8ZSM | pdb_00008zsm

Complex I from respirasome closed state 1 bound by metformin (SC-MetC1-iii)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Hydrophilic metformin and hydrophobic biguanides inhibit mitochondrial complex I by distinct mechanisms.

He, Z.Teng, F.Yang, Y.Guo, R.Wu, M.Han, F.Tian, H.Wang, J.Hu, Y.Jiang, Y.Zhang, L.Xu, C.Yang, F.Zhou, J.Zhang, S.Letts, J.A.Zhou, R.Zhou, L.

(2026) Nat Struct Mol Biol 33: 100-111

  • DOI: https://doi.org/10.1038/s41594-025-01710-6
  • Primary Citation Related Structures: 
    8ZO8, 8ZOU, 8ZSK, 8ZSL, 8ZSM, 8ZSN, 8ZSO, 8ZSQ, 8ZXZ, 9J6H, 9J6W

  • PubMed Abstract: 

    Metformin is the only antihyperglycemic biguanide targeting type 2 diabetes mellitus with proven safety. Although a mechanism of action involving tight inhibition of the respiratory complex I has been proposed for hydrophobic biguanides, it remains elusive for the hydrophilic metformin, whose excellent pharmacological tolerance depends on weak complex I inhibition without competitive nature. Here we solved cryo-electron microscopy structures of the metformin-bound porcine respirasome. Our structural and kinetic data are consistent with a model in which metformin enters complex I only in its open state and becomes trapped at the ubiquinone redox site by ubiquinone-induced conformational closing of the enzyme. By contrast, the hydrophobic proguanil alone occupies both the entrance and the redox site of the ubiquinone channel in open and closed complex I and is kinetically consistent with competitive inhibition with conformation-dependent affinities. Our data provide the molecular basis for metformin's well-known superior properties, such as a wide therapeutic window and positive ubiquinone cooperativity, leading to its clinical success and facilitating future therapeutic developments.


  • Organizational Affiliation
    • Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.

Macromolecule Content 

  • Total Structure Weight: 992.49 kDa 
  • Atom Count: 68,795 
  • Modeled Residue Count: 8,245 
  • Deposited Residue Count: 8,299 
  • Unique protein chains: 44

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
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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
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2C [auth A2]85Sus scrofaMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3D [auth A3]83Sus scrofaMutation(s): 0 
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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 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Complex I-B14.5aG [auth A7]112Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8H [auth A8]171Sus scrofaMutation(s): 0 
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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 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Acyl carrier proteinJ [auth AB],
K [auth AC]
87Sus scrofaMutation(s): 0 
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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 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11M [auth AL]140Sus scrofaMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12N [auth AM]144Sus scrofaMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13O [auth AN]142Sus scrofaMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1P [auth B1]56Sus scrofaMutation(s): 0 
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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
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3R [auth B3]80Sus scrofaMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4S [auth B4]128Sus scrofaMutation(s): 0 
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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 
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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 
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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 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9X [auth B9]178Sus scrofaMutation(s): 0 
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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 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialAA [auth CA]49Sus scrofaMutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2BA [auth CB]121Sus scrofaMutation(s): 0 
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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
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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
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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
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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
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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
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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
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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
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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
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
Complex I-30kDKA [auth S3]208Sus scrofaMutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialLA [auth S4]124Sus scrofaMutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5MA [auth S5]105Sus scrofaMutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialNA [auth S6]96Sus scrofaMutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialOA [auth S7]156Sus scrofaMutation(s): 0 
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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
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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
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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
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Find proteins for A0A287BG40 (Sus scrofa)
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit V3SA [auth V3]42Sus scrofaMutation(s): 0 
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Reference Sequence

Small Molecules

Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

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Download:Ideal Coordinates CCD File
DB [auth AL]
EB [auth AL]
FC [auth N4]
HC [auth N5]
IC [auth N5]
DB [auth AL],
EB [auth AL],
FC [auth N4],
HC [auth N5],
IC [auth N5],
MB [auth B5],
SB [auth CB],
TA [auth 4L],
TB [auth N1],
UA [auth A1],
XB [auth N2]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1

Query on PC1



Download:Ideal Coordinates CCD File
BC [auth N3]
CC [auth N3]
JB [auth AN]
NB [auth B5]
PB [auth B8]
BC [auth N3],
CC [auth N3],
JB [auth AN],
NB [auth B5],
PB [auth B8],
VA [auth A3],
WA [auth A3]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
PLX

Query on PLX



Download:Ideal Coordinates CCD File
AC [auth N3]
EC [auth N4]
GB [auth AL]
LB [auth B5]
QB [auth CB]
AC [auth N3],
EC [auth N4],
GB [auth AL],
LB [auth B5],
QB [auth CB],
RC [auth S7],
UB [auth N1]
(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



Download:Ideal Coordinates CCD File
GC [auth N4],
KB [auth B4],
RB [auth CB]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP

Query on NDP



Download:Ideal Coordinates CCD File
XA [auth A9]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PEE

Query on PEE



Download:Ideal Coordinates CCD File
CB [auth AK]
DC [auth N4]
FB [auth AL]
HB [auth AL]
IB [auth AN]
CB [auth AK],
DC [auth N4],
FB [auth AL],
HB [auth AL],
IB [auth AN],
JC [auth N5],
OB [auth B6],
UC [auth S8],
VB [auth N1],
WB [auth N2],
YA [auth A9],
YB [auth N2],
ZB [auth N3]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
ZMP
(Subject of Investigation/LOI)

Query on ZMP



Download:Ideal Coordinates CCD File
AB [auth AC],
ZA [auth AB]
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
(Subject of Investigation/LOI)

Query on FMN



Download:Ideal Coordinates CCD File
WC [auth V1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
ADP

Query on ADP



Download:Ideal Coordinates CCD File
BB [auth AK]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
KC [auth S1]
LC [auth S1]
QC [auth S7]
SC [auth S8]
TC [auth S8]
KC [auth S1],
LC [auth S1],
QC [auth S7],
SC [auth S8],
TC [auth S8],
VC [auth V1]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
(Subject of Investigation/LOI)

Query on FES



Download:Ideal Coordinates CCD File
MC [auth S1],
XC [auth V2]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MF8
(Subject of Investigation/LOI)

Query on MF8



Download:Ideal Coordinates CCD File
OC [auth S2]Metformin
C4 H11 N5
XZWYZXLIPXDOLR-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
PC [auth S6]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
NC [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: 3.25 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 governmentZJU100 Young Professor

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2026-02-04
    Changes: Data collection, Database references