4WZ7

Crystal structure of mitochondrial NADH:ubiquinone oxidoreductase from Yarrowia lipolytica.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.316 
  • R-Value Observed: 0.317 

wwPDB Validation 3D Report Full Report



Literature

Structural biology. Mechanistic insight from the crystal structure of mitochondrial complex I.

Zickermann, V.Wirth, C.Nasiri, H.Siegmund, K.Schwalbe, H.Hunte, C.Brandt, U.

(2015) Science 347: 44-49

  • DOI: 10.1126/science.1259859
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Proton-pumping complex I of the mitochondrial respiratory chain is among the largest and most complicated membrane protein complexes. The enzyme contributes substantially to oxidative energy conversion in eukaryotic cells. Its malfunctions are implic ...

    Proton-pumping complex I of the mitochondrial respiratory chain is among the largest and most complicated membrane protein complexes. The enzyme contributes substantially to oxidative energy conversion in eukaryotic cells. Its malfunctions are implicated in many hereditary and degenerative disorders. We report the x-ray structure of mitochondrial complex I at a resolution of 3.6 to 3.9 angstroms, describing in detail the central subunits that execute the bioenergetic function. A continuous axis of basic and acidic residues running centrally through the membrane arm connects the ubiquinone reduction site in the hydrophilic arm to four putative proton-pumping units. The binding position for a substrate analogous inhibitor and blockage of the predicted ubiquinone binding site provide a model for the "deactive" form of the enzyme. The proposed transition into the active form is based on a concerted structural rearrangement at the ubiquinone reduction site, providing support for a two-state stabilization-change mechanism of proton pumping.


    Organizational Affiliation

    Cluster of Excellence Frankfurt "Macromolecular Complexes," Goethe-University, 60438 Frankfurt am Main, Germany. Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Center, 6525 GA Nijmegen, Netherlands. zickermann@med.uni-frankfurt.de carola.hunte@biochemie.uni-freiburg.de ulrich.brandt@radboudumc.nl.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 11327Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
39-kDa subunitE195Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
NUGM proteinG133Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Subunit NUHM of protein NADH:Ubiquinone Oxidoreductase (Complex I)H154Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I)I137Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I)K183Yarrowia lipolyticaMutation(s): 0 
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 4LL89Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for Q9B6D4 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
unknown subunits 1D, Z57Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
unknown subunits 2F54Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsJ63Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsM29Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase subunit 22438Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsN50Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsO70Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsP46Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsQ51Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsR30Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsS69Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAH, T15Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsU26Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsV22Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAB, AY, BE, W9Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 3389Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAJ, AV, BH, X16Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAR, AT, Y13Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAA, AW, BB, BG18Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAC, AD47Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAE48Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAF35Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAG25Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAI, AL36Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAK, AN76Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAM17Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 44470Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAO32Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAP, AS11Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAQ, BA8Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAU58Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAX39Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsAZ40Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsBC20Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsBD, BF19Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
unknown subunitsBI905Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 55619Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 66185Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for Q9B6E9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q9B6E9 
Go to UniProtKB:  Q9B6E9
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
NUAM proteinA628Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
NUBM proteinB370Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
NUCM proteinC444Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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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: 3.60 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.316 
  • R-Value Observed: 0.317 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 317.74α = 90
b = 317.74β = 90
c = 818.97γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
iMOSFLMdata reduction
SHARPphasing
Cootmodel building
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Excellence Initiative of the German Federal and State GovernmentsGermanyEXC 294 BIOSS
German Research FoundationGermanyCRC 746
German Research FoundationGermanyZI 552/3-1
Excellence Initiative of the German Federal and State GovernmentsGermanyEXC 115

Revision History 

  • Version 1.0: 2015-03-25
    Type: Initial release