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- EMDB-32191: Membrane arm of deactive state CI from Q10 dataset -

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Basic information

Entry
Database: EMDB / ID: EMD-32191
TitleMembrane arm of deactive state CI from Q10 dataset
Map data
Sample
  • Complex: Respiratory complex I
    • Protein or peptide: x 15 types
  • Protein or peptide: x 14 types
  • Ligand: x 6 types
Keywordsmammalian / mitochondrial / respiratory / complex I / ELECTRON TRANSPORT
Function / homology
Function and homology information


Mitochondrial Fatty Acid Beta-Oxidation / Glyoxylate metabolism and glycine degradation / protein lipoylation / Mitochondrial protein import / Complex I biogenesis / Respiratory electron transport / cellular response to oxygen levels / Neutrophil degranulation / gliogenesis / neural precursor cell proliferation ...Mitochondrial Fatty Acid Beta-Oxidation / Glyoxylate metabolism and glycine degradation / protein lipoylation / Mitochondrial protein import / Complex I biogenesis / Respiratory electron transport / cellular response to oxygen levels / Neutrophil degranulation / gliogenesis / neural precursor cell proliferation / [2Fe-2S] cluster assembly / mitochondrial large ribosomal subunit / oxygen sensor activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / aerobic respiration / reactive oxygen species metabolic process / mitochondrial intermembrane space / fatty acid biosynthetic process / NAD binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / response to oxidative stress / membrane => GO:0016020 / mitochondrial matrix / nuclear speck / ubiquitin protein ligase binding / endoplasmic reticulum / mitochondrion / nucleoplasm / cytoplasm
Similarity search - Function
NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / Tim17/Tim22/Tim23/Pmp24 family / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 ...NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / Tim17/Tim22/Tim23/Pmp24 family / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase subunit 2 C-terminus / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / GRIM-19 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / GRIM-19 protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NDUFB9, LYR domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / Deoxynucleoside kinase domain / Deoxynucleoside kinase / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / Complex 1 LYR protein domain / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / Complex 1 protein (LYR family) / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / CHCH / CHCH domain / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / [NiFe]-hydrogenase, large subunit / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 ...Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4
Similarity search - Component
Biological speciesSus scrofa (pig) / pig (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGu JK / Yang MJ
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504600 and 2016YFA0501100 China
National Natural Science Foundation of China (NSFC)31625008 China
National Natural Science Foundation of China (NSFC)32030056, 21532004 and 31570733 and 31800620 China
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: The coupling mechanism of mammalian mitochondrial complex I.
Authors: Jinke Gu / Tianya Liu / Runyu Guo / Laixing Zhang / Maojun Yang /
Abstract: Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in ...Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in mitochondria. In the present study, we report cryo-electron microscopy structures of CI from Sus scrofa in six treatment conditions at a resolution of 2.4-3.5 Å, in which CI structures of each condition can be classified into two biochemical classes (active or deactive), with a notably higher proportion of active CI particles. These structures illuminate how hydrophobic ubiquinone-10 (Q10) with its long isoprenoid tail is bound and reduced in a narrow Q chamber comprising four different Q10-binding sites. Structural comparisons of active CI structures from our decylubiquinone-NADH and rotenone-NADH datasets reveal that Q10 reduction at site 1 is not coupled to proton pumping in the membrane arm, which might instead be coupled to Q10 oxidation at site 2. Our data overturn the widely accepted previous proposal about the coupling mechanism of CI.
History
DepositionNov 13, 2021-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateJun 7, 2023-
Current statusJun 7, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32191.png

Downloads & links

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Map

FileDownload / File: emd_32191.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0742 Å
Density
Contour LevelBy AUTHOR: 0.0238
Minimum - Maximum-0.057419486 - 0.108358845
Average (Standard dev.)0.0002899445 (±0.0034188312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 354.48602 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Respiratory complex I

EntireName: Respiratory complex I
Components
  • Complex: Respiratory complex I
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
    • Protein or peptide: NADH dehydrogenase 1 beta subcomplex 6
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
    • Protein or peptide: Complex I-KFYI
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 subunit C2
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 4L
    • Protein or peptide: Complex I-B15
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
  • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
  • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
  • Protein or peptide: Acyl carrier protein
  • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
  • Protein or peptide: Complex I-ESSS
  • Protein or peptide: NADH-ubiquinone oxidoreductase chain 2
  • Protein or peptide: ND3
  • Protein or peptide: NADH-ubiquinone oxidoreductase chain 5
  • Protein or peptide: NADH-ubiquinone oxidoreductase chain 6
  • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
  • Protein or peptide: NADH-ubiquinone oxidoreductase chain 4
  • Protein or peptide: NADH-ubiquinone oxidoreductase chain 1
  • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
  • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: CARDIOLIPIN
  • Ligand: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
  • Ligand: (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
  • Ligand: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Respiratory complex I

SupramoleculeName: Respiratory complex I / type: complex / ID: 1 / Parent: 0
Macromolecule list: #1-#2, #5, #7-#8, #10-#12, #14-#16, #19, #23-#24, #27
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 53.735777 KDa
SequenceString: MVPVSLWRGK MAALRALCSL RGVAAQVLRP GAGARLPIQP SRGARQWQPD VEWAEQFGGA VMYPTKETAH WKPPPWNDVD PPKDTLVSN LTLNFGPQHP AAHGVLRLVM ELSGEMVRKC DPHIGLLH(2MR)G TEKLIEYKTY LQALPYFDRL DYVSMMC NE QAYSLAVEKL ...String:
MVPVSLWRGK MAALRALCSL RGVAAQVLRP GAGARLPIQP SRGARQWQPD VEWAEQFGGA VMYPTKETAH WKPPPWNDVD PPKDTLVSN LTLNFGPQHP AAHGVLRLVM ELSGEMVRKC DPHIGLLH(2MR)G TEKLIEYKTY LQALPYFDRL DYVSMMC NE QAYSLAVEKL LNIQPPPRAQ WIRVLFGEIT RLLNHIMAVT THALDIGAMT PFFWMFEERE KMFEFYERVS GARMHAAY I RPGGVHQDLP LGLLDDIYEF SKNFSFRIDE LEEMLTNNRI WRNRTVDIGV VTAEDALNYG FSGVMLRGSG IQWDLRKTQ PYDVYDQVEF DVPIGSRGDC YDRYLCRVEE MRQSLRIISQ CLNKMPPGEI KVDDAKVSPP KRAEMKTSME SLIHHFKLYT EGYQVPPGA TYTAIEAPKG EFGVYLVSDG SSRPYRCKIK APGFAHLAGL DKMSKGHMLA DVVAIIGTQD IVFGEVDR

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Macromolecule #2: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 8.088424 KDa
SequenceString:
MWFEILPGIA VMAACLFIPG MATAHIHKFT NGGKEKRVAH FSYQWNLMER DRRISGVNRY HVTKGLENID

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Macromolecule #3: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 9.225567 KDa
SequenceString:
MAGRIASFLK NAWAKEPVLV ASFAIGGLAI ILPSLSPYTN YAIRINRATP YNYPVPLRDD GNMPDVPSHP QDPQGPSLEW LKNL

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Macromolecule #4: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 14.686894 KDa
SequenceString:
MAKTLLHKYS DIPEGTECHR KAYASTSIGG ATGLIVSAYS IALKPPASFL EGVARTGRYT FTSAAIGAIF GLTSCISAQV REKPDDPLN YFIGGCAGGL TLGARTRSYG IGAAACAYMG LTAALVKMGQ LEGWQVFAEP KV

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Macromolecule #5: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 16.911611 KDa
SequenceString:
MAASKVKQDM PPPGGYGPID YKRNLPRRGL SGYSMFAVGI GTLLFGYWSM MKWNRERRRL QIEDFEARIA LMPLFQAEKD RRVLQMLRE NLEEEAIIMK DVPDWKVGES VFHTTRWVTP MMGELYGLRT NEEILSATYG FIWYT

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Macromolecule #6: Acyl carrier protein

MacromoleculeName: Acyl carrier protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 17.308186 KDa
SequenceString:
MAARVLCACV RRLPAAFAPL PRIPTVVAAR PLSTTLFPTG AQARSRALQP ALVLAQAPGG VTQLCRRYSD APPLTLEAIK DRVLYVLKL YDKIDPEKLS VNSHFMKDLG LDSLDQVEII MAMEDEFGFE IPDIDAEKLM CPQEIVDYIA DKKDVYE

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Macromolecule #7: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 11.939366 KDa
SequenceString:
MSPLQRLAPF TRVGGRFLRG RGAGVAGGGG VRHAGGGVHI EPRYRQFPQL TRSQLIQAEF FSATMWFWIL WRFWHDSDAV LGHFPYPDP SQWTDEELGI LPDDED

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Macromolecule #8: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 11.128515 KDa
SequenceString:
MAHGHGHEHG HSKMELPDYK QWKIEGTPLE TVQEKLAARG LRDPWGRNEA WRYSGGFANN VSFVGALLKG FKWGFAAFVV AVGAEYYLE SQNKDKKHH

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Macromolecule #9: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 21.587006 KDa
SequenceString:
MAAMSLLQRA SVTAVATLSR SRLGTRFGFG GFLTHGFPKT GAPVRHSGDH GKRLFIIKPS GFYDRRFLKL MRFYILLTGI PVAIGITLV NVFIGEAELA DIPEGYVPEH WEYFKHPISR WIARTFYDGP EKNYEKTMAI LQIEAEKAEL RLKELEVRRL M RARGDGPW YQYPTIDKAL IDHSPKTTPD N

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Macromolecule #10: NADH dehydrogenase 1 beta subcomplex 6

MacromoleculeName: NADH dehydrogenase 1 beta subcomplex 6 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 15.603177 KDa
SequenceString:
MSGYTPDEKL RLQQLRELRR RWLKDQELSP REPVLPPRRV WPMEQFWNKF LQDGAPWKNV IYKTYRHSIF AVTHVLIPVW IIHYYLKYH VTAKPYTVVE RKPRIFPGDT ILETGEVIPL MKEFPDQHH

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Macromolecule #11: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 21.702543 KDa
SequenceString:
MAAAKAGVLG VRWLQRAARK VVPLGARTAS HVTKDMFPGP YPKTPEERAA AAKKYNMRVE DYEPYPDDGM GYGDYPKLPD RSQQERDPW YDWDHPDLRL NWGEPIHWDL DMYIRNRVDT SPTPVSWNTM CKHLFGFVAF MLFMFWVGEI YPSYQPVGPK Q YPYNDLYL ERGGDPTKEP EPVVHYEI

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Macromolecule #12: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 20.944768 KDa
SequenceString:
MPDSWDKDVY PEPPRRTPAP APQTSLPNPV TYLTKIFDLL VDRPVTLARE FIEQQHAKNR YYYYHREFRR VPDITECEEK DILCMFEAE MQWRRDYKVD QEIVNIIQER LKACQQREGE SYRQNCAKEL EQFTQVSKAF QDRYSDLGAH YSARKCLAKQ K QRMLAERK AAKEAAAA

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Macromolecule #13: Complex I-ESSS

MacromoleculeName: Complex I-ESSS / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 17.384729 KDa
SequenceString:
MAAGVLGLCA RRLLAAAATR GLPAARVRWE SGSSRAVIAP SALVGKRPPE PTIRLQEDPD PEDENLYEKN PDSHGYDKDP IVDLWNMRV VFFFGFSIVL VLGSTFVAYL PDYRMQEWAR REAERLVKYR EANGLPLMES NCFDPNKIQL PEDED

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Macromolecule #14: Complex I-KFYI

MacromoleculeName: Complex I-KFYI / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 8.664053 KDa
SequenceString:
MAASALFRPF SKLLSSARLP SGSSARSKFY IREPPHGSPD WLKVGLTLGT SVFLWIYLIK QHKEDVLEYK RRNGLE

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Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 subunit C2

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 subunit C2 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 14.327655 KDa
SequenceString:
MTMMSGRPGR VPLQFLPNEA RSLPPPKLTD PRLVYMGFLG YCSGLIDNAI RRRPVVSAGL HRQLLYVTSF VFFGYYLLKR QDYMYALRD HDMFAYVKSH PEDFPEKDKK TYGEILEEFH PVR

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Macromolecule #16: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 12.506591 KDa
SequenceString:
MPFFDVQKRL GLDLDRWMTI QSAEQPHKIP GRCHAFEKEW IECAHGIGGI RAEKECKIEF DDFVECLLRQ KTMKRLSAIK RQRDKLIKE GKYTPPPHHL GKEDPRP

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Macromolecule #17: NADH-ubiquinone oxidoreductase chain 2

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 2 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 39.077504 KDa
SequenceString: MNPIIYTTLI MTVMSGTMLV MISSHWLLIW IGFEMNLLAM IPVLMKNFNP RATEAATKYF LTQATASMML MMAIIINLLY SGQWTITKM FNPVAMTMMT MALAMKLGLS PFHFWVPEVT QGISLQAGLL LLTWQKLAPL SVLCQISQSI NPNLMLTMAM L SILIGGWG ...String:
MNPIIYTTLI MTVMSGTMLV MISSHWLLIW IGFEMNLLAM IPVLMKNFNP RATEAATKYF LTQATASMML MMAIIINLLY SGQWTITKM FNPVAMTMMT MALAMKLGLS PFHFWVPEVT QGISLQAGLL LLTWQKLAPL SVLCQISQSI NPNLMLTMAM L SILIGGWG GLNQTQLRKI MAYSSIAHMG WMTAVLPYNT TMTILNLLIY ITMTLAMFML LIHSSATTTL SLSHTWNKMP VI TSLMMVT LLSMGGLPPL SGFMPKWMII QEMTKNESII MPTLMAMTAL LNLYFYMRLA YSSSLTMFPS TNNMKMKWQF EHT KQMKLL PTMIVLSTLV LPMTPALSSL N

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Macromolecule #18: ND3

MacromoleculeName: ND3 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 12.798257 KDa
SequenceString:
MNIMLTLLTN VTLASLLVLI AFWLPQLNAY SEKTSPYECG FDPMGSARLP FSMKFFLVAI TFLLFDLEIA LLLPLPWASQ TNNLKTMLT MALFLLILLA ASLAYEWTQK GLEW

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Macromolecule #19: NADH-ubiquinone oxidoreductase chain 4L

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 4L / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 10.827253 KDa
SequenceString:
MPLVYMNIIM AFAIALAGLL MYRSHLMSSL LCLEGMMLSL FIMSTLIILN THFTLANMMP IILLVFAACE AALGLSLLVM VSNTYGTDY VQNLNLLQC

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Macromolecule #20: NADH-ubiquinone oxidoreductase chain 5

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 5 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 68.267031 KDa
SequenceString: MNPFASLTLT TLTILTIPIM MSNSNIYKTN LYPNYVKTTV SYAFTLSLVP LLMFMHTGQE MIISNWHWMT LQTVELSLSF KMDYFSVMF IPVALFVTWS IMEFSMWYMH SDPFINRFFK YLLLFLITMM ILVTANNLFQ LFIGWEGVGI MSFLLIGWWH G RTDANTAA ...String:
MNPFASLTLT TLTILTIPIM MSNSNIYKTN LYPNYVKTTV SYAFTLSLVP LLMFMHTGQE MIISNWHWMT LQTVELSLSF KMDYFSVMF IPVALFVTWS IMEFSMWYMH SDPFINRFFK YLLLFLITMM ILVTANNLFQ LFIGWEGVGI MSFLLIGWWH G RTDANTAA LQAILYNRIG DIGFVLSMAW FLTHSNAWDL QQIFMLNNEC PNMPLIGLLL AAAGKSAQFG LHPWLPSAME GP TPVSALL HSSTMVVAGV FLLIRFYPLM ETNKLVQTMT LCLGAITTLF TALCAITQND IKKIVAFSTS SQLGLMMVTI GIN QPHLAF LHICMHAFFK AMLFMCSGSI IHSLNDEQDI RKMGGLYKAM PFTTTALIIG SLALTGMPYL TGFYSKDLII EAVN MSYTN AWALLMTLIA TSLTAAYSTR IIFFAFLGKP RFPPLVLINE NNPLLINSIK RLLIGSIFAG FIISNNIPPM TVPNT TMPL YMKMTALIVT IMGFMLALEL NNTTYYLKFK YPSQTYKFSN MLGYYPSIMH RLPTYHNLSM SQKSASSLLD LIWLET ILP KTTSFIQMKM SIMVSNQKGL IKLYFLSFLI TIMISMTLFN

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Macromolecule #21: NADH-ubiquinone oxidoreductase chain 6

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 6 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 19.021332 KDa
SequenceString:
MTMYIAFILS TIFVIGFVGF SSKPSPIYGG LGLIVSGGVG CGIVLNFGGS FLGLMVFLIY LGGMLVVFGY TTAMATEMYP EVWVSNKTV FGAFVSGLMM EFCMVYYALK EEEVEIIFKF NGLGDWVIYD TGDSGFFSEE AMGIAALYSY GTWLVIVTGW S LLIGVVVI MEITRGN

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Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 7.044278 KDa
SequenceString:
MMNVLQIVRD HWVHILVPVG FVFGCYLDRR SDEKLTAFRN KSLLFKRELR PNEEVTWK

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Macromolecule #23: Complex I-B15

MacromoleculeName: Complex I-B15 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 15.11735 KDa
SequenceString:
MSFPKYKPSR LATLPATLDP AEYDISPETR KAQAERLAIR SRLKREYLLQ YNDPNRLGVI EDPALIRWTY ARSANIYPNF RPTPKTSLL GALFGIGPLF FWYYVFKTDR DKKEKLIQEG KLDQTFNISY

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Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 21.864906 KDa
SequenceString:
MAFSAPAAYL THQQKVLRLY KRALRHLESW CVHRDKYRYF ACLMRARFDE HKNEKDMVKA TQLLRQAEEE FWYGQHPQPY IFPESPGGT SYERYECYKV PEWCLDDWHP SEKAMYPDYF AKREQWKRLR RESWEREVKQ LQEETPPGGP RTEALPPARK E GDLPPLWW HIVTRPRERP M

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Macromolecule #25: NADH-ubiquinone oxidoreductase chain 4

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 4 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 51.853355 KDa
SequenceString: MLKIIIPTTM LLPMTWMSKH NMIWINATVH SLLISLISLS LLNQLGENSL NFSLTFFSDS LSAPLLVLTT WLLPLMLMAS QSHLSKETT TRKKLYITML ILLQLFLIMT FTATELILFY ILFEATLVPT LIIITRWGNQ TERLNAGLYF LFYTLAGSLP L LVALVYIQ ...String:
MLKIIIPTTM LLPMTWMSKH NMIWINATVH SLLISLISLS LLNQLGENSL NFSLTFFSDS LSAPLLVLTT WLLPLMLMAS QSHLSKETT TRKKLYITML ILLQLFLIMT FTATELILFY ILFEATLVPT LIIITRWGNQ TERLNAGLYF LFYTLAGSLP L LVALVYIQ NTTGSLNFLI IHYWSHPLSN SWSNIFMWLA CIMAFMVKMP LYGLHLWLPK AHVEAPIAGS MVLAAVLLKL GG YGMMRIT TILNPLTNYM AYPFLMLSMW GMIMTSSICL RQTDLKSLIA YSSVSHMALV IVAIMIQTPW SFMGATALMI AHG LTSSML FCLANTNYER VHSRTMILAR GLQTLLPLMA TWWLVASLTN LALPPSINLI GELFIITASF SWSNITIILM GMNM MITAL YSLYMLITTQ RGKYTHHINN IKPSFTRENA LMALHILPLL LLTLNPKMIL GPLY

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Macromolecule #26: NADH-ubiquinone oxidoreductase chain 1

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 1 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 35.66752 KDa
SequenceString: MFMINILSLI IPILLAVAFL TLVERKVLGY MQLRKGPNVV GPYGLLQPIA DALKLFTKEP LRPATSSISM FIIAPILALS LALTMWVPL PMPYPLINMN LGVLFMLAMS SLAVYSILWS GWASNSKYAL IGALRAVAQT ISYEVTLAII LLSVLLMNGS Y TLSTLITT ...String:
MFMINILSLI IPILLAVAFL TLVERKVLGY MQLRKGPNVV GPYGLLQPIA DALKLFTKEP LRPATSSISM FIIAPILALS LALTMWVPL PMPYPLINMN LGVLFMLAMS SLAVYSILWS GWASNSKYAL IGALRAVAQT ISYEVTLAII LLSVLLMNGS Y TLSTLITT QEHIWMIFTS WPLAMMWFIS TLAETNRAPF DLTEGESELV SGFNVEYAAG PFAMFFMAEY ANIIMMNAFT AI LFLGASH DPHTPELYTI NFVLKTLALT ITFLWIRASY PRFRYDQLMH LLWKSFLPLT LALCMWHISL PIMTASIPPQ S

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Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 20.064096 KDa
SequenceString:
MPGIVELPTL EDLKVQEVKV SSSVLKAAAH HYGAQCDKPN KEFMLCRWEE KDPRRCLEEG KLVNQCALDF FRQIKRHCAE PFTEYWTCI DYSGLQLFRH CRKQQAKFDE CVLDKLGWVR PDLGELSKVT KVKTDRPLPE NPYHSRARPE PNPEAEGDLK P AKHGSRLF FWTM

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Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 16.35669 KDa
SequenceString:
GAHLARRYLG DASKEPDPLR MPTFPPDYGF PERKEREMVA TQQEMNDAQL MLQQRDYCAH YLIQLLKCKR DSFPNFLACK HEQHDWDYC EHLDYVKRMK EFERERRLLQ RKKRREQREA EMARGQGPGE VAPEMAL

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Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 40.476082 KDa
SequenceString: MALRLLRLAP ASASAVPRGL GAVAQRVGGI HTGAPCRLQY GPLAFVLGER TTRKLTETSK VITVDGNICS GKGRLAREIA EKLGLRHFP EAGIHYADST TGDGKPLDVQ LSGNCSLEKF YDDPKSNDGN SYRLQSWLYA SRLLQYADAL EHLLSTGQGV V LERSIYSD ...String:
MALRLLRLAP ASASAVPRGL GAVAQRVGGI HTGAPCRLQY GPLAFVLGER TTRKLTETSK VITVDGNICS GKGRLAREIA EKLGLRHFP EAGIHYADST TGDGKPLDVQ LSGNCSLEKF YDDPKSNDGN SYRLQSWLYA SRLLQYADAL EHLLSTGQGV V LERSIYSD FVFLEAMYRQ GFIRKQCVEH YNEVKKVTAC EYLPPHVVVY VDVPVPEIQS RIQKKGNPHE MKITAAYLQD IE NAYKKTF LPEMSEKCEV LQYSAREAED AEKVVEDIEY LKCDKGPWPD QDDRTFHRLR MLVQNKLEVL NYTTIPVYLP EIT IGAHQS DRVFQKFTEL PGRKYSPGYN EDVGDKWIWL K

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Macromolecule #30: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 30 / Number of copies: 8 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM / Discrete optimized protein energy

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Macromolecule #31: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 31 / Number of copies: 8 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #32: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...

MacromoleculeName: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
type: ligand / ID: 32 / Number of copies: 1 / Formula: 8Q1
Molecular weightTheoretical: 540.651 Da
Chemical component information

ChemComp-8Q1:
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate

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Macromolecule #33: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,...

MacromoleculeName: (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
type: ligand / ID: 33 / Number of copies: 5 / Formula: PLX
Molecular weightTheoretical: 767.132 Da
Chemical component information

ChemComp-PLX:
(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 / phospholipid*YM

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Macromolecule #34: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer

MacromoleculeName: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer / type: ligand / ID: 34 / Number of copies: 1 / Formula: UQ
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-UQ:
Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer

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Macromolecule #35: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 35 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 193234

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