8ESW

Structure of mitochondrial complex I from Drosophila melanogaster, Flexible-class 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Resting mitochondrial complex I from Drosophila melanogaster adopts a helix-locked state.

Padavannil, A.Murari, A.Rhooms, S.K.Owusu-Ansah, E.Letts, J.A.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.84415
  • Primary Citation of Related Structures:  
    8ESW, 8ESZ

  • PubMed Abstract: 

    Respiratory complex I is a proton-pumping oxidoreductase key to bioenergetic metabolism. Biochemical studies have found a divide in the behavior of complex I in metazoans that aligns with the evolutionary split between Protostomia and Deuterostomia. Complex I from Deuterostomia including mammals can adopt a biochemically defined off-pathway 'deactive' state, whereas complex I from Protostomia cannot. The presence of off-pathway states complicates the interpretation of structural results and has led to considerable mechanistic debate. Here, we report the structure of mitochondrial complex I from the thoracic muscles of the model protostome Drosophila melanogaster . We show that although D. melanogaster complex I ( Dm -CI) does not have a NEM-sensitive deactive state, it does show slow activation kinetics indicative of an off-pathway resting state. The resting-state structure of Dm -CI from the thoracic muscle reveals multiple conformations. We identify a helix-locked state in which an N-terminal α-helix on the NDUFS4 subunit wedges between the peripheral and membrane arms. Comparison of the Dm -CI structure and conformational states to those observed in bacteria, yeast, and mammals provides insight into the roles of subunits across organisms, explains why the Dm -CI off-pathway resting state is NEM insensitive, and raises questions regarding current mechanistic models of complex I turnover.


  • Organizational Affiliation

    Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12A [auth AN]142Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialB [auth S6]126Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9VMU0 (Drosophila melanogaster)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialC [auth S1]731Drosophila melanogasterMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialD [auth S3]265Drosophila melanogasterMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform AE [auth V2]242Drosophila melanogasterMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
LD31474pF [auth S7]221Drosophila melanogasterMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase (ubiquinone) 23 kDa subunitG [auth S8]217Drosophila melanogasterMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3H [auth 3]117Drosophila melanogasterMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1I [auth 1]315Drosophila melanogasterMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4J [auth 4]446Drosophila melanogasterMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5K [auth 5]577Drosophila melanogasterMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8L [auth A8]175Drosophila melanogasterMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1M [auth A1]123Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13N [auth AO]154Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5O [auth S5]101Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11P [auth AM]170Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10Q [auth BL]159Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6R [auth B6]167Drosophila melanogasterMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4S [auth B4]113Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7T [auth B7]117Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialU [auth B5]186Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9V [auth B9]144Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialW [auth BM]150Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialX [auth B8]175Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3Y [auth B3]110Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialQA [auth AB],
Z [auth AC]
152Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2AA [auth C2]116Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1BA [auth B1]56Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialCA [auth S4]183Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform ADA [auth A9]416Drosophila melanogasterMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
GEO11417p1EA [auth B2]94Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-49kDFA [auth S2]468Drosophila melanogasterMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3GA [auth V3]27Drosophila melanogasterMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialHA [auth V1]474Drosophila melanogasterMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2IA [auth 2]341Drosophila melanogasterMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LJA [auth 4L]96Drosophila melanogasterMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6KA [auth 6]174Drosophila melanogasterMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7LA [auth A7]103Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase (Ubiquinone) 13 kDa B subunitMA [auth A5]124Drosophila melanogasterMutation(s): 0 
EC: 1.6.99.3
Membrane Entity: Yes 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
RH45008pNA [auth A3]77Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6OA [auth A6]124Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialPA [auth AL]407Drosophila melanogasterMutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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DC [auth A9]
EC [auth A9]
LB [auth 5]
PB [auth 5]
RA [auth AN]
DC [auth A9],
EC [auth A9],
LB [auth 5],
PB [auth 5],
RA [auth AN],
XB [auth B6],
YA [auth S7],
ZB [auth B5]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
Query on PC1

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AB [auth S7]
BC [auth C2]
DB [auth 1]
EB [auth 4]
FB [auth 4]
AB [auth S7],
BC [auth C2],
DB [auth 1],
EB [auth 4],
FB [auth 4],
IC [auth 2],
JC [auth 2],
KC [auth 6],
LC [auth 6],
RB [auth AM],
UB [auth AM],
VB [auth B6],
YB [auth B4],
ZA [auth S7]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

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GB [auth 4]
HB [auth 4]
HC [auth 2]
IB [auth 5]
JB [auth 5]
GB [auth 4],
HB [auth 4],
HC [auth 2],
IB [auth 5],
JB [auth 5],
KB [auth 5],
MB [auth 5],
NB [auth 5],
OB [auth 5],
QB [auth AM],
SB [auth AM],
TB [auth AM],
WB [auth B6]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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CC [auth A9]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
ZMP
Query on ZMP

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AC [auth B9],
NC [auth AB]
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
C25 H49 N2 O8 P S
HDTINWYIVVMRIN-HSZRJFAPSA-N
DGT
Query on DGT

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MC [auth AL]2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
FMN
Query on FMN

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FC [auth V1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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BB [auth S8]
CB [auth S8]
GC [auth V1]
TA [auth S1]
UA [auth S1]
BB [auth S8],
CB [auth S8],
GC [auth V1],
TA [auth S1],
UA [auth S1],
XA [auth S7]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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VA [auth S1],
WA [auth V2]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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SA [auth S6]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesGM137929

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references