5J8K

Architecture of supercomplex I-III2

• PDB DOI: https://doi.org/10.2210/pdb5J8K/pdb
• EM Map EMD-8129: EMDB EMDataResource

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


• Deposited: 2016-04-08 Released: 2016-09-21 
• Deposition Author(s): Letts, J.A., Fiedorczuk, K., Sazanov, L.A.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The architecture of respiratory supercomplexes.

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

(2016) Nature 537: 644-648

• PubMed: 27654913 
• 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 ₂ CIV (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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 76-mer - A13B11C8D6E6F3G2H2I2J2K2L2M2N2O2P2Q2R2S2T2U1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 76-mer - AA5AB4AC3AD2AE2AF2AG2AH2AI2AJ2AK2AL2AM2AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1BB1BC1BD1BE1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - H2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - I2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - O2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - Q2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - R2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 16-mer - J2K2L2M2N2P2S2T2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1,080.95 kDa 
• Atom Count: 55,850 
• Modelled Residue Count: 11,157 
• Deposited Residue Count: 11,289 
• Unique protein chains: 61

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ND3	A	102	Ovis aries	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I PSST/NDUFS7	B	154	Ovis aries	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 30KDA/NDUFS3	C	194	Ovis aries	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 49KDA/NDUFS2	D	384	Ovis aries	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 24KDA/NDUFV2	E	189	Ovis aries	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 51KDA/NDUFV1	F	429	Ovis aries	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 75KDA/NDUFS1	G	652	Ovis aries	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ND1	H	297	Ovis aries	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I TYKY/NDUFS8	I	171	Ovis aries	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ND6	J	171	Ovis aries	Mutation(s): 0

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ND4L	K	93	Ovis aries	Mutation(s): 0

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ND5	L	575	Ovis aries	Mutation(s): 0

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ND4	M	455	Ovis aries	Mutation(s): 0

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ND2	N	345	Ovis aries	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 18KDA/NDUFS6	O	104	Ovis aries	Mutation(s): 0

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 13KDA/NDUFS6	P	85	Ovis aries	Mutation(s): 0

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 15KDA/NDUFS5	Q	66	Ovis aries	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I MWFE/NDUFA1	R	29	Ovis aries	Mutation(s): 0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B8/NDUFA2	DA [auth d], S	80	Ovis aries	Mutation(s): 0

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B9/NDUFA3	T	53	Ovis aries	Mutation(s): 0

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B13/NDUFA5	U	96	Ovis aries	Mutation(s): 0

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B14/NDUFA6	V	112	Ovis aries	Mutation(s): 0

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I PGIV/NDUFA8	W	103	Ovis aries	Mutation(s): 0

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 39KDA/NDUFA9	X	309	Ovis aries	Mutation(s): 0

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I 42KDA/NDUFA10	Y	322	Ovis aries	Mutation(s): 0

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B14.7/NDUFA11	Z	119	Ovis aries	Mutation(s): 0

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B17.2/NDUFA12	AA [auth a]	111	Ovis aries	Mutation(s): 0

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B16.6/NDUFA13	BA [auth b]	92	Ovis aries	Mutation(s): 0

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I SDAP/NDUFAB1	CA [auth c]	79	Ovis aries	Mutation(s): 0

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B15/NDUFB4	EA [auth e]	55	Ovis aries	Mutation(s): 0

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B18/NDUFB7	FA [auth f]	59	Ovis aries	Mutation(s): 0

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B22/NDUFB9	GA [auth g]	130	Ovis aries	Mutation(s): 0

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I PDSW/NDUFB10	HA [auth h], UA [auth 9], VA [auth z]	63	Ovis aries	Mutation(s): 0

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I ESSS/NDUFB11	IA [auth i]	70	Ovis aries	Mutation(s): 0

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I KFYI/NDUFC1	JA [auth j]	44	Ovis aries	Mutation(s): 0

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I B14.5B/NDUFC2	KA [auth k]	83	Ovis aries	Mutation(s): 0

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 1	LA [auth 0]	36	Ovis aries	Mutation(s): 0

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 2	MA [auth 1]	30	Ovis aries	Mutation(s): 0

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 3	NA [auth 2]	38	Ovis aries	Mutation(s): 0

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 4	OA [auth 3], PA [auth 4]	28	Ovis aries	Mutation(s): 0

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 5	QA [auth 5]	34	Ovis aries	Mutation(s): 0

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 6	RA [auth 6]	21	Ovis aries	Mutation(s): 0

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 7	SA [auth 7]	39	Ovis aries	Mutation(s): 0

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 8	TA [auth 8]	27	Ovis aries	Mutation(s): 0

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

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

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

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

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

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

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
UniProt
Find proteins for W5Q5G6 (Ovis aries) Explore W5Q5G6  Go to UniProtKB:  W5Q5G6

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

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
UniProt
Find proteins for P24959 (Ovis aries) Explore P24959  Go to UniProtKB:  P24959

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

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

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
UniProt
Find proteins for W5P642 (Ovis aries) Explore W5P642  Go to UniProtKB:  W5P642

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
UniProt
Find proteins for W5PUP9 (Ovis aries) Explore W5PUP9  Go to UniProtKB:  W5PUP9

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

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

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

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	GC [auth AC], HC [auth AC], IC [auth AD], KC [auth AN], LC [auth AN], MC [auth AO]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SF4	AC [auth F], BC [auth G], CC [auth G], EC [auth I], FC [auth I], YB [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
FES	DC [auth G], JC [auth AE], NC [auth AP], ZB [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	1.4
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Letts, J.A., Fiedorczuk, K., Sazanov, L.A.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MC_U105674180

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2016-10-05
  Changes: Database references
• Version 1.2: 2017-08-02
  Changes: Data collection, Experimental preparation, Structure summary
• Version 1.3: 2019-12-11
  Changes: Advisory, Other