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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 11335Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Find proteins for Q9B6E8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 2,NADH dehydrogenase subunit 22434Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Find proteins for Q9B6C8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 33110Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Find proteins for Q9B6C7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 44470Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Find proteins for Q9B6D6 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 55616Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Find proteins for Q9B6D3 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 66184Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Find proteins for Q9B6E9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
NUAM proteinA634Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuam
EC: 1.6.99.3
Find proteins for Q9UUU3 (Yarrowia lipolytica)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialB370Yarrowia 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)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
NUCM proteinC383Yarrowia lipolyticaMutation(s): 0 
Gene Names: nucmB0I71DRAFT_131656YALI1_F22993g
EC: 1.6.99.3
Find proteins for Q9UUU1 (Yarrowia lipolytica)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
NUEM proteinE195Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
NUGM proteinG133Yarrowia lipolyticaMutation(s): 0 
Gene Names: nugm
EC: 1.6.99.3
Find proteins for Q9UUU0 (Yarrowia lipolytica)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)H154Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)I140Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuim
EC: 1.6.99.3
Find proteins for Q9UUT8 (Yarrowia lipolytica)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I)K147Yarrowia lipolyticaMutation(s): 1 
Gene Names: nukmB0I71DRAFT_136033YALI1_F09003g
EC: 1.6.99.3
Find proteins for Q9UUT7 (Yarrowia lipolytica)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 4LL79Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Find proteins for Q9B6D4 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideZ, r17Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideAF, Y40Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideU10Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideX57Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideW54Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideV63Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideAI, T, m20Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideAJ, AL, S19Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideR50Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideQ70Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideP28Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideAC, AH, AM, F, f18Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideO, l25Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideM51Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideD30Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideJ69Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideN15Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptidea, i26Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideb22Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideAE, AK, AO, c, g9Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideAB, AN, d, o16Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptidee, w, z13Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideh47Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptidej48Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptidek, s23Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptiden, q36Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptidep76Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptidet45Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideu32Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptidev, y11Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideAG, x8Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideAA58Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Unknown polypeptideAD39Yarrowia lipolyticaMutation(s): 0 
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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

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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