9IHO | pdb_00009iho

Open state without NUQM and without flavoprotein (classification state 4) of Pichia pastoris mitochondrial complex I in cMSP26 nanodiscs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Global conformations of Pichia pastoris complex I are distinguished by the binding of a unique interdomain bridging subunit.

Lee, C.S.Grba, D.N.Wright, J.J.Ivanov, B.S.Hirst, J.

(2025) Sci Adv 11: eadz0693-eadz0693

  • DOI: https://doi.org/10.1126/sciadv.adz0693
  • Primary Citation of Related Structures:  
    9IHO, 9IHP, 9IHQ, 9IHR

  • PubMed Abstract: 

    Complex I (CI; NADH ubiquinone oxidoreductase) is central to energy generation and metabolic homeostasis in mammalian cells but contributes to adverse outcome pathways under challenging conditions. During ischemia, mammalian CI transitions from a turnover-ready, structurally "closed" state toward a dormant "open" state that prevents it from functioning in reverse during reperfusion to produce reactive oxygen species. Unfortunately, simpler, genetically tractable CI models do not recapitulate the same regulatory behavior, compromising mechanistic studies. Here, we report the structure of isolated CI from the yeast Pichia pastoris ( Pp -CI) and identify distinct closed and open states that resemble those of mammalian CI. Notably, a hitherto-unknown protein (NUQM) completes an interdomain bridge in only the closed state, implying that NUQM stabilizes it by restricting the conformational changes of opening. The direct correlation of NUQM binding with closed/open status in Pp -CI provides opportunities for investigating regulatory mechanisms relevant to reversible catalysis and ischemia-reperfusion injury.


  • Organizational Affiliation
    • The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3141Komagataella pastorisMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BA75_00622T0204Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NUGM (30 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)289Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NUCM (49 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)482Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NUAM (75 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)E [auth G]726Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1F [auth H]353Komagataella pastorisMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NUIM (TYKY) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)G [auth I]222Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6H [auth J]161Komagataella pastorisMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NULM (ND4L) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)I [auth K]82Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5J [auth L]642Komagataella pastorisMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4K [auth M]491Komagataella pastorisMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2L [auth N]523Komagataella pastorisMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NUXM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)M [auth O]193Komagataella pastorisMutation(s): 1 
EC: 1.6.5.3
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NUEM (39 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)N [auth P]384Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialO [auth Q]159Komagataella pastorisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NUMM (13 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)P [auth R]139Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NI8M (B8) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)Q [auth S]90Komagataella pastorisMutation(s): 1 
EC: 1.6.5.3
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinR [auth T]138Komagataella pastorisMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinS [auth U]130Komagataella pastorisMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NUFM (B13) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)T [auth V]134Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
BA75_04796T0U [auth W]122Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductaseV [auth X]184Komagataella pastorisMutation(s): 1 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NUJM (B14.7) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)W [auth Y]216Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13X [auth Z]147Komagataella pastorisMutation(s): 1 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1Y [auth a]150Komagataella pastorisMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NI9M (B9) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)Z [auth b]79Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
BA75_00589T0AA [auth c]182Komagataella pastorisMutation(s): 1 
EC: 1.6.5.3
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Pichia pastoris NADH-ubiquinone oxidoreductase subunit NEBMBA [auth d]78Komagataella pastorisMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
BA75_05084T0CA [auth e]106Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NUTM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)DA [auth f]86Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NESM (ESSS) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)EA [auth g]239Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NUSM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)FA [auth h]182Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NUUM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)GA [auth i]74Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)HA [auth j]59Komagataella pastorisMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NB2M (B12) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)IA [auth k]61Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NIAM (ASHI) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)JA [auth l]156Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NB5M (B15) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)KA [auth m]81Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9LA [auth n]111Komagataella pastorisMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7MA [auth o]87Komagataella pastorisMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NIDM (PDSW) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)NA [auth p]92Komagataella pastorisMutation(s): 0 
EC: 1.6.5.3
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UniProt GroupE1UWC9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunitOA [auth q]140Komagataella pastorisMutation(s): 1 
UniProt
Find proteins for E1UWE0 (Komagataella pastoris)
Explore E1UWE0 
Go to UniProtKB:  E1UWE0
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1UWE0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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AC [auth Z],
DC [auth b],
OB [auth O],
OC [auth q]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
3PE
Query on 3PE

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AB [auth L]
BB [auth L]
CB [auth L]
DB [auth L]
EB [auth L]
AB [auth L],
BB [auth L],
CB [auth L],
DB [auth L],
EB [auth L],
EC [auth b],
FB [auth L],
FC [auth b],
JB [auth M],
JC [auth h],
KB [auth M],
KC [auth j],
LC [auth m],
NB [auth N],
VB [auth Y],
YA [auth J],
YB [auth Z]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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PB [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PLC
Query on PLC

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BC [auth a]
CC [auth b]
GB [auth L]
GC [auth d]
HB [auth L]
BC [auth a],
CC [auth b],
GB [auth L],
GC [auth d],
HB [auth L],
HC [auth d],
IB [auth L],
IC [auth g],
LB [auth M],
MB [auth M],
MC [auth q],
NC [auth q],
QA [auth B],
QB [auth P],
RA [auth D],
RB [auth P],
VA [auth H],
WB [auth Y],
XB [auth Y],
ZA [auth L],
ZB [auth Z]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
EHZ
Query on EHZ

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TB [auth T],
UB [auth U]
~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate
C25 H49 N2 O9 P S
JYSKQPQRUCZFIQ-REWPJTCUSA-N
SF4
Query on SF4

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PA [auth B],
SA [auth G],
TA [auth G],
WA [auth I],
XA [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

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SB [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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UA [auth G]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A
L-PEPTIDE LINKINGC6 H11 N O3 SMET
2MR
Query on 2MR
D
L-PEPTIDE LINKINGC8 H18 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00015/2

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release