [auth 2]	38	Ovis aries	Mutation(s): 0
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 2	OA [auth 3], PA [auth 4]	28	Ovis aries	Mutation(s): 0
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 3	QA [auth 5]	34	Ovis aries	Mutation(s): 0
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 4	RA [auth 6]	21	Ovis aries	Mutation(s): 0
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 5	SA [auth 7]	39	Ovis aries	Mutation(s): 0
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 6	TA [auth 8]	27	Ovis aries	Mutation(s): 0
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 11	WA [auth y]	46	Ovis aries	Mutation(s): 0
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 12	XA [auth x]	13	Ovis aries	Mutation(s): 0
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 13	YA [auth w]	24	Ovis aries	Mutation(s): 0
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 14	ZA [auth v]	18	Ovis aries	Mutation(s): 0
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 15	AB [auth u]	16	Ovis aries	Mutation(s): 0
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 16	BB [auth t]	12	Ovis aries	Mutation(s): 0
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX III SUBUNIT 1 / CORE 1	CB [auth AA], NB [auth AL]	446	Ovis aries	Mutation(s): 0
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UniProt Group	W5Q5G6
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX III SUBUNIT 2 / CORE 2	DB [auth AB], OB [auth AM]	423	Ovis aries	Mutation(s): 0
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	EB [auth AC], PB [auth AN]	378	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
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UniProt Group	P24959
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX III SUBUNIT 4 / CYTOCHROME C1	FB [auth AD], QB [auth AO]	241	Ovis aries	Mutation(s): 0
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	GB [auth AE], RB [auth AP]	196	Ovis aries	Mutation(s): 0 EC: 1.10.2.2
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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX III SUBUNIT 7 / 14KDA	HB [auth AF], SB [auth AQ]	105	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
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Find proteins for W5P642 (Ovis aries) Explore W5P642 Go to UniProtKB: W5P642
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UniProt Group	W5P642
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX III SUBUNIT 8 / QP-C	IB [auth AG], TB [auth AR]	75	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
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UniProt Group	W5PUP9
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Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 6	JB [auth AH], UB [auth AS]	67	Ovis aries	Mutation(s): 0
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Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	KB [auth AI], VB [auth AT]	57	Ovis aries	Mutation(s): 0 EC: 1.10.2.2
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Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX III SUBUNIT 9 / 7.2KDA	LB [auth AJ], WB [auth AU]	60	Ovis aries	Mutation(s): 0
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Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX III SUBUNIT 10 / 6.4KDA	MB [auth AK], XB [auth AV]	51	Ovis aries	Mutation(s): 0
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Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	YB [auth BN]	514	Ovis aries	Mutation(s): 0 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for O78749 (Ovis aries) Explore O78749 Go to UniProtKB: O78749
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O78749
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Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	ZB [auth BO]	227	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
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Find proteins for O78750 (Ovis aries) Explore O78750 Go to UniProtKB: O78750
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UniProt Group	O78750
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Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	AC [auth BC]	259	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
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UniProt Group	O21619
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Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX IV COX4	BC [auth BD]	144	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
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Find proteins for W5PPE8 (Ovis aries) Explore W5PPE8 Go to UniProtKB: W5PPE8
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UniProt Group	W5PPE8
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Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX IV COX5A	CC [auth BE]	105	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
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Find proteins for W5NXT8 (Ovis aries) Explore W5NXT8 Go to UniProtKB: W5NXT8
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UniProt Group	W5NXT8
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Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX IV COX5B	DC [auth BP]	98	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for W5PW27 (Ovis aries) Explore W5PW27 Go to UniProtKB: W5PW27
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UniProt Group	W5PW27
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Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6A, mitochondrial	EC [auth BG]	84	Ovis aries	Mutation(s): 0
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Entity ID: 69
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX IV COX6B1	FC [auth BH]	79	Ovis aries	Mutation(s): 0
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Entity ID: 70
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX IV COX6C	GC [auth BI]	73	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
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Find proteins for W5PXG3 (Ovis aries) Explore W5PXG3 Go to UniProtKB: W5PXG3
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UniProt Group	W5PXG3
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Entity ID: 71
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7A1, mitochondrial	HC [auth BJ]	58	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
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Find proteins for W5P5H0 (Ovis aries) Explore W5P5H0 Go to UniProtKB: W5P5H0
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UniProt Group	W5P5H0
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Entity ID: 72
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX IV COX7B	IC [auth BK]	49	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
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Find proteins for W5QE72 (Ovis aries) Explore W5QE72 Go to UniProtKB: W5QE72
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UniProt Group	W5QE72
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 73
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX IV COX7C	JC [auth BL]	46	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A6P7E5B2 (Ovis aries) Explore A0A6P7E5B2 Go to UniProtKB: A0A6P7E5B2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6P7E5B2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 74
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX IV COX8B	KC [auth BM]	43	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for W5PFK9 (Ovis aries) Explore W5PFK9 Go to UniProtKB: W5PFK9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W5PFK9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEA Query on HEA Download Ideal Coordinates CCD File SDF format, chain CD [auth BN] SDF format, chain DD [auth BN] MOL2 format, chain CD [auth BN] MOL2 format, chain DD [auth BN]	CD [auth BN], DD [auth BN]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain CD [auth BN] Focus chain DD [auth BN] Interactions & Density Focus chain CD [auth BN] Focus chain DD [auth BN]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain TC [auth AC] SDF format, chain UC [auth AC] SDF format, chain VC [auth AD] SDF format, chain XC [auth AN] SDF format, chain YC [auth AN] SDF format, chain ZC [auth AO] MOL2 format, chain TC [auth AC] MOL2 format, chain UC [auth AC] MOL2 format, chain VC [auth AD] MOL2 format, chain XC [auth AN] MOL2 format, chain YC [auth AN] MOL2 format, chain ZC [auth AO]	TC [auth AC] UC [auth AC] VC [auth AD] XC [auth AN] YC [auth AN] TC [auth AC], UC [auth AC], VC [auth AD], XC [auth AN], YC [auth AN], ZC [auth AO]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain TC [auth AC] Focus chain UC [auth AC] Focus chain VC [auth AD] Focus chain XC [auth AN] Focus chain YC [auth AN] Focus chain ZC [auth AO] Interactions & Density Focus chain TC [auth AC] Focus chain UC [auth AC] Focus chain VC [auth AD] Focus chain XC [auth AN] Focus chain YC [auth AN] Focus chain ZC [auth AO]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain LC [auth B] SDF format, chain NC [auth F] SDF format, chain OC [auth G] SDF format, chain PC [auth G] SDF format, chain RC [auth I] SDF format, chain SC [auth I] MOL2 format, chain LC [auth B] MOL2 format, chain NC [auth F] MOL2 format, chain OC [auth G] MOL2 format, chain PC [auth G] MOL2 format, chain RC [auth I] MOL2 format, chain SC [auth I]	LC [auth B] NC [auth F] OC [auth G] PC [auth G] RC [auth I] LC [auth B], NC [auth F], OC [auth G], PC [auth G], RC [auth I], SC [auth I]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain LC [auth B] Focus chain NC [auth F] Focus chain OC [auth G] Focus chain PC [auth G] Focus chain RC [auth I] Focus chain SC [auth I] Interactions & Density Focus chain LC [auth B] Focus chain NC [auth F] Focus chain OC [auth G] Focus chain PC [auth G] Focus chain RC [auth I] Focus chain SC [auth I]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain AD [auth AP] SDF format, chain MC [auth E] SDF format, chain QC [auth G] SDF format, chain WC [auth AE] MOL2 format, chain AD [auth AP] MOL2 format, chain MC [auth E] MOL2 format, chain QC [auth G] MOL2 format, chain WC [auth AE]	AD [auth AP], MC [auth E], QC [auth G], WC [auth AE]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain AD [auth AP] Focus chain MC [auth E] Focus chain QC [auth G] Focus chain WC [auth AE] Interactions & Density Focus chain AD [auth AP] Focus chain MC [auth E] Focus chain QC [auth G] Focus chain WC [auth AE]
CUA Query on CUA Download Ideal Coordinates CCD File SDF format, chain ED [auth BO] MOL2 format, chain ED [auth BO]	ED [auth BO]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain ED [auth BO] Interactions & Density Focus chain ED [auth BO]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain BD [auth BN] MOL2 format, chain BD [auth BN]	BD [auth BN]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain BD [auth BN] Interactions & Density Focus chain BD [auth BN]