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- EMDB-13214: Complex I from E. coli, DDM-purified, with NADH, Resting state -

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Basic information

Entry
Database: EMDB / ID: EMD-13214
TitleComplex I from E. coli, DDM-purified, with NADH, Resting state
Map data
Sample
  • Complex: Complex I
    • Protein or peptide: x 13 types
  • Ligand: x 7 types
KeywordsComplex I / NADH / Quinone / PROTON TRANSPORT
Function / homology
Function and homology information


: / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase complex / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / NADH dehydrogenase activity / electron transport coupled proton transport ...: / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase complex / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / NADH dehydrogenase activity / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / aerobic respiration / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / iron ion binding / membrane / metal ion binding / plasma membrane
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-quinone oxidoreductase, chain I / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain M/4 / 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-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 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / : / NADH-quinone oxidoreductase, subunit D / Aspartate decarboxylase-like domain superfamily / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / 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, 75kDa subunit, conserved site / 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 / Proton-conducting membrane transporter / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / 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. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / 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-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / 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 / Respiratory-chain NADH dehydrogenase 51 Kd subunit / 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 M / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase subunit C/D / NADH-quinone oxidoreductase subunit N / NADH-quinone oxidoreductase subunit A / Proton-translocating NADH-quinone oxidoreductase, chain L / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit E ...NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit M / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase subunit C/D / NADH-quinone oxidoreductase subunit N / NADH-quinone oxidoreductase subunit A / Proton-translocating NADH-quinone oxidoreductase, chain L / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit E / NADH-quinone oxidoreductase / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit K
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKravchuk V / Kampjut D / Sazanov L
Funding support Austria, 1 items
OrganizationGrant numberCountry
Not funded25541 Austria
CitationJournal: Nature / Year: 2022
Title: A universal coupling mechanism of respiratory complex I.
Authors: Vladyslav Kravchuk / Olga Petrova / Domen Kampjut / Anna Wojciechowska-Bason / Zara Breese / Leonid Sazanov /
Abstract: Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria. Complex I couples the transfer of two electrons from NADH to quinone ...Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a 'domino effect' series of proton transfers and electrostatic interactions: the forward wave ('dominoes stacking') primes the pump, and the reverse wave ('dominoes falling') results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes.
History
DepositionJul 15, 2021-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13214.png

Downloads & links

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Map

FileDownload / File: emd_13214.map.gz / Format: CCP4 / Size: 25.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 141 pix.
= 149.601 Å		1.06 Å/pix.
x 208 pix.
= 220.688 Å		1.06 Å/pix.
x 224 pix.
= 237.664 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.1289223 - 0.9288209
Average (Standard dev.)0.0075633363 (±0.033839412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions208224141
Spacing141208224
CellA: 149.601 Å / B: 220.688 Å / C: 237.664 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DDM NADH PA focused

Fileemd_13214_additional_1.map
AnnotationDDM NADH PA focused
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DDM NADH MD focused

Fileemd_13214_additional_2.map
AnnotationDDM NADH MD focused
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex I

EntireName: Complex I
Components
  • Complex: Complex I
    • Protein or peptide: NADH-quinone oxidoreductase subunit F
    • Protein or peptide: NADH dehydrogenase I subunit E
    • Protein or peptide: NADH-quinone oxidoreductase
    • Protein or peptide: NADH-quinone oxidoreductase subunit C/D
    • Protein or peptide: NADH-quinone oxidoreductase subunit B
    • Protein or peptide: NADH-quinone oxidoreductase subunit I
    • Protein or peptide: Proton-translocating NADH-quinone oxidoreductase, chain L
    • Protein or peptide: NADH dehydrogenase I subunit M
    • Protein or peptide: NADH-quinone oxidoreductase subunit N
    • Protein or peptide: NADH-quinone oxidoreductase subunit H
    • Protein or peptide: NADH-quinone oxidoreductase subunit A
    • Protein or peptide: NADH-quinone oxidoreductase subunit K
    • Protein or peptide: NADH-quinone oxidoreductase subunit J
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: CALCIUM ION
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: Ubiquinone-8

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Supramolecule #1: Complex I

SupramoleculeName: Complex I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BL21-DE3

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Macromolecule #1: NADH-quinone oxidoreductase subunit F

MacromoleculeName: NADH-quinone oxidoreductase subunit F / 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 BL21(DE3) (bacteria) / Strain: DE3
Molecular weightTheoretical: 48.879812 KDa
SequenceString: MKNIIRTPET HPLTWRLRDD KQPVWLDEYR SKNGYEGARK ALTGLSPDEI VNQVKDAGLK GRGGAGFSTG LKWSLMPKDE SMNIRYLLC NADEMEPGTY KDRLLMEQLP HLLVEGMLIS AFALKAYRGY IFLRGEYIEA AVNLRRAIAE ATEAGLLGKN I MGTGFDFE ...String:
MKNIIRTPET HPLTWRLRDD KQPVWLDEYR SKNGYEGARK ALTGLSPDEI VNQVKDAGLK GRGGAGFSTG LKWSLMPKDE SMNIRYLLC NADEMEPGTY KDRLLMEQLP HLLVEGMLIS AFALKAYRGY IFLRGEYIEA AVNLRRAIAE ATEAGLLGKN I MGTGFDFE LFVHTGAGRY ICGEETALIN SLEGRRANPR SKPPFPATSG AWGKPTCVNN VETLCNVPAI LANGVEWYQN IS KSKDAGT KLMGFSGRVK NPGLWELPFG TTAREILEDY AGGMRDGLKF KAWQPGGAGT DFLTEAHLDL PMEFESIGKA GSR LGTALA MAVDHEINMV SLVRNLEEFF ARESCGWCTP CRDGLPWSVK ILRALERGEG QPGDIETLEQ LCRFLGPGKT FCAH APGAV EPLQSAIKYF REEFEAGIKQ PFSNTHLING IQPNLLK

UniProtKB: NADH-quinone oxidoreductase subunit F

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Macromolecule #2: NADH dehydrogenase I subunit E

MacromoleculeName: NADH dehydrogenase I subunit E / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: DE3
Molecular weightTheoretical: 17.38977 KDa
SequenceString:
AFELSAAERE AIEHEMHHYE DPRAASIEAL KIVQKQRGWV PDGAIHAIAD VLGIPASDVE GVATFYSQIF RQPVGRHVIR YCDSVVCHI NGYQGIQAAL EKKLNIKPGQ TTFDGRFTLL PTCCLGNCDK GPNMMIDEDT HAHLTPEAIP ELLERYK

UniProtKB: NADH-quinone oxidoreductase subunit E

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Macromolecule #3: NADH-quinone oxidoreductase

MacromoleculeName: NADH-quinone oxidoreductase / 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 BL21(DE3) (bacteria) / Strain: DE3
Molecular weightTheoretical: 99.961672 KDa
SequenceString: ATIHVDGKEY EVNGADNLLE ACLSLGLDIP YFCWHPALGS VGACRQCAVK QYQNAEDTRG RLVMSCMTPA SDGTFISIDD EEAKQFRES VVEWLMTNHP HDCPVCEEGG NCHLQDMTVM TGHSFRRYRF TKRTHRNQDL GPFISHEMNR CIACYRCVRY Y KDYAGGTD ...String:
ATIHVDGKEY EVNGADNLLE ACLSLGLDIP YFCWHPALGS VGACRQCAVK QYQNAEDTRG RLVMSCMTPA SDGTFISIDD EEAKQFRES VVEWLMTNHP HDCPVCEEGG NCHLQDMTVM TGHSFRRYRF TKRTHRNQDL GPFISHEMNR CIACYRCVRY Y KDYAGGTD LGVYGAHDNV YFGRPEDGTL ESEFSGNLVE ICPTGVFTDK THSERYNRKW DMQFAPSICQ QCSIGCNISP GE RYGELRR IENRYNGTVN HYFLCDRGRF GYGYVNLKDR PRQPVQRRGD DFITLNAEQA MQGAADILRQ SKKVIGIGSP RAS VESNFA LRELVGEENF YTGIAHGEQE RLQLALKVLR EGGIYTPALR EIESYDAVLV LGEDVTQTGA RVALAVRQAV KGKA REMAA AQKVADWQIA AILNIGQRAK HPLFVTNVDD TRLDDIAAWT YRAPVEDQAR LGFAIAHALD NSAPAVDGIE PELQS KIDV IVQALAGAKK PLIISGTNAG SLEVIQAAAN VAKALKGRGA DVGITMIARS VNSMGLGIMG GGSLEEALTE LETGRA DAV VVLENDLHRH ASATRVNAAL AKAPLVMVVD HQRTAIMENA HLVLSAASFA ESDGTVINNE GRAQRFFQVY DPAYYDS KT VMLESWRWLH SLHSTLLSRE VDWTQLDHVI DAVVAKIPEL AGIKDAAPDA TFRIRGQKLA REPHRYSGRT AMRANISV H EPRQPQDIDT MFTFSMEGNN QPTAHRSQVP FAWAPGWNSP QAWNKFQDEV GGKLRFGDPG VRLFETSENG LDYFTSVPA RFQPQDGKWR IAPYYHLFGS DELSQRAPVF QSRMPQPYIK LNPADAAKLG VNAGTRVSFS YDGNTVTLPV EIAEGLTAGQ VGLPMGMSG IAPVLAGAHL EDLKEA

UniProtKB: NADH-quinone oxidoreductase

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Macromolecule #4: NADH-quinone oxidoreductase subunit C/D

MacromoleculeName: NADH-quinone oxidoreductase subunit C/D / 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 BL21(DE3) (bacteria) / Strain: B / BL21-DE3
Molecular weightTheoretical: 68.8105 KDa
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 IRT PSYAHLQQIP AAIRGSLVSD LIVYLGSIDF VMSDVDR

UniProtKB: NADH-quinone oxidoreductase subunit C/D

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Macromolecule #5: NADH-quinone oxidoreductase subunit B

MacromoleculeName: NADH-quinone oxidoreductase subunit B / 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 BL21(DE3) (bacteria) / Strain: DE3
Molecular weightTheoretical: 25.081809 KDa
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 #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 BL21(DE3) (bacteria) / Strain: DE3
Molecular weightTheoretical: 16.69009 KDa
SequenceString:
PEEPVYLPPR YRGRIVLTRD PDGEERCVAC NLCAVACPVG CISLQKAETK DGRWYPEFFR INFSRCIFCG LCEEACPTTA IQLTPDFEM GEYKRQDLVY EKEDLLISGP GKYPEYNFYR MAGMAIDGKD KGEAENEAKP IDVKSLLP

UniProtKB: NADH-quinone oxidoreductase subunit I

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Macromolecule #7: Proton-translocating NADH-quinone oxidoreductase, chain L

MacromoleculeName: Proton-translocating NADH-quinone oxidoreductase, chain L
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3
Molecular weightTheoretical: 66.513633 KDa
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 SAPGRLLSTW WYNAWGFDWL YDKVFVKPFL GIAWLL KRD PLNSMMNIPA VLSRFAGKGL LLSENGYLRW YVASMSIGAV VVLALLMVLR

UniProtKB: Proton-translocating NADH-quinone oxidoreductase, chain L

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Macromolecule #8: NADH dehydrogenase I subunit M

MacromoleculeName: NADH dehydrogenase I subunit M / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: DE3
Molecular weightTheoretical: 56.002473 KDa
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

UniProtKB: NADH-quinone oxidoreductase subunit M

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Macromolecule #9: NADH-quinone oxidoreductase subunit N

MacromoleculeName: NADH-quinone oxidoreductase subunit N / 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 BL21(DE3) (bacteria) / Strain: DE3
Molecular weightTheoretical: 52.072672 KDa
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 #10: NADH-quinone oxidoreductase subunit H

MacromoleculeName: NADH-quinone oxidoreductase subunit H / 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 BL21(DE3) (bacteria) / Strain: B / BL21-DE3
Molecular weightTheoretical: 36.240922 KDa
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 #11: NADH-quinone oxidoreductase subunit A

MacromoleculeName: NADH-quinone oxidoreductase subunit A / 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 BL21(DE3) (bacteria) / Strain: B / BL21-DE3
Molecular weightTheoretical: 16.474283 KDa
SequenceString:
MSMSTSTEVI AHHWAFAIFL IVAIGLCCLM LVGGWFLGGR ARARSKNVPF ESGIDSVGSA RLRLSAKFYL VAMFFVIFDV EALYLFAWS TSIRESGWVG FVEAAIFIFV LLAGLVYLVR IGALDWTPAR SRRERMNPET NSIANRQR

UniProtKB: NADH-quinone oxidoreductase subunit A

+
Macromolecule #12: NADH-quinone oxidoreductase subunit K

MacromoleculeName: NADH-quinone oxidoreductase subunit K / 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 BL21(DE3) (bacteria) / Strain: DE3
Molecular weightTheoretical: 10.852961 KDa
SequenceString:
MIPLQHGLIL AAILFVLGLT GLVIRRNLLF MLIGLEIMIN ASALAFVVAG SYWGQTDGQV MYILAISLAA AEASIGLALL LQLHRRRQN LNIDSVSEMR G

UniProtKB: NADH-quinone oxidoreductase subunit K

+
Macromolecule #13: NADH-quinone oxidoreductase subunit J

MacromoleculeName: NADH-quinone oxidoreductase subunit J / 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 BL21(DE3) (bacteria) / Strain: DE3
Molecular weightTheoretical: 18.834361 KDa
SequenceString:
MEFAFYICGL IAILATLRVI THTNPVHALL YLIISLLAIS GVFFSLGAYF AGALEIIVYA GAIMVLFVFV VMMLNLGGSE IEQERQWLK PQVWIGPAIL SAIMLVVIVY AILGVNDQGI DGTPISAKAV GITLFGPYVL AVELASMLLL AGLVVAFHVG R EERAGEVL SNRKDDS

UniProtKB: NADH-quinone oxidoreductase subunit J

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Macromolecule #14: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 14 / Number of copies: 7 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #15: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 15 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #16: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

MacromoleculeName: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / type: ligand / ID: 16 / Number of copies: 1 / Formula: NAI
Molecular weightTheoretical: 665.441 Da
Chemical component information

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

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Macromolecule #17: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 17 / 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 #18: CALCIUM ION

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

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Macromolecule #19: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 19 / Number of copies: 2 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

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

+
Macromolecule #20: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 20 / Number of copies: 1 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

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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 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
20.0 mMC6H13NO4SMES
2.0 mMCaCl2calcium chloride
250.0 mMNaClsodium chloride
0.4 %C24H46O11DDM
5.0 mMC21H27N7O14P2NADH
GridModel: Quantifoil R0.6/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 3492 / Average electron dose: 89.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 441374
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4hea

Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 145253
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4hea

source_name: PDB, initial_model_type: experimental model

3rko

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: ML
Output model

PDB-7p61:
Complex I from E. coli, DDM-purified, with NADH, Resting state

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