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- EMDB-52895: Cryo-EM structure of E. coli complex I variant V96P/N142M (NuoE) -

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Basic information

Entry
Database: EMDB / ID: EMD-52895
TitleCryo-EM structure of E. coli complex I variant V96P/N142M (NuoE)
Map dataComposite map of the entire complex, including the peripheral arm, the membrane arm, and the junction.
Sample
  • Complex: Respiratory complex I
    • Protein or peptide: x 13 types
  • Ligand: x 7 types
KeywordsRespiratory chain / Complex I / NADH ubiquinone oxidoreductase / electron transport / proton transport / MEMBRANE PROTEIN
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / cellular respiration / molybdopterin cofactor binding / 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 ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / cellular respiration / molybdopterin cofactor binding / 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 / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
NADH dehydrogenase, subunit CD / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. ...NADH dehydrogenase, subunit CD / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain I / 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 / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH ubiquinone oxidoreductase, F subunit / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / : / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 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 / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / Aspartate decarboxylase-like domain superfamily / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
NADH-quinone oxidoreductase subunit A / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit E / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit M / NADH-quinone oxidoreductase subunit N / NADH-quinone oxidoreductase subunit F ...NADH-quinone oxidoreductase subunit A / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit E / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit M / NADH-quinone oxidoreductase subunit N / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit C/D / NADH-quinone oxidoreductase subunit G / NADH-quinone oxidoreductase subunit L
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsSeifermann T / Wohlwend D / Friedrich T
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FR 1140/11-2 Germany
German Research Foundation (DFG)278002225 Germany
CitationJournal: Structure / Year: 2026
Title: Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I.
Authors: Daniel Wohlwend / Thilo Seifermann / Emmanuel Gnandt / Marta Vranas / Stefan Gerhardt / Thorsten Friedrich /
Abstract: Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. ...Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. Electrons are transferred from the primary acceptor flavin mononucleotide via a chain of iron-sulfur clusters to quinone. The enigmatic cluster N1a is conserved, but not part of this electron transfer chain. We reported on variants of the complex in which N1a is not detectable by EPR spectroscopy. This was tentatively attributed to the lower redox potential of the variant N1a. However, it remained an open question, whether the variants contain this cluster at all. Here, we determined the structures of these variants by X-ray crystallography and cryogenic-electron microscopy. Cluster N1a is present in all variants and the shift of its redox potential is explained by nearby structural changes. A role of the cluster for the mechanism of the complex is discussed.
History
DepositionFeb 24, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52895.png

Downloads & links

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Map

FileDownload / File: emd_52895.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the entire complex, including the peripheral arm, the membrane arm, and the junction.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 400 pix.
= 457.6 Å		1.14 Å/pix.
x 400 pix.
= 457.6 Å		1.14 Å/pix.
x 400 pix.
= 457.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.144 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.17127518 - 1.3170265
Average (Standard dev.)0.011277668 (±0.025946422)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 457.60004 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-quinone oxidoreductase subunit A
    • Protein or peptide: NADH-quinone oxidoreductase subunit B
    • Protein or peptide: NADH-quinone oxidoreductase subunit C/D
    • Protein or peptide: NADH-quinone oxidoreductase subunit E
    • Protein or peptide: NADH-quinone oxidoreductase subunit F
    • Protein or peptide: NADH-quinone oxidoreductase subunit G
    • Protein or peptide: NADH-quinone oxidoreductase subunit H
    • Protein or peptide: NADH-quinone oxidoreductase subunit I
    • Protein or peptide: NADH-quinone oxidoreductase subunit J
    • Protein or peptide: NADH-quinone oxidoreductase subunit K
    • Protein or peptide: NADH-quinone oxidoreductase subunit L
    • Protein or peptide: NADH-quinone oxidoreductase subunit M
    • Protein or peptide: NADH-quinone oxidoreductase subunit N
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: CALCIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: Respiratory complex I

SupramoleculeName: Respiratory complex I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 542 KDa

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Macromolecule #1: NADH-quinone oxidoreductase subunit A

MacromoleculeName: NADH-quinone oxidoreductase subunit A / 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 (E. coli)
Molecular weightTheoretical: 16.474283 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString:
MSMSTSTEVI AHHWAFAIFL IVAIGLCCLM LVGGWFLGGR ARARSKNVPF ESGIDSVGSA RLRLSAKFYL VAMFFVIFDV EALYLFAWS TSIRESGWVG FVEAAIFIFV LLAGLVYLVR IGALDWTPAR SRRERMNPET NSIANRQR

UniProtKB: NADH-quinone oxidoreductase subunit A

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Macromolecule #2: NADH-quinone oxidoreductase subunit B

MacromoleculeName: NADH-quinone oxidoreductase subunit B / 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 (E. coli)
Molecular weightTheoretical: 25.081809 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString: MDYTLTRIDP NGENDRYPLQ KQEIVTDPLE QEVNKNVFMG KLNDMVNWGR KNSIWPYNFG LSCCYVEMVT SFTAVHDVAR FGAEVLRAS PRQADLMVVA GTCFTKMAPV IQRLYDQMLE PKWVISMGAC ANSGGMYDIY SVVQGVDKFI PVDVYIPGCP P RPEAYMQA ...String:
MDYTLTRIDP NGENDRYPLQ KQEIVTDPLE QEVNKNVFMG KLNDMVNWGR KNSIWPYNFG LSCCYVEMVT SFTAVHDVAR FGAEVLRAS PRQADLMVVA GTCFTKMAPV IQRLYDQMLE PKWVISMGAC ANSGGMYDIY SVVQGVDKFI PVDVYIPGCP P RPEAYMQA LMLLQESIGK ERRPLSWVVG DQGVYRANMQ SERERKRGER IAVTNLRTPD EI

UniProtKB: NADH-quinone oxidoreductase subunit B

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Macromolecule #3: NADH-quinone oxidoreductase subunit C/D

MacromoleculeName: NADH-quinone oxidoreductase subunit C/D / 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 (E. coli)
Molecular weightTheoretical: 68.321945 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString: MTDLTAQEPA WQTRDHLDDP VIGELRNRFG PDAFTVQATR TGVPVVWIKR EQLLEVGDFL KKLPKPYVML FDLHGMDERL RTHREGLPA ADFSVFYHLI SIDRNRDIML KVALAENDLH VPTFTKLFPN ANWYERETWD LFGITFDGHP NLRRIMMPQT W KGHPLRKD ...String:
MTDLTAQEPA WQTRDHLDDP VIGELRNRFG PDAFTVQATR TGVPVVWIKR EQLLEVGDFL KKLPKPYVML FDLHGMDERL RTHREGLPA ADFSVFYHLI SIDRNRDIML KVALAENDLH VPTFTKLFPN ANWYERETWD LFGITFDGHP NLRRIMMPQT W KGHPLRKD YPARATEFSP FELTKAKQDL EMEALTFKPE EWGMKRGTEN EDFMFLNLGP NHPSAHGAFR IVLQLDGEEI VD CVPDIGY HHRGAEKMGE RQSWHSYIPY TDRIEYLGGC VNEMPYVLAV EKLAGITVPD RVNVIRVMLS ELFRINSHLL YIS TFIQDV GAMTPVFFAF TDRQKIYDLV EAITGFRMHP AWFRIGGVAH DLPRGWDRLL REFLDWMPKR LASYEKAALQ NTIL KGRSQ GVAAYGAKEA LEWGTTGAGL RATGIDFDVR KARPYSGYEN FDFEIPVGGG VSDCYTRVML KVEELRQSLR ILEQC LNNM PEGPFKADHP LTTPPPKERT LQHIETLITH FLQVSWGPVM PANESFQMIE ATKGINSYYL TSDGSTMSYR TRVRTP SFA HLQQIPAAIR GSLVSDLIVY LGSIDFVMSD VDR

UniProtKB: NADH-quinone oxidoreductase subunit C/D

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Macromolecule #4: NADH-quinone oxidoreductase subunit E

MacromoleculeName: NADH-quinone oxidoreductase subunit E / type: protein_or_peptide / ID: 4
Details: Point mutations V96P and N142M have been introduced by means of site-directed mutagenesis
Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.629125 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString:
MHENQQPQTE AFELSAAERE AIEHEMHHYE DPRAASIEAL KIVQKQRGWV PDGAIHAIAD VLGIPASDVE GVATFYSQIF RQPVGRHVI RYCDSVPCHI NGYQGIQAAL EKKLNIKPGQ TTFDGRFTLL PTCCLGNCDK GPMMMIDEDT HAHLTPEAIP E LLERYK

UniProtKB: NADH-quinone oxidoreductase subunit E

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Macromolecule #5: NADH-quinone oxidoreductase subunit F

MacromoleculeName: NADH-quinone oxidoreductase subunit F / type: protein_or_peptide / ID: 5
Details: The sequence MRGSHHHHHHTDPALRA was added in cloning and is an affinity sequence used for immobilized metal ion affinity chromatography, followed by an eight-amino-acid linker preceding the N-terminus of NuoF.
Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 51.208352 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString: MRGSHHHHHH TDPALRAKNI IRTPETHPLT WRLRDDKQPV WLDEYRSKNG YEGARKALTG LSPDEIVNQV KDAGLKGRGG AGFSTGLKW SLMPKDESMN IRYLLCNADE MEPGTYKDRL LMEQLPHLLV EGMLISAFAL KAYRGYIFLR GEYIEAAVNL R RAIAEATE ...String:
MRGSHHHHHH TDPALRAKNI IRTPETHPLT WRLRDDKQPV WLDEYRSKNG YEGARKALTG LSPDEIVNQV KDAGLKGRGG AGFSTGLKW SLMPKDESMN IRYLLCNADE MEPGTYKDRL LMEQLPHLLV EGMLISAFAL KAYRGYIFLR GEYIEAAVNL R RAIAEATE AGLLGKNIMG TGFDFELFVH TGAGRYICGE ETALINSLEG RRANPRSKPP FPATSGAWGK PTCVNNVETL CN VPAILAN GVEWYQNISK SKDAGTKLMG FSGRVKNPGL WELPFGTTAR EILEDYAGGM RDGLKFKAWQ PGGAGTDFLT EAH LDLPME FESIGKAGSR LGTALAMAVD HEINMVSLVR NLEEFFARES CGWCTPCRDG LPWSVKILRA LERGEGQPGD IETL EQLCR FLGPGKTFCA HAPGAVEPLQ SAIKYFREEF EAGIKQPFSN THLINGIQPN LLKERW

UniProtKB: NADH-quinone oxidoreductase subunit F

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Macromolecule #6: NADH-quinone oxidoreductase subunit G

MacromoleculeName: NADH-quinone oxidoreductase subunit G / 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 (E. coli)
Molecular weightTheoretical: 100.419211 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString: MATIHVDGKE YEVNGADNLL EACLSLGLDI PYFCWHPALG SVGACRQCAV KQYQNAEDTR GRLVMSCMTP ASDGTFISID DEEAKQFRE SVVEWLMTNH PHDCPVCEEG GNCHLQDMTV MTGHSFRRYR FTKRTHRNQD LGPFISHEMN RCIACYRCVR Y YKDYADGT ...String:
MATIHVDGKE YEVNGADNLL EACLSLGLDI PYFCWHPALG SVGACRQCAV KQYQNAEDTR GRLVMSCMTP ASDGTFISID DEEAKQFRE SVVEWLMTNH PHDCPVCEEG GNCHLQDMTV MTGHSFRRYR FTKRTHRNQD LGPFISHEMN RCIACYRCVR Y YKDYADGT DLGVYGAHDN VYFGRPEDGT LESEFSGNLV EICPTGVFTD KTHSERYNRK WDMQFAPSIC QQCSIGCNIS PG ERYGELR RIENRYNGTV NHYFLCDRGR FGYGYVNLKD RPRQPVQRRG DDFITLNAEQ AMQGAADILR QSKKVIGIGS PRA SVESNF ALRELVGEEN FYTGIAHGEQ ERLQLALKVL REGGIYTPAL REIESYDAVL VLGEDVTQTG ARVALAVRQA VKGK AREMA AAQKVADWQI AAILNIGQRA KHPLFVTNVD DTRLDDIAAW TYRAPVEDQA RLGFAIAHAL DNSAPAVDGI EPELQ SKID VIVQALAGAK KPLIISGTNA GSLEVIQAAA NVAKALKGRG ADVGITMIAR SVNSMGLGIM GGGSLEEALT ELETGR ADA VVVLENDLHR HASAIRVNAA LAKAPLVMVV DHQRTAIMEN AHLVLSAASF AESDGTVINN EGRAQRFFQV YDPAYYD SK TVMLESWRWL HSLHSTLLSR EVDWTQLDHV IDAVVAKIPE LAGIKDAAPD ATFRIRGQKL AREPHRYSGR TAMRANIS V HEPRQPQDID TMFTFSMEGN NQPTAHRSQV PFAWAPGWNS PQAWNKFQDE VGGKLRFGDP GVRLFETSEN GLDYFTSVP ARFQPQDGKW RIAPYYHLFG SDELSQRAPV FQSRMPQPYI KLNPADAAKL GVNAGTRVSF SYDGNTVTLP VEIAEGLTAG QVGLPMGMS GIAPVLAGAH LEDLKEAQQ

UniProtKB: NADH-quinone oxidoreductase subunit G

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Macromolecule #7: NADH-quinone oxidoreductase subunit H

MacromoleculeName: NADH-quinone oxidoreductase subunit H / 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 (E. coli)
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 #8: NADH-quinone oxidoreductase subunit I

MacromoleculeName: NADH-quinone oxidoreductase subunit I / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.562771 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString:
MTLKELLVGF GTQVRSIWMI GLHAFAKRET RMYPEEPVYL PPRYRGRIVL TRDPDGEERC VACNLCAVAC PVGCISLQKA ETKDGRWYP EFFRINFSRC IFCGLCEEAC PTTAIQLTPD FEMGEYKRQD LVYEKEDLLI SGPGKYPEYN FYRMAGMAID G KDKGEAEN EAKPIDVKSL LP

UniProtKB: NADH-quinone oxidoreductase subunit I

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Macromolecule #9: NADH-quinone oxidoreductase subunit J

MacromoleculeName: NADH-quinone oxidoreductase subunit J / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli (E. coli)
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 #10: NADH-quinone oxidoreductase subunit K

MacromoleculeName: NADH-quinone oxidoreductase subunit K / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli (E. coli)
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 #11: NADH-quinone oxidoreductase subunit L

MacromoleculeName: NADH-quinone oxidoreductase subunit L / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli (E. coli)
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

+
Macromolecule #12: NADH-quinone oxidoreductase subunit M

MacromoleculeName: NADH-quinone oxidoreductase subunit M / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli (E. coli)
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

+
Macromolecule #13: NADH-quinone oxidoreductase subunit N

MacromoleculeName: NADH-quinone oxidoreductase subunit N / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Escherichia coli (E. coli)
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

+
Macromolecule #14: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 14 / Number of copies: 10 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

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

+
Macromolecule #15: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 15 / Number of copies: 7 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #16: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 16 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

+
Macromolecule #17: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 17 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

+
Macromolecule #18: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #19: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 19 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

+
Macromolecule #20: water

MacromoleculeName: water / type: ligand / ID: 20 / Number of copies: 116 / 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

Concentration10.00 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
50.0 mMNaClsodium chloride
50.0 mMC6H13NO4SMES
5.0 mMMgCl2magnesium chloride
10.0 %C3H8O3glycerol
0.005 %C47H88O22lauryl maltose neopentyl glycol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Details: BLOTTING TIME FOR 6 S WITH FILTER PAPER.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k 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: 2.2 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7z7s

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: UCSF ChimeraX (ver. 1.7.1)
Details: THE COMPOSITE MAP WAS CREATED IN UCSF CHIMERAX USING THREE FOCUSED MAPS AND THE CONSENSUS MAP.
Number images used: 95103
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
Image processing #2

Image processing ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7z7s

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: UCSF ChimeraX (ver. 1.7.1)
Details: THE COMPOSITE MAP WAS CREATED IN UCSF CHIMERAX USING THREE FOCUSED MAPS AND THE CONSENSUS MAP.
Number images used: 95103
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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