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 
  • R-Value Observed: 0.361 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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

    Cluster of Excellence Macromolecular Complexes, Goethe-University, Max von Laue Str. 9, 60438, Frankfurt am Main, Germany. ulrich.brandt@radboudumc.nl.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 1
1
335Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Find proteins for Q9B6E8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6E8

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 2,NADH dehydrogenase subunit 2
2
434Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Find proteins for Q9B6C8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6C8

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 3
3
110Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Find proteins for Q9B6C7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6C7

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 4
4
470Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Find proteins for Q9B6D6 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6D6

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 5
5
616Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Find proteins for Q9B6D3 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6D3

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 6
6
184Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Find proteins for Q9B6E9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6E9

Find similar proteins by: Sequence  |  Structure

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

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
B
370Yarrowia lipolyticaMutation(s): 0 
Gene Names: nubm
EC: 1.6.99.3 (PDB Primary Data), 7.1.1.2 (PDB Primary Data)
Find proteins for Q9UUU2 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUU2

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
NUCM protein
C
383Yarrowia lipolyticaMutation(s): 0 
Gene Names: nucmB0I71DRAFT_131656YALI1_F22993g
EC: 1.6.99.3
Find proteins for Q9UUU1 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUU1

Find similar proteins by: Sequence  |  Structure

Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
NUEM protein
E
195Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

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

Find similar proteins by: Sequence  |  Structure

Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
H
154Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

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

Find similar proteins by: Sequence  |  Structure

Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
K
147Yarrowia lipolyticaMutation(s): 1 
Gene Names: nukmB0I71DRAFT_136033YALI1_F09003g
EC: 1.6.99.3
Find proteins for Q9UUT7 (Yarrowia lipolytica)
Go to UniProtKB:  Q9UUT7

Find similar proteins by: Sequence  |  Structure

Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 4L
L
79Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Find proteins for Q9B6D4 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Go to UniProtKB:  Q9B6D4
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
Z, r
17Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
AF, Y
40Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
U
10Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
X
57Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
W
54Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
V
63Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
AI, T, m
20Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
AJ, AL, S
19Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
R
50Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
Q
70Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
P
28Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
AC, AH, AM, F, f
18Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
O, l
25Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
M
51Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
D
30Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
J
69Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
N
15Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
a, i
26Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
b
22Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
AE, AK, AO, c, g
9Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
AB, AN, d, o
16Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
e, w, z
13Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
h
47Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
j
48Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
k, s
23Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
n, q
36Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
p
76Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
t
45Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
u
32Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
v, y
11Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
AG, x
8Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
AA
58Yarrowia lipolyticaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptide
AD
39Yarrowia lipolyticaMutation(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 CCD File 
A, B, I, K
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

Download CCD File 
A, H
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.79 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.361 
  • R-Value Observed: 0.361 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 316.31α = 90
b = 316.31β = 90
c = 819.18γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
AutoPROCdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



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