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- EMDB-55752: Local refinement of E. coli Complex I D79N NuoA mutant hydrophili... -

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Basic information

Entry
Database: EMDB / ID: EMD-55752
TitleLocal refinement of E. coli Complex I D79N NuoA mutant hydrophilic domain in LMNG
Map data
Sample
  • Complex: NADH-quinone oxidoreductase, Complex I D79N NuoA mutant
    • Protein or peptide: x 6 types
  • Ligand: x 5 types
KeywordsPROTON TRANSPORT / bioenergetics / Leigh's syndrome
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 / molybdopterin cofactor binding / cellular respiration / electron transport coupled proton transport / oxidoreductase activity, acting on NAD(P)H / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding ...NADH dehydrogenase (quinone) (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase complex / molybdopterin cofactor binding / cellular respiration / electron transport coupled proton transport / oxidoreductase activity, acting on NAD(P)H / 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 / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
NADH dehydrogenase, subunit CD / 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-quinone oxidoreductase, chain I ...NADH dehydrogenase, subunit CD / 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-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / 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. / 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:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / 2Fe-2S iron-sulfur cluster binding domain / 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. / 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 / Aspartate decarboxylase-like domain superfamily / 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 B / NADH-quinone oxidoreductase subunit E / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit C/D / NADH-quinone oxidoreductase subunit G
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 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: To Be Published
Title: A Carboxylate Switch Point Controls Long-Range Energy Transduction in Respiratory Complex I
Authors: Beghiah A / Saura P / Kovalova T / Hoeser F / Friedrich F / Kaila VRI
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_55752.png

Downloads & links

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Map

FileDownload / File: emd_55752.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

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.9963874 - 2.932855
Average (Standard dev.)-0.00047079605 (±0.041003425)
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_55752_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_55752_additional_1.map
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Half map: #2

Fileemd_55752_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_55752_half_map_2.map
Projections & Slices
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Sample components

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Entire : NADH-quinone oxidoreductase, Complex I D79N NuoA mutant

EntireName: NADH-quinone oxidoreductase, Complex I D79N NuoA mutant
Components
  • Complex: NADH-quinone oxidoreductase, Complex I D79N NuoA mutant
    • 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 I
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: CALCIUM ION
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: water

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Supramolecule #1: NADH-quinone oxidoreductase, Complex I D79N NuoA mutant

SupramoleculeName: NADH-quinone oxidoreductase, Complex I D79N NuoA mutant
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Escherichia coli BW25113 (bacteria)

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Macromolecule #1: NADH-quinone oxidoreductase subunit B

MacromoleculeName: NADH-quinone oxidoreductase subunit B / 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: 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 #2: NADH-quinone oxidoreductase subunit C/D

MacromoleculeName: NADH-quinone oxidoreductase subunit C/D / 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: 68.780477 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString: MVNNMTDLTA QEPAWQTRDH LDDPVIGELR NRFGPDAFTV QATRTGVPVV WIKREQLLEV GDFLKKLPKP YVMLFDLHGM DERLRTHRE GLPAADFSVF YHLISIDRNR DIMLKVALAE NDLHVPTFTK LFPNANWYER ETWDLFGITF DGHPNLRRIM M PQTWKGHP ...String:
MVNNMTDLTA QEPAWQTRDH LDDPVIGELR NRFGPDAFTV QATRTGVPVV WIKREQLLEV GDFLKKLPKP YVMLFDLHGM DERLRTHRE GLPAADFSVF YHLISIDRNR DIMLKVALAE NDLHVPTFTK LFPNANWYER ETWDLFGITF DGHPNLRRIM M PQTWKGHP LRKDYPARAT EFSPFELTKA KQDLEMEALT FKPEEWGMKR GTENEDFMFL NLGPNHPSAH GAFRIVLQLD GE EIVDCVP DIGYHHRGAE KMGERQSWHS YIPYTDRIEY LGGCVNEMPY VLAVEKLAGI TVPDRVNVIR VMLSELFRIN SHL LYISTF IQDVGAMTPV FFAFTDRQKI YDLVEAITGF RMHPAWFRIG GVAHDLPRGW DRLLREFLDW MPKRLASYEK AALQ NTILK GRSQGVAAYG AKEALEWGTT GAGLRATGID FDVRKARPYS GYENFDFEIP VGGGVSDCYT RVMLKVEELR QSLRI LEQC LNNMPEGPFK ADHPLTTPPP KERTLQHIET LITHFLQVSW GPVMPANESF QMIEATKGIN SYYLTSDGST MSYRTR VRT PSFAHLQQIP AAIRGSLVSD LIVYLGSIDF VMSDVDR

UniProtKB: NADH-quinone oxidoreductase subunit C/D

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Macromolecule #3: NADH-quinone oxidoreductase subunit E

MacromoleculeName: NADH-quinone oxidoreductase subunit E / 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: 18.614049 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString:
MHENQQPQTE AFELSAAERE AIEHEMHHYE DPRAASIEAL KIVQKQRGWV PDGAIHAIAD VLGIPASDVE GVATFYSQIF RQPVGRHVI RYCDSVVCHI NGYQGIQAAL EKKLNIKPGQ TTFDGRFTLL PTCCLGNCDK GPNMMIDEDT HAHLTPEAIP E LLERYK

UniProtKB: NADH-quinone oxidoreductase subunit E

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Macromolecule #4: NADH-quinone oxidoreductase subunit F

MacromoleculeName: NADH-quinone oxidoreductase subunit F / 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: 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 #5: NADH-quinone oxidoreductase subunit G

MacromoleculeName: NADH-quinone oxidoreductase subunit G / 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: 100.66357 KDa
Recombinant expressionOrganism: Escherichia coli BW25113 (bacteria)
SequenceString: MLMATIHVDG KEYEVNGADN LLEACLSLGL DIPYFCWHPA LGSVGACRQC AVKQYQNAED TRGRLVMSCM TPASDGTFIS IDDEEAKQF RESVVEWLMT NHPHDCPVCE EGGNCHLQDM TVMTGHSFRR YRFTKRTHRN QDLGPFISHE MNRCIACYRC V RYYKDYAD ...String:
MLMATIHVDG KEYEVNGADN LLEACLSLGL DIPYFCWHPA LGSVGACRQC AVKQYQNAED TRGRLVMSCM TPASDGTFIS IDDEEAKQF RESVVEWLMT NHPHDCPVCE EGGNCHLQDM TVMTGHSFRR YRFTKRTHRN QDLGPFISHE MNRCIACYRC V RYYKDYAD GTDLGVYGAH DNVYFGRPED GTLESEFSGN LVEICPTGVF TDKTHSERYN RKWDMQFAPS ICQQCSIGCN IS PGERYGE LRRIENRYNG TVNHYFLCDR GRFGYGYVNL KDRPRQPVQR RGDDFITLNA EQAMQGAADI LRQSKKVIGI GSP RASVES NFALRELVGE ENFYTGIAHG EQERLQLALK VLREGGIYTP ALREIESYDA VLVLGEDVTQ TGARVALAVR QAVK GKARE MAAAQKVADW QIAAILNIGQ RAKHPLFVTN VDDTRLDDIA AWTYRAPVED QARLGFAIAH ALDNSAPAVD GIEPE LQSK IDVIVQALAG AKKPLIISGT NAGSLEVIQA AANVAKALKG RGADVGITMI ARSVNSMGLG IMGGGSLEEA LTELET GRA DAVVVLENDL HRHASAIRVN AALAKAPLVM VVDHQRTAIM ENAHLVLSAA SFAESDGTVI NNEGRAQRFF QVYDPAY YD SKTVMLESWR WLHSLHSTLL SREVDWTQLD HVIDAVVAKI PELAGIKDAA PDATFRIRGQ KLAREPHRYS GRTAMRAN I SVHEPRQPQD IDTMFTFSME GNNQPTAHRS QVPFAWAPGW NSPQAWNKFQ DEVGGKLRFG DPGVRLFETS ENGLDYFTS VPARFQPQDG KWRIAPYYHL FGSDELSQRA PVFQSRMPQP YIKLNPADAA KLGVNAGTRV SFSYDGNTVT LPVEIAEGLT AGQVGLPMG MSGIAPVLAG AHLEDLKEAQ Q

UniProtKB: NADH-quinone oxidoreductase subunit G

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Macromolecule #6: NADH-quinone oxidoreductase subunit I

MacromoleculeName: NADH-quinone oxidoreductase subunit I / 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: 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 #7: IRON/SULFUR CLUSTER

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

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #8: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 8 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #9: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 9 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #10: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 10 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 296 / 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: 2.59 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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Atomic model buiding 1

Initial modelChain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9tan:
Local refinement of E. coli Complex I D79N NuoA mutant hydrophilic domain in LMNG

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