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- EMDB-55753: Local refinement of E. coli Complex I D79N NuoA mutant membrane d... -

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Basic information

Entry
Database: EMDB / ID: EMD-55753
TitleLocal refinement of E. coli Complex I D79N NuoA mutant membrane domain in LMNG
Map data
Sample
  • Complex: NADH-quinone oxidoreductase, Complex I
    • Protein or peptide: x 7 types
  • Ligand: x 5 types
KeywordsPROTON TRANSPORT / bioenergetics
Function / homology
Function and homology information


NADH dehydrogenase (quinone) (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport ...NADH dehydrogenase (quinone) (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / proton transmembrane transport / aerobic respiration / respiratory electron transport chain / membrane / plasma membrane
Similarity search - Function
NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L ...NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / 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
Similarity search - Domain/homology
NADH-quinone oxidoreductase subunit A / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit M / NADH-quinone oxidoreductase subunit N / NADH-quinone oxidoreductase subunit L
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsBeghiah A / Kovalova T / Kaila VRI
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation2024.0220 Sweden
Swedish Research Council2020-04081 Sweden
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionNov 18, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55753.png

Downloads & links

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Map

FileDownload / File: emd_55753.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 710 pix.
= 585.75 Å		0.83 Å/pix.
x 710 pix.
= 585.75 Å		0.83 Å/pix.
x 710 pix.
= 585.75 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-1.2486751 - 1.9254462
Average (Standard dev.)-0.00047609457 (±0.038180307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions710710710
Spacing710710710
CellA=B=C: 585.75 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55753_msk_1.map
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Additional map: #1

Fileemd_55753_additional_1.map
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Half map: #2

Fileemd_55753_half_map_1.map
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Half map: #1

Fileemd_55753_half_map_2.map
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Sample components

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Entire : NADH-quinone oxidoreductase, Complex I

EntireName: NADH-quinone oxidoreductase, Complex I
Components
  • Complex: NADH-quinone oxidoreductase, Complex I
    • Protein or peptide: NADH-quinone oxidoreductase subunit H
    • Protein or peptide: NADH-quinone oxidoreductase subunit K
    • Protein or peptide: NADH-quinone oxidoreductase subunit L
    • Protein or peptide: NADH-quinone oxidoreductase subunit A
    • Protein or peptide: NADH-quinone oxidoreductase subunit J
    • Protein or peptide: NADH-quinone oxidoreductase subunit M
    • Protein or peptide: NADH-quinone oxidoreductase subunit N
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
  • Ligand: CARDIOLIPIN
  • Ligand: Ubiquinone-8
  • Ligand: water

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Supramolecule #1: NADH-quinone oxidoreductase, Complex I

SupramoleculeName: NADH-quinone oxidoreductase, Complex I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Escherichia coli BW25113 (bacteria)

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Macromolecule #1: NADH-quinone oxidoreductase subunit H

MacromoleculeName: NADH-quinone oxidoreductase subunit H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 36.240922 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString: MSWISPELIE ILLTILKAVV ILLVVVTCGA FMSFGERRLL GLFQNRYGPN RVGWGGSLQL VADMIKMFFK EDWIPKFSDR VIFTLAPMI AFTSLLLAFA IVPVSPGWVV ADLNIGILFF LMMAGLAVYA VLFAGWSSNN KYSLLGAMRA SAQTLSYEVF L GLSLMGVV ...String:
MSWISPELIE ILLTILKAVV ILLVVVTCGA FMSFGERRLL GLFQNRYGPN RVGWGGSLQL VADMIKMFFK EDWIPKFSDR VIFTLAPMI AFTSLLLAFA IVPVSPGWVV ADLNIGILFF LMMAGLAVYA VLFAGWSSNN KYSLLGAMRA SAQTLSYEVF L GLSLMGVV AQAGSFNMTD IVNSQAHVWN VIPQFFGFIT FAIAGVAVCH RHPFDQPEAE QELADGYHIE YSGMKFGLFF VG EYIGIVT ISALMVTLFF GGWQGPLLPP FIWFALKTAF FMMMFILIRA SLPRPRYDQV MSFGWKICLP LTLINLLVTA AVI LWQAQ

UniProtKB: NADH-quinone oxidoreductase subunit H

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Macromolecule #2: NADH-quinone oxidoreductase subunit K

MacromoleculeName: NADH-quinone oxidoreductase subunit K / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 10.852961 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString:
MIPLQHGLIL AAILFVLGLT GLVIRRNLLF MLIGLEIMIN ASALAFVVAG SYWGQTDGQV MYILAISLAA AEASIGLALL LQLHRRRQN LNIDSVSEMR G

UniProtKB: NADH-quinone oxidoreductase subunit K

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Macromolecule #3: NADH-quinone oxidoreductase subunit L

MacromoleculeName: NADH-quinone oxidoreductase subunit L / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 66.483609 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString: MNMLALTIIL PLIGFVLLAF SRGRWSENVS AIVGVGSVGL AALVTAFIGV DFFANGEQTY SQPLWTWMSV GDFNIGFNLV LDGLSLTML SVVTGVGFLI HMYASWYMRG EEGYSRFFAY TNLFIASMVV LVLADNLLLM YLGWEGVGLC SYLLIGFYYT D PKNGAAAM ...String:
MNMLALTIIL PLIGFVLLAF SRGRWSENVS AIVGVGSVGL AALVTAFIGV DFFANGEQTY SQPLWTWMSV GDFNIGFNLV LDGLSLTML SVVTGVGFLI HMYASWYMRG EEGYSRFFAY TNLFIASMVV LVLADNLLLM YLGWEGVGLC SYLLIGFYYT D PKNGAAAM KAFVVTRVGD VFLAFALFIL YNELGTLNFR EMVELAPAHF ADGNNMLMWA TLMLLGGAVG KSAQLPLQTW LA DAMAGPT PVSALIHAAT MVTAGVYLIA RTHGLFLMTP EVLHLVGIVG AVTLLLAGFA ALVQTDIKRV LAYSTMSQIG YMF LALGVQ AWDAAIFHLM THAFFKALLF LASGSVILAC HHEQNIFKMG GLRKSIPLVY LCFLVGGAAL SALPLVTAGF FSKD EILAG AMANGHINLM VAGLVGAFMT SLYTFRMIFI VFHGKEQIHA HAVKGVTHSL PLIVLLILST FVGALIVPPL QGVLP QTTE LAHGSMLTLE ITSGVVAVVG ILLAAWLWLG KRTLVTSIAN SAPGRLLGTW WYNAWGFDWL YDKVFVKPFL GIAWLL KRD PLNSMMNIPA VLSRFAGKGL LLSENGYLRW YVASMSIGAV VVLALLMVLR

UniProtKB: NADH-quinone oxidoreductase subunit L

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Macromolecule #4: NADH-quinone oxidoreductase subunit A

MacromoleculeName: NADH-quinone oxidoreductase subunit A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 16.473299 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString:
MSMSTSTEVI AHHWAFAIFL IVAIGLCCLM LVGGWFLGGR ARARSKNVPF ESGIDSVGSA RLRLSAKFYL VAMFFVIFNV EALYLFAWS TSIRESGWVG FVEAAIFIFV LLAGLVYLVR IGALDWTPAR SRRERMNPET NSIANRQR

UniProtKB: NADH-quinone oxidoreductase subunit A

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Macromolecule #5: NADH-quinone oxidoreductase subunit J

MacromoleculeName: NADH-quinone oxidoreductase subunit J / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 19.889551 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString:
MEFAFYICGL IAILATLRVI THTNPVHALL YLIISLLAIS GVFFSLGAYF AGALEIIVYA GAIMVLFVFV VMMLNLGGSE IEQERQWLK PQVWIGPAIL SAIMLVVIVY AILGVNDQGI DGTPISAKAV GITLFGPYVL AVELASMLLL AGLVVAFHVG R EERAGEVL SNRKDDSAKR KTEEHA

UniProtKB: NADH-quinone oxidoreductase subunit J

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Macromolecule #6: NADH-quinone oxidoreductase subunit M

MacromoleculeName: NADH-quinone oxidoreductase subunit M / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 56.56009 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString: MLLPWLILIP FIGGFLCWQT ERFGVKVPRW IALITMGLTL ALSLQLWLQG GYSLTQSAGI PQWQSEFDMP WIPRFGISIH LAIDGLSLL MVVLTGLLGV LAVLCSWKEI EKYQGFFHLN LMWILGGVIG VFLAIDMFLF FFFWEMMLVP MYFLIALWGH K ASDGKTRI ...String:
MLLPWLILIP FIGGFLCWQT ERFGVKVPRW IALITMGLTL ALSLQLWLQG GYSLTQSAGI PQWQSEFDMP WIPRFGISIH LAIDGLSLL MVVLTGLLGV LAVLCSWKEI EKYQGFFHLN LMWILGGVIG VFLAIDMFLF FFFWEMMLVP MYFLIALWGH K ASDGKTRI TAATKFFIYT QASGLVMLIA ILALVFVHYN ATGVWTFNYE ELLNTPMSSG VEYLLMLGFF IAFAVKMPVV PL HGWLPDA HSQAPTAGSV DLAGILLKTA AYGLLRFSLP LFPNASAEFA PIAMWLGVIG IFYGAWMAFA QTDIKRLIAY TSV SHMGFV LIAIYTGSQL AYQGAVIQMI AHGLSAAGLF ILCGQLYERI HTRDMRMMGG LWSKMKWLPA LSLFFAVATL GMPG TGNFV GEFMILFGSF QVVPVITVIS TFGLVFASVY SLAMLHRAYF GKAKSQIASQ ELPGMSLREL FMILLLVVLL VLLGF YPQP ILDTSHSAIG NIQQWFVNSV TTTRP

UniProtKB: NADH-quinone oxidoreductase subunit M

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Macromolecule #7: NADH-quinone oxidoreductase subunit N

MacromoleculeName: NADH-quinone oxidoreductase subunit N / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 52.072672 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString: MTITPQNLIA LLPLLIVGLT VVVVMLSIAW RRNHFLNATL SVIGLNAALV SLWFVGQAGA MDVTPLMRVD GFAMLYTGLV LLASLATCT FAYPWLEGYN DNKDEFYLLV LIAALGGILL ANANHLASLF LGIELISLPL FGLVGYAFRQ KRSLEASIKY T ILSAAASS ...String:
MTITPQNLIA LLPLLIVGLT VVVVMLSIAW RRNHFLNATL SVIGLNAALV SLWFVGQAGA MDVTPLMRVD GFAMLYTGLV LLASLATCT FAYPWLEGYN DNKDEFYLLV LIAALGGILL ANANHLASLF LGIELISLPL FGLVGYAFRQ KRSLEASIKY T ILSAAASS FLLFGMALVY AQSGDLSFVA LGKNLGDGML NEPLLLAGFG LMIVGLGFKL SLVPFHLWTP DVYQGAPAPV ST FLATASK IAIFGVVMRL FLYAPVGDSE AIRVVLAIIA FASIIFGNLM ALSQTNIKRL LGYSSISHLG YLLVALIALQ TGE MSMEAV GVYLAGYLFS SLGAFGVVSL MSSPYRGPDA DSLFSYRGLF WHRPILAAVM TVMMLSLAGI PMTLGFIGKF YVLA VGVQA HLWWLVGAVV VGSAIGLYYY LRVAVSLYLH APEQPGRDAP SNWQYSAGGI VVLISALLVL VLGVWPQPLI SIVRL AMPL M

UniProtKB: NADH-quinone oxidoreductase subunit N

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Macromolecule #8: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 8 / Number of copies: 12 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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Macromolecule #9: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate

MacromoleculeName: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
type: ligand / ID: 9 / Number of copies: 5 / Formula: 7PH
Molecular weightTheoretical: 564.732 Da
Chemical component information

ChemComp-7PH:
(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate

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Macromolecule #10: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 10 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #11: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 11 / Number of copies: 2 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

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Macromolecule #12: water

MacromoleculeName: water / type: ligand / ID: 12 / Number of copies: 177 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration4.0 mg/mL
BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 86927
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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