6H8K

Crystal structure of a variant (Q133C in PSST) of Yarrowia lipolytica complex I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.79 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.361 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Locking loop movement in the ubiquinone pocket of complex I disengages the proton pumps.

Cabrera-Orefice, A.Yoga, E.G.Wirth, C.Siegmund, K.Zwicker, K.Guerrero-Castillo, S.Zickermann, V.Hunte, C.Brandt, U.

(2018) Nat Commun 9: 4500-4500

  • DOI: 10.1038/s41467-018-06955-y

  • PubMed Abstract: 
  • Complex I (proton-pumping NADH:ubiquinone oxidoreductase) is the largest enzyme of the mitochondrial respiratory chain and a significant source of reactive oxygen species (ROS). We hypothesized that during energy conversion by complex I, electron tra ...

    Complex I (proton-pumping NADH:ubiquinone oxidoreductase) is the largest enzyme of the mitochondrial respiratory chain and a significant source of reactive oxygen species (ROS). We hypothesized that during energy conversion by complex I, electron transfer onto ubiquinone triggers the concerted rearrangement of three protein loops of subunits ND1, ND3, and 49-kDa thereby generating the power-stoke driving proton pumping. Here we show that fixing loop TMH1-2 ND3 to the nearby subunit PSST via a disulfide bridge introduced by site-directed mutagenesis reversibly disengages proton pumping without impairing ubiquinone reduction, inhibitor binding or the Active/Deactive transition. The X-ray structure of mutant complex I indicates that the disulfide bridge immobilizes but does not displace the tip of loop TMH1-2 ND3 . We conclude that movement of loop TMH1-2 ND3 located at the ubiquinone-binding pocket is required to drive proton pumping corroborating one of the central predictions of our model for the mechanism of energy conversion by complex I proposed earlier.


    Organizational Affiliation

    Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525, GA, Nijmegen, The Netherlands.,Institute of Biochemistry I, Medical School, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.,Institute for Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg im Breisgau, Germany.,Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525, GA, Nijmegen, The Netherlands. ulrich.brandt@radboudumc.nl.,Cluster of Excellence Macromolecular Complexes, Goethe-University, Max von Laue Str. 9, 60438, Frankfurt am Main, Germany. ulrich.brandt@radboudumc.nl.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Max von Laue Str. 9, 60438, Frankfurt am Main, Germany.,Institute of Biochemistry II, Medical School, Goethe University, Max von Laue Str. 9, 60438, Frankfurt am Main, Germany.,Cluster of Excellence Macromolecular Complexes, Goethe-University, Max von Laue Str. 9, 60438, Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 1
1
335Yarrowia lipolytica (strain CLIB 122 / E 150)Mutation(s): 0 
Gene Names: ND1
EC: 7.1.1.2
Find proteins for Q9B6E8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6E8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 2,NADH dehydrogenase subunit 2
2
434Yarrowia lipolytica (strain CLIB 122 / E 150)Mutation(s): 0 
Gene Names: ND2
EC: 7.1.1.2
Find proteins for Q9B6C8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6C8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 3
3
110Yarrowia lipolytica (strain CLIB 122 / E 150)Mutation(s): 0 
Gene Names: ND3
EC: 7.1.1.2
Find proteins for Q9B6C7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6C7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 4
4
470Yarrowia lipolytica (strain CLIB 122 / E 150)Mutation(s): 0 
Gene Names: ND4
EC: 7.1.1.2
Find proteins for Q9B6D6 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6D6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 5
5
616Yarrowia lipolytica (strain CLIB 122 / E 150)Mutation(s): 0 
Gene Names: ND5
EC: 7.1.1.2
Find proteins for Q9B6D3 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6D3
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 6
6
184Yarrowia lipolytica (strain CLIB 122 / E 150)Mutation(s): 0 
Gene Names: ND6
EC: 7.1.1.2
Find proteins for Q9B6E9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6E9
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
NUAM protein
A
634Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuam
EC: 1.6.99.3
Find proteins for Q9UUU3 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUU3
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
B
370Yarrowia lipolyticaMutation(s): 0 
Gene Names: nubm (NUO51)
EC: 1.6.99.3, 7.1.1.2
Find proteins for Q9UUU2 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUU2
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
NUCM protein
C
383Yarrowia lipolyticaMutation(s): 0 
Gene Names: nucm
EC: 1.6.99.3
Find proteins for Q9UUU1 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUU1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
NUEM protein
E
195N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
NUGM protein
G
133Yarrowia lipolyticaMutation(s): 0 
Gene Names: nugm
EC: 1.6.99.3
Find proteins for Q9UUU0 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUU0
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
H
154N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
I
140Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuim
EC: 1.6.99.3
Find proteins for Q9UUT8 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUT8
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
K
147Yarrowia lipolyticaMutation(s): 1 
Gene Names: nukm
EC: 1.6.99.3
Find proteins for Q9UUT7 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUT7
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 4L
L
79Yarrowia lipolytica (strain CLIB 122 / E 150)Mutation(s): 0 
Gene Names: ND4L
EC: 7.1.1.2
Find proteins for Q9B6D4 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6D4
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
Z, r
17N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
Y, AF
40N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
U
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
X
57N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
W
54N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
V
63N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
T, m, AI
20N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
S, AJ, AL
19N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
R
50N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
Q
70N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
P
28N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
F, f, AC, AH, AM
18N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
O, l
25N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
M
51N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
D
30N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
J
69N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
N
15N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
a, i
26N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
b
22N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
c, g, AE, AK, AO
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
d, o, AB, AN
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
e, w, z
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
h
47N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
j
48N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
k, s
23N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
n, q
36N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
p
76N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
t
45N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
u
32N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
v, y
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
x, AG
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
AA
58N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
AD
39N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B, I, K
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
A, H
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
2, 4, 5, 6, a, A, AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, b, B, c, D, d, e, E, f, F, g, G, H, h, I, i, j, J, k, l, m, M, n, N, o, O, P, p, Q, q, r, R, S, s, T, t, U, u, v, V, w, W, x, X, Y, y, Z, z
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.79 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.361 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 316.310α = 90.00
b = 316.310β = 90.00
c = 819.180γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
AutoPROCdata scaling
Cootmodel building
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
GermanyEXC 294 BIOSS
German Research FoundationGermanyZI552/4-1

Revision History 

  • Version 1.0: 2018-12-26
    Type: Initial release