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


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
  • Primary Citation of Related Structures:  
    6H8K

  • 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 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 ...

    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 LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1A [auth 1]335Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6E8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2,NADH dehydrogenase subunit 2B [auth 2]434Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6C8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3C [auth 3]110Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6C7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4D [auth 4]470Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6D6 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5E [auth 5]616Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6D3 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6F [auth 6]184Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NUAM proteinG [auth A]634Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuam
EC: 1.6.99.3
UniProt
Find proteins for Q9UUU3 (Yarrowia lipolytica)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialH [auth B]370Yarrowia lipolyticaMutation(s): 0 
Gene Names: nubm
EC: 1.6.99.3 (PDB Primary Data), 7.1.1.2 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for Q9UUU2 (Yarrowia lipolytica)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NUCM proteinI [auth C]383Yarrowia lipolyticaMutation(s): 0 
Gene Names: nucmB0I71DRAFT_131656YALI1_F22993g
EC: 1.6.99.3
UniProt
Find proteins for Q9UUU1 (Yarrowia lipolytica)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NUEM proteinJ [auth E]195Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NUGM proteinK [auth G]133Yarrowia lipolyticaMutation(s): 0 
Gene Names: nugm
EC: 1.6.99.3
UniProt
Find proteins for Q9UUU0 (Yarrowia lipolytica)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)L [auth H]154Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)M [auth I]140Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuim
EC: 1.6.99.3
UniProt
Find proteins for Q9UUT8 (Yarrowia lipolytica)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I)N [auth K]147Yarrowia lipolyticaMutation(s): 1 
Gene Names: nukmB0I71DRAFT_136033YALI1_F09003g
EC: 1.6.99.3
UniProt
Find proteins for Q9UUT7 (Yarrowia lipolytica)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LO [auth L]79Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6D4 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideP [auth Z], XA [auth r]17Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideLB [auth AF], Q [auth Y]40Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideR [auth U]10Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideS [auth X]57Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideT [auth W]54Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideU [auth V]63Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideOB [auth AI], V [auth T], SA [auth m]20Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptidePB [auth AJ], RB [auth AL], W [auth S]19Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideX [auth R]50Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideY [auth Q]70Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideZ [auth P]28Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideIB [auth AC], NB [auth AH], SB [auth AM], AA [auth F], LA [auth f]18Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideBA [auth O], RA [auth l]25Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideCA [auth M]51Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideDA [auth D]30Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideEA [auth J]69Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideFA [auth N]15Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideGA [auth a], OA [auth i]26Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideHA [auth b]22Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideKB [auth AE], QB [auth AK], UB [auth AO], IA [auth c], MA [auth g]9Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideHB [auth AB], TB [auth AN], JA [auth d], UA [auth o]16Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideKA [auth e], CB [auth w], FB [auth z]13Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideNA [auth h]47Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptidePA [auth j]48Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideQA [auth k], YA [auth s]23Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideTA [auth n], WA [auth q]36Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideVA [auth p]76Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideZA [auth t]45Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideAB [auth u]32Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideBB [auth v], EB [auth y]11Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideMB [auth AG], DB [auth x]8Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideGB [auth AA]58Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown polypeptideJB [auth AD]39Yarrowia lipolyticaMutation(s): 0 
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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 
  • 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  (Full details and data files)

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