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: https://doi.org/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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1A [auth 1]327Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 2B [auth 2]438Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3C [auth 3]89Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4D [auth 4]470Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5E [auth 5]619Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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))
Explore Q9B6E9 
Go to UniProtKB:  Q9B6E9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9B6E9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NUAM proteinG [auth A]628Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NUBM proteinH [auth B]370Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NUCM proteinI [auth C]444Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
39-kDa subunitJ [auth E]195Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NUGM proteinK [auth G]133Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore Q9UUT7 
Go to UniProtKB:  Q9UUT7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UUT7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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))
Explore Q9B6D4 
Go to UniProtKB:  Q9B6D4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9B6D4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunits 1P [auth Z],
Q [auth D]
57Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunits 2R [auth F]54Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsS [auth J]63Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsT [auth M]29Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsU [auth N]50Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsV [auth O]70Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsW [auth P]46Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsX [auth Q]51Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsY [auth R]30Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsZ [auth S]69Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsAA [auth T],
NA [auth AH]
15Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsBA [auth U]26Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsCA [auth V]22Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsDA [auth W],
EB [auth AY],
HA [auth AB],
KB [auth BE]
9Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsBB [auth AV],
EA [auth X],
NB [auth BH],
PA [auth AJ]
16Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsFA [auth Y],
XA [auth AR],
ZA [auth AT]
13Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsCB [auth AW],
GA [auth AA],
HB [auth BB],
MB [auth BG]
18Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsIA [auth AC],
JA [auth AD]
47Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsKA [auth AE]48Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsLA [auth AF]35Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsMA [auth AG]25Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsOA [auth AI],
RA [auth AL]
36Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsQA [auth AK],
TA [auth AN]
76Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsSA [auth AM]17Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsUA [auth AO]32Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsVA [auth AP],
YA [auth AS]
11Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsGB [auth BA],
WA [auth AQ]
8Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsAB [auth AU]58Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsDB [auth AX]39Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsFB [auth AZ]40Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsIB [auth BC]20Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsJB [auth BD],
LB [auth BF]
19Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
unknown subunitsOB [auth BI]905Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
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