8ZSR | pdb_00008zsr

Complex I form respirasome open state bound by proguanil (SC-ProgO)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

structural basis for inhibition of mammalian respirasome by metformin and proguanil

Teng, F.He, Z.X.Yang, Y.Q.Guo, R.Y.Hu, Y.Q.Xu, C.Y.Zhou, R.H.Zhang, X.Zhang, S.Zhou, L.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LA [auth 4L]98Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1B [auth A1]70Sus scrofaMutation(s): 0 
UniProt
Find proteins for K7GR43 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2C [auth A2]85Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RGE3 (Sus scrofa)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3D [auth A3]83Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VPG4 (Sus scrofa)
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UniProt GroupA0A4X1VPG4
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5E [auth A5]112Sus scrofaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6F [auth A6]114Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-B14.5aG [auth A7]112Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VLA2 (Sus scrofa)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8H [auth A8]171Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialI [auth A9]341Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinJ [auth AB],
K [auth AC]
87Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialL [auth AK]321Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11M [auth AL]140Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12N [auth AM]144Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13O [auth AN]142Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1P [auth B1]56Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D2CGH8 (Sus scrofa)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialQ [auth B2]67Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A5G2QW32 (Sus scrofa)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3R [auth B3]80Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VD84 (Sus scrofa)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4S [auth B4]128Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1T6M0 (Sus scrofa)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialT [auth B5]138Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SGC6 (Sus scrofa)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6U [auth B6]126Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480KM09 (Sus scrofa)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7V [auth B7]125Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SCH1 (Sus scrofa)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialW [auth B8]156Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RWL7 (Sus scrofa)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9X [auth B9]178Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10Y [auth BK]176Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialZ [auth BL]102Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1EYI7 (Sus scrofa)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialAA [auth CA]49Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupA1XQS6
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2BA [auth CB]121Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480JRW3 (Sus scrofa)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1CA [auth N1]318Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for O79874 (Sus scrofa)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2DA [auth N2]347Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for O79875 (Sus scrofa)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3EA [auth N3]115Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for O79880 (Sus scrofa)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4FA [auth N4]459Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for Q7IIB7 (Sus scrofa)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5GA [auth N5]603Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for Q71K68 (Sus scrofa)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6HA [auth N6]174Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for O79882 (Sus scrofa)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialIA [auth S1]689Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for A0A4X1V1H9 (Sus scrofa)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialJA [auth S2]430Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for F1S1A8 (Sus scrofa)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-30kDKA [auth S3]208Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZNN4 (Sus scrofa)
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialLA [auth S4]124Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1SN37 (Sus scrofa)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5MA [auth S5]105Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SV23 (Sus scrofa)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialNA [auth S6]96Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1S031 (Sus scrofa)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialOA [auth S7]156Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1TL60 (Sus scrofa)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialPA [auth S8]176Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for A0A287BDC0 (Sus scrofa)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialQA [auth V1]431Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for A0A4X1SZP7 (Sus scrofa)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialRA [auth V2]217Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for A0A287BG40 (Sus scrofa)
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UniProt GroupA0A287BG40
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit V3SA [auth V3]42Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BEK4 (Sus scrofa)
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
BB [auth AL]
BC [auth N4]
CB [auth AL]
EC [auth N5]
FC [auth N5]
BB [auth AL],
BC [auth N4],
CB [auth AL],
EC [auth N5],
FC [auth N5],
JB [auth B4],
LB [auth B5],
SC [auth S8],
TA [auth 4L],
VA [auth A7],
WA [auth A8],
WB [auth N2]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
Query on PC1

Download Ideal Coordinates CCD File 
FB [auth AL]
MB [auth B5]
NB [auth B7]
PC [auth S7]
RB [auth N1]
FB [auth AL],
MB [auth B5],
NB [auth B7],
PC [auth S7],
RB [auth N1],
SB [auth N1]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
PLX (Subject of Investigation/LOI)
Query on PLX

Download Ideal Coordinates CCD File 
AC [auth N4]
GB [auth AM]
HB [auth AM]
KB [auth B5]
QB [auth CB]
AC [auth N4],
GB [auth AM],
HB [auth AM],
KB [auth B5],
QB [auth CB],
YB [auth N3],
ZB [auth N4]
(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL
C42 H89 N O8 P
YVNJQRQLQPWVSQ-IWSHAHEXSA-O
3PE
Query on 3PE

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DB [auth AL],
OB [auth B8],
PB [auth CA]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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XA [auth A9]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PEE
Query on PEE

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CC [auth N5]
DC [auth N5]
EB [auth AL]
GC [auth N5]
HC [auth N5]
CC [auth N5],
DC [auth N5],
EB [auth AL],
GC [auth N5],
HC [auth N5],
IB [auth B4],
UA [auth A3],
UB [auth N1],
VB [auth N1],
XB [auth N2]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
ZMP (Subject of Investigation/LOI)
Query on ZMP

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YA [auth AB],
ZA [auth AC]
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
C25 H49 N2 O8 P S
HDTINWYIVVMRIN-HSZRJFAPSA-N
FMN
Query on FMN

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UC [auth V1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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AB [auth AK]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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IC [auth S1]
JC [auth S1]
OC [auth S7]
QC [auth S8]
RC [auth S8]
IC [auth S1],
JC [auth S1],
OC [auth S7],
QC [auth S8],
RC [auth S8],
TC [auth V1]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
XEW (Subject of Investigation/LOI)
Query on XEW

Download Ideal Coordinates CCD File 
MC [auth S2],
TB [auth N1]
N-(4-chlorophenyl)-N'-(propan-2-yl)triimidodicarbonic diamide
C11 H16 Cl N5
SSOLNOMRVKKSON-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
KC [auth S1],
VC [auth V2]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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NC [auth S6]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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LC [auth S1]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
2MR
Query on 2MR
JA [auth S2]L-PEPTIDE LINKINGC8 H18 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONcryoSPARCv4.4.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaZJU100 Young Professor

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release