8UEU

In-situ complex I, Deactive class03

  • Classification: ELECTRON TRANSPORT
  • Organism(s): Sus scrofa
  • Mutation(s): Yes 

  • Deposited: 2023-10-02 Released: 2024-06-19 
  • Deposition Author(s): Zheng, W., Zhu, J., Zhang, K.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

High-resolution in situ structures of mammalian respiratory supercomplexes.

Zheng, W.Chai, P.Zhu, J.Zhang, K.

(2024) Nature 631: 232-239

  • DOI: https://doi.org/10.1038/s41586-024-07488-9
  • Primary Citation of Related Structures:  
    8UD1, 8UEO, 8UEP, 8UEQ, 8UER, 8UES, 8UET, 8UEU, 8UEV, 8UEW, 8UEX, 8UEY, 8UEZ, 8UGD, 8UGE, 8UGF, 8UGG, 8UGH, 8UGI, 8UGJ, 8UGK, 8UGL, 8UGN, 8UGP, 8UGR

  • PubMed Abstract: 

    Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes 1-4 . Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: I 1 III 2 IV 1 , I 1 III 2 IV 2 , I 2 III 2 IV 2 and I 2 III 4 IV 2 , which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context.


  • Organizational Affiliation

    School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3A [auth 1A]115Sus scrofaMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialB [auth 1B]258Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupA0A4X1VVS8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialC [auth 1C]264Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialD [auth 1D]476Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialE [auth 1E]249Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialF [auth 1F]464Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialG [auth 1G]727Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287ARY3 (Sus scrofa)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1H [auth 1H]318Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for A0A0U1RS44 (Sus scrofa)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialI [auth 1I]239Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZUN9 (Sus scrofa)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6J [auth 1J]175Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for O79882 (Sus scrofa)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LK [auth 1K]98Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for P56632 (Sus scrofa)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5L [auth 1L]606Sus scrofaMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4M [auth 1M]459Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2N [auth 1N]347Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialO [auth 1O]357Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A9P [auth 1P]377Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialQ [auth 1Q]175Sus scrofaMutation(s): 0 
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Find proteins for A0A4X1SN37 (Sus scrofa)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialR [auth 1R]123Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1THU2 (Sus scrofa)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2S [auth 1S]99Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1FN21 (Sus scrofa)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit AB1T [auth 1T],
U [auth 1U]
156Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1KH26 (Sus scrofa)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1V [auth 1V]116Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6W [auth 1W]128Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480VKQ8 (Sus scrofa)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8X [auth 1X]172Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11Y [auth 1Y]141Sus scrofaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A13Z [auth 1Z]144Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1AA [auth 1a]70Sus scrofaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3BA [auth 1b]84Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialCA [auth 1c]76Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2DA [auth 1d]123Sus scrofaMutation(s): 1 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5EA [auth 1e]106Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 [Sus scrofa]FA [auth 1f]135Sus scrofaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialGA [auth 1g]154Sus scrofaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialHA [auth 1h]189Sus scrofaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6IA [auth 1i]128Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B2JA [auth 1j]105Sus scrofaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3KA [auth 1k]98Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialLA [auth 1l]186Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4MA [auth 1m]129Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9NA [auth 1n]179Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7OA [auth 1o]137Sus scrofaMutation(s): 0 
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UniProt GroupF1SCH1
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10PA [auth 1p]176Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D0R7A9 (Sus scrofa)
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UniProt GroupA0A8D0R7A9
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12QA [auth 1q]145Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SQP4 (Sus scrofa)
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UniProt GroupF1SQP4
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7RA [auth 1r]114Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8W4F7N8 (Sus scrofa)
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UniProt GroupA0A8W4F7N8
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialSA [auth 1s]471Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TE42 (Sus scrofa)
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UniProt GroupA0A4X1TE42
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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LB [auth 1N],
XB [auth 1r]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
Query on PC1

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CB [auth 1H],
FB [auth 1I],
JB [auth 1M],
TA [auth 1A],
UB [auth 1g]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
PGT
Query on PGT

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IB [auth 1M](1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
3PE
Query on 3PE

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GB [auth 1L]
HB [auth 1L]
KB [auth 1N]
RB [auth 1Y]
SB [auth 1Y]
GB [auth 1L],
HB [auth 1L],
KB [auth 1N],
RB [auth 1Y],
SB [auth 1Y],
TB [auth 1b]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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OB [auth 1P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
EHZ
Query on EHZ

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QB [auth 1W],
WB [auth 1n]
~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate
C25 H49 N2 O9 P S
JYSKQPQRUCZFIQ-REWPJTCUSA-N
GTP
Query on GTP

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MB [auth 1O]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
FMN
Query on FMN

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WA [auth 1F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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DB [auth 1I]
EB [auth 1I]
UA [auth 1B]
XA [auth 1F]
YA [auth 1G]
DB [auth 1I],
EB [auth 1I],
UA [auth 1B],
XA [auth 1F],
YA [auth 1G],
ZA [auth 1G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MYR
Query on MYR

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VB [auth 1l]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
FES
Query on FES

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AB [auth 1G],
VA [auth 1E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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PB [auth 1R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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BB [auth 1G]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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NB [auth 1O]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A [auth 1A]L-PEPTIDE LINKINGC6 H11 N O3 SMET
SAC
Query on SAC
IA [auth 1i]L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM142959

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-07-17
    Changes: Data collection, Database references