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


This is version 1.0 of the entry. See complete history


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
  • Primary Citation of Related Structures:  
    4WZ7

  • 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 implicated in many hereditary and degenerative disorders ...

    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 LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1A [auth 1]327Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 2B [auth 2]438Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3C [auth 3]89Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4D [auth 4]470Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5E [auth 5]619Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6F [auth 6]185Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6E9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NUAM proteinG [auth A]628Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NUBM proteinH [auth B]370Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NUCM proteinI [auth C]444Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
39-kDa subunitJ [auth E]195Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NUGM proteinK [auth G]133Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUHM of protein NADH:Ubiquinone Oxidoreductase (Complex I)L [auth H]154Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I)M [auth I]137Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I)N [auth K]183Yarrowia lipolyticaMutation(s): 0 
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]89Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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 subunits 1Q [auth D], P [auth Z]57Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunits 2R [auth F]54Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsS [auth J]63Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsT [auth M]29Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsU [auth N]50Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsV [auth O]70Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsW [auth P]46Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsX [auth Q]51Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsY [auth R]30Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsZ [auth S]69Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsNA [auth AH], AA [auth T]15Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsBA [auth U]26Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsCA [auth V]22Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsHA [auth AB], EB [auth AY], KB [auth BE], DA [auth W]9Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsPA [auth AJ], BB [auth AV], NB [auth BH], EA [auth X]16Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsXA [auth AR], ZA [auth AT], FA [auth Y]13Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsGA [auth AA], CB [auth AW], HB [auth BB], MB [auth BG]18Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsIA [auth AC], JA [auth AD]47Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsKA [auth AE]48Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsLA [auth AF]35Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsMA [auth AG]25Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsOA [auth AI], RA [auth AL]36Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsQA [auth AK], TA [auth AN]76Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsSA [auth AM]17Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsUA [auth AO]32Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsVA [auth AP], YA [auth AS]11Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsWA [auth AQ], GB [auth BA]8Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsAB [auth AU]58Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsDB [auth AX]39Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsFB [auth AZ]40Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsIB [auth BC]20Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsJB [auth BD], LB [auth BF]19Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsOB [auth BI]905Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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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

View Full Validation Report




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  (Full details and data files)

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