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- EMDB-11235: Respiratory complex I from Thermus thermophilus, NAD+ dataset, ma... -

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Basic information

Entry
Database: EMDB / ID: EMD-11235
TitleRespiratory complex I from Thermus thermophilus, NAD+ dataset, major state
Map dataPostprocessed map, NAD dataset, major state
Sample
  • Complex: Respiratory complex I from Thermus thermophilus
    • Protein or peptide: x 15 types
  • Ligand: x 3 types
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / iron-sulfur cluster assembly / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / ferric iron binding ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / iron-sulfur cluster assembly / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / ferric iron binding / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / metal ion binding / plasma membrane
Similarity search - Function
NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Frataxin/CyaY superfamily / Soluble ligand binding domain / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / SLBB domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain ...NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Frataxin/CyaY superfamily / Soluble ligand binding domain / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / SLBB domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Cro/C1-type helix-turn-helix domain / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / 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-quinone oxidoreductase, chain M/4 / Aspartate decarboxylase-like domain superfamily / NADH-ubiquinone oxidoreductase chain 4L/K / 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 / 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 / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / 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 / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Thioredoxin-like [2Fe-2S] ferredoxin / 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 7 / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 / NADH-quinone oxidoreductase subunit 3 / NADH-quinone oxidoreductase subunit 9 / NADH-quinone oxidoreductase subunit 10 / NADH-quinone oxidoreductase subunit 11 ...NADH-quinone oxidoreductase subunit 7 / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 / NADH-quinone oxidoreductase subunit 3 / NADH-quinone oxidoreductase subunit 9 / NADH-quinone oxidoreductase subunit 10 / NADH-quinone oxidoreductase subunit 11 / NADH-quinone oxidoreductase subunit 12 / NADH-quinone oxidoreductase subunit 13 / NADH-quinone oxidoreductase subunit 14 / NADH-quinone oxidoreductase subunit 15 / NADH-quinone oxidoreductase subunit 8
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKaszuba K / Tambalo M / Gallagher GT / Sazanov LA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105674180 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Key role of quinone in the mechanism of respiratory complex I.
Authors: Javier Gutiérrez-Fernández / Karol Kaszuba / Gurdeep S Minhas / Rozbeh Baradaran / Margherita Tambalo / David T Gallagher / Leonid A Sazanov /
Abstract: Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in ...Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.
History
DepositionJun 29, 2020-
Header (metadata) releaseSep 2, 2020-
Map releaseSep 2, 2020-
UpdateSep 2, 2020-
Current statusSep 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.23
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.23
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zjl
  • Surface level: 0.23
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11235.png

Downloads & links

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Map

FileDownload / File: emd_11235.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map, NAD dataset, major state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 512 pix.
= 880.64 Å		1.72 Å/pix.
x 512 pix.
= 880.64 Å		1.72 Å/pix.
x 512 pix.
= 880.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23 / Movie #1: 0.23
Minimum - Maximum-0.71455026 - 1.7128719
Average (Standard dev.)-0.00000185219 (±0.038882803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 880.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.721.721.72
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z880.640880.640880.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.7151.713-0.000

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Supplemental data

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Sample components

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Entire : Respiratory complex I from Thermus thermophilus

EntireName: Respiratory complex I from Thermus thermophilus
Components
  • Complex: Respiratory complex I from Thermus thermophilus
    • Protein or peptide: NADH-quinone oxidoreductase subunit 1
    • Protein or peptide: NADH-quinone oxidoreductase subunit 2
    • Protein or peptide: NADH-quinone oxidoreductase subunit 3
    • Protein or peptide: NADH-quinone oxidoreductase subunit 4
    • Protein or peptide: NADH-quinone oxidoreductase subunit 5
    • Protein or peptide: NADH-quinone oxidoreductase subunit 6
    • Protein or peptide: NADH-quinone oxidoreductase subunit 9
    • Protein or peptide: NADH-quinone oxidoreductase subunit 15
    • Protein or peptide: NADH-quinone oxidoreductase subunit 7
    • Protein or peptide: NADH-quinone oxidoreductase subunit 10
    • Protein or peptide: NADH-quinone oxidoreductase subunit 11
    • Protein or peptide: NADH-quinone oxidoreductase subunit 12
    • Protein or peptide: NADH-quinone oxidoreductase subunit 13
    • Protein or peptide: NADH-quinone oxidoreductase subunit 14
    • Protein or peptide: NADH-quinone oxidoreductase subunit 8
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

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Supramolecule #1: Respiratory complex I from Thermus thermophilus

SupramoleculeName: Respiratory complex I from Thermus thermophilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Thermus thermophilus (bacteria) / Strain: HB8
Molecular weightTheoretical: 530 KDa

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Macromolecule #1: NADH-quinone oxidoreductase subunit 1

MacromoleculeName: NADH-quinone oxidoreductase subunit 1 / 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: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 48.693715 KDa
SequenceString: MTGPILSGLD PRFERTLYAH VGKEGSWTLD YYLRHGGYET AKRVLKEKTP DEVIEEVKRS GLRGRGGAGF PTGLKWSFMP KDDGKQHYL ICNADESEPG SFKDRYILED VPHLLIEGMI LAGYAIRATV GYIYVRGEYR RAADRLEQAI KEARARGYLG K NLFGTDFS ...String:
MTGPILSGLD PRFERTLYAH VGKEGSWTLD YYLRHGGYET AKRVLKEKTP DEVIEEVKRS GLRGRGGAGF PTGLKWSFMP KDDGKQHYL ICNADESEPG SFKDRYILED VPHLLIEGMI LAGYAIRATV GYIYVRGEYR RAADRLEQAI KEARARGYLG K NLFGTDFS FDLHVHRGAG AYICGEETAL MNSLEGLRAN PRLKPPFPAQ SGLWGKPTTI NNVETLASVV PIMERGADWF AQ MGTEQSK GMKLYQISGP VKRPGVYELP MGTTFRELIY EWAGGPLEPI QAIIPGGSST PPLPFTEEVL DTPMSYEHLQ AKG SMLGTG GVILIPERVS MVDAMWNLTR FYAHESCGKC TPCREGVAGF MVNLFAKIGT GQGEEKDVEN LEALLPLIEG RSFC PLADA AVWPVKGSLR HFKDQYLALA REKRPVPRPS LWR

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Macromolecule #2: NADH-quinone oxidoreductase subunit 2

MacromoleculeName: NADH-quinone oxidoreductase subunit 2 / 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: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 20.309162 KDa
SequenceString:
MGFFDDKQDF LEETFAKYPP EGRRAAIMPL LRRVQQEEGW IRPERIEEIA RLVGTTPTEV MGVASFYSYY QFVPTGKYHL QVCATLSCK LAGAEELWDY LTETLGIGPG EVTPDGLFSV QKVECLGSCH TAPVIQVNDE PYVECVTRAR LEALLAGLRA G KRLEEIEL PGKCGHHVHE VEV

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Macromolecule #3: NADH-quinone oxidoreductase subunit 3

MacromoleculeName: NADH-quinone oxidoreductase subunit 3 / 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: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 86.656203 KDa
SequenceString: MVRVKVNDRI VEVPPGTSVM DAVFHAGYDV PLFCSEKHLS PIGACRMCLV RIGLPKKGPD GKPLLNEKGE PEIQWQPKLA ASCVTAVAD GMVVDTLSDV VREAQAGMVE FTLLNHPLDC PTCDKGGACE LQDRTVEYGL YEKYYQKGPL ELPVYTRFEF T RRHVDKHH ...String:
MVRVKVNDRI VEVPPGTSVM DAVFHAGYDV PLFCSEKHLS PIGACRMCLV RIGLPKKGPD GKPLLNEKGE PEIQWQPKLA ASCVTAVAD GMVVDTLSDV VREAQAGMVE FTLLNHPLDC PTCDKGGACE LQDRTVEYGL YEKYYQKGPL ELPVYTRFEF T RRHVDKHH PLSPFVILDR ERCIHCKRCV RYFEEVPGDE VLDFIERGVH TFIGTMDFGL PSGFSGNITD ICPVGALLDL TA RFRARNW EMEETPTTCA LCPVGCGITA DTRSGELLRI RAREVPEVNE IWICDAGRFG HEWADQNRLK TPLVRKEGRL VEA TWEEAF LALKEGLKEA RGEEVGLYLA HDATLEEGLL ASELAKALKT PHLDFQGRTA APASLFPPAS LEDLLQADFA LVLG DPTEE APILHLRLSE FVRDLKPPHR YNHGTPFADL QIKERMPRRT DKMALFAPYR APLMKWAAIH EVHRPGEERE ILLAL LGDK EGSEMVAKAK EAWEKAKNPV LILGAGVLQD TVAAERARLL AERKGAKVLA MTPAANARGL EAMGVLPGAK GASWDE PGA LYAYYGFVPP EEALKGKRFV VMHLSHLHPL AERYAHVVLP APTFYEKRGH LVNLEGRVLP LSPAPIENGE AEGALQV LA LLAEALGVRP PFRLHLEAQK ALKARKVPEA MGRLSFRLKE LRPKERKGAF YLRPTMWKAH QAVGKAQEAA RAELWAHP E TARAEALPEG AQVAVETPFG RVEARVVHRE DVPKGHLYLS ALGPAAGLRV EGRVLVPAGG EA

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Macromolecule #4: NADH-quinone oxidoreductase subunit 4

MacromoleculeName: NADH-quinone oxidoreductase subunit 4 / 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: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 46.428027 KDa
SequenceString: MREEFLEEIP LDAPPEEAKE LRTEVMTLNV GPQHPSTHGV LRLMVTLSGE EVLEVVPHIG YLHTGFEKTM EHRTYLQNIT YTPRMDYLH SFAHDLAYAL AVEKLLGAVV PPRAETIRVI LNELSRLASH LVFLGTGLLD LGALTPFFYA FRERETILDL F EWVTGQRF ...String:
MREEFLEEIP LDAPPEEAKE LRTEVMTLNV GPQHPSTHGV LRLMVTLSGE EVLEVVPHIG YLHTGFEKTM EHRTYLQNIT YTPRMDYLH SFAHDLAYAL AVEKLLGAVV PPRAETIRVI LNELSRLASH LVFLGTGLLD LGALTPFFYA FRERETILDL F EWVTGQRF HHNYIRIGGV KEDLPEEFVP ELKKLLEVLP HRIDEYEALF AESPIFYERA RGVGVIPPEV AIDLGLTGGS LR ASGVNYD VRKAYPYSGY ETYTFDVPLG ERGDVFDRML VRIREMRESV KIIKQALERL EPGPVRDPNP QITPPPRHLL ETS MEAVIY HFKHYTEGFH PPKGEVYVPT ESARGELGYY IVSDGGSMPY RVKVRAPSFV NLQSLPYACK GEQVPDMVAI IASL DPVMG DVDR

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Macromolecule #5: NADH-quinone oxidoreductase subunit 5

MacromoleculeName: NADH-quinone oxidoreductase subunit 5 / 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: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 23.893254 KDa
SequenceString: MRLERVLEEA RAKGYPIEDN GLGNLWVVLP RERFKEEMAH YKAMGFNFLA DIVGLDYLTY PDPRPERFAV VYELVSLPGW KDGDGSRFF VRVYVPEEDP RLPTVTDLWG SANFLEREVY DLFGIVFEGH PDLRKILTPE DLEGHPLRKD YPLGETPTLF R EGRYIIPA ...String:
MRLERVLEEA RAKGYPIEDN GLGNLWVVLP RERFKEEMAH YKAMGFNFLA DIVGLDYLTY PDPRPERFAV VYELVSLPGW KDGDGSRFF VRVYVPEEDP RLPTVTDLWG SANFLEREVY DLFGIVFEGH PDLRKILTPE DLEGHPLRKD YPLGETPTLF R EGRYIIPA EFRAALTGKD PGLTFYKGGS RKGYRSLWAD LKKAREVKG

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Macromolecule #6: NADH-quinone oxidoreductase subunit 6

MacromoleculeName: NADH-quinone oxidoreductase subunit 6 / 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: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 20.262564 KDa
SequenceString:
MALKDLFERD VQELEREGIL FTTLEKLVAW GRSNSLWPAT FGLACCAIEM MASTDARNDL ARFGSEVFRA SPRQADVMIV AGRLSKKMA PVMRRVWEQM PDPKWVISMG ACASSGGMFN NYAIVQNVDS VVPVDVYVPG CPPRPEALIY AVMQLQKKVR G QAYNERGE RLPPVAAWKR TRG

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Macromolecule #7: NADH-quinone oxidoreductase subunit 9

MacromoleculeName: NADH-quinone oxidoreductase subunit 9 / 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: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 20.106309 KDa
SequenceString:
MTLKALAQSL GITLKYLFSK PVTVPYPDAP VALKPRFHGR HVLTRHPNGL EKCIGCSLCA AACPAYAIYV EPAENDPENP VSAGERYAK VYEINMLRCI FCGLCEEACP TGAIVLGYDF EMADYEYSDL VYGKEDMLVD VVGTKPQRRE AKRTGKPVKV G YVVPYVRP ELEGFKAPTE GGKR

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Macromolecule #8: NADH-quinone oxidoreductase subunit 15

MacromoleculeName: NADH-quinone oxidoreductase subunit 15 / 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: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 14.812074 KDa
SequenceString:
MSASSERELY EAWVELLSWM REYAQAKGVR FEKEADFPDF IYRMERPYDL PTTIMTASLS DGLGEPFLLA DVSPRHAKLK RIGLRLPRA HIHLHAHYEP GKGLVTGKIP LTKERFFALA DRAREALAFA

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Macromolecule #9: NADH-quinone oxidoreductase subunit 7

MacromoleculeName: NADH-quinone oxidoreductase subunit 7 / 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: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 13.154656 KDa
SequenceString:
MAPIQEYVGT LIYVGVALFI GVAALLVGAL LGPKKPGRAK LMPYESGNDP AGEVKRFPVH FYVVAMLFIL FDVEVAFLWP YAVSAGGLG LYGFLGVLAF TLLLFVGFLY EWWKGVMRWH

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Macromolecule #10: NADH-quinone oxidoreductase subunit 10

MacromoleculeName: NADH-quinone oxidoreductase subunit 10 / 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: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 18.56333 KDa
SequenceString:
MSLLEGLALF LLLLSGVLVV TLRNAIHAAL ALILNFLVLA GVYVALDARF LGFIQVIVYA GAIVVLFLFV IMLLFAAQGE IGFDPLVRS RPLAALLALG VAGILAAGLW GLDLAFTQDL KGGLPQALGP LLYGDWLFVL LAVGFLLMAA TVVAVALVEP G KASRAKEA EKREEVAR

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Macromolecule #11: NADH-quinone oxidoreductase subunit 11

MacromoleculeName: NADH-quinone oxidoreductase subunit 11 / 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: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 10.002788 KDa
SequenceString:
MSYLLTSALL FALGVYGVLT RRTAILVFLS IELMLNAANL SLVGFARAYG LDGQVAALMV IAVAAAEVAV GLGLIVAIFR HRESTAVDD LSELRG

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Macromolecule #12: NADH-quinone oxidoreductase subunit 12

MacromoleculeName: NADH-quinone oxidoreductase subunit 12 / 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: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 65.18993 KDa
SequenceString: MALLGTILLP LLGFALLGLF GKRMREPLPG VLASGLVLAS FLLGAGLLLS GGARFQAEWL PGIPFSLLLD NLSGFMLLIV TGVGFLIHV YAIGYMGGDP GYSRFFAYFN LFIAMMLTLV LADSYPVMFI GWEGVGLASF LLIGFWYKNP QYADSARKAF I VNRIGDLG ...String:
MALLGTILLP LLGFALLGLF GKRMREPLPG VLASGLVLAS FLLGAGLLLS GGARFQAEWL PGIPFSLLLD NLSGFMLLIV TGVGFLIHV YAIGYMGGDP GYSRFFAYFN LFIAMMLTLV LADSYPVMFI GWEGVGLASF LLIGFWYKNP QYADSARKAF I VNRIGDLG FMLGMAILWA LYGTLSISEL KEAMEGPLKN PDLLALAGLL LFLGAVGKSA QIPLMVWLPD AMAGPTPVSA LI HAATMVT AGVYLIARSS FLYSVLPDVS YAIAVVGLLT AAYGALSAFG QTDIKKIVAY STISQLGYMF LAAGVGAYWV ALF HVFTHA FFKALLFLAS GSVIHALGGE QDVRKMGGLW KHLPQTRWHA LIGALALGGL PLLSGFWSKD AILAATLTYP FGGV GFYVG ALLVAVLTAM YAMRWFVLVF LGEERGHHHP HEAPPVMLWP NHLLALGSVL AGYLALPHPL PNVLEPFLKP ALAEV EAHH LSLGAEWGLI ALSAAVALLG LWAGFVFFQR KVFPAWYLAF EAASREAFYV DRAYNALIVN PLKALAEALF YGDRGL LSG YFGLGGAARS LGQGLARLQT GYLRVYALLF VLGALLLLGV MRW

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Macromolecule #13: NADH-quinone oxidoreductase subunit 13

MacromoleculeName: NADH-quinone oxidoreductase subunit 13 / 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: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 49.247117 KDa
SequenceString: MVVLAVLLPV VFGALLLLGL PRALGVLGAG LSFLLNLYLF LTHPGGVAHA FQAPLLPGAG VYWAFGLDGL SALFFLTIAL TVFLGALVA RVEGRFLGLA LLMEGLLLGL FAARDLLVFY VFFEAALIPA LLMLYLYGGE GRTRALYTFV LFTLVGSLPM L AAVLGARL ...String:
MVVLAVLLPV VFGALLLLGL PRALGVLGAG LSFLLNLYLF LTHPGGVAHA FQAPLLPGAG VYWAFGLDGL SALFFLTIAL TVFLGALVA RVEGRFLGLA LLMEGLLLGL FAARDLLVFY VFFEAALIPA LLMLYLYGGE GRTRALYTFV LFTLVGSLPM L AAVLGARL LSGSPTFLLE DLLAHPLQEE AAFWVFLGFA LAFAIKTPLF PLHAWLPPFH QENHPSGLAD ALGTLYKVGV FA FFRFAIP LAPEGFAQAQ GLLLFLAALS ALYGAWVAFA AKDFKTLLAY AGLSHMGVAA LGVFSGTPEG AMGGLYLLAA SGV YTGGLF LLAGRLYERT GTLEIGRYRG LAQSAPGLAA LALILFLAMV GLPGLSGFPG EFLTLLGAYK ASPWLAALAF LSVI ASAAY ALTAFQKTFW EEGGSGVKDL AGAEWGFALL SVLALLLMGV FPGYFARGLH PLAEAFAKLL GGGA

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Macromolecule #14: NADH-quinone oxidoreductase subunit 14

MacromoleculeName: NADH-quinone oxidoreductase subunit 14 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 44.463895 KDa
SequenceString: MTLAILAVFS VALTLLGFVL PPQGVKRATL LGLALALASL LLTWGKPFAF GPYAVDGVSQ VFTLLALLGA LWTVGLVRSG RFEFYLLVL YAALGMHLLA STRHLLLMLV ALEALSLPLY ALATWRRGQG LEAALKYFLL GALAAAFFLY GAALFYGATG S LVLGAPGE ...String:
MTLAILAVFS VALTLLGFVL PPQGVKRATL LGLALALASL LLTWGKPFAF GPYAVDGVSQ VFTLLALLGA LWTVGLVRSG RFEFYLLVL YAALGMHLLA STRHLLLMLV ALEALSLPLY ALATWRRGQG LEAALKYFLL GALAAAFFLY GAALFYGATG S LVLGAPGE GPLYALALGL LLVGLGFKAA LAPFHFWTPD VYQGSPTPVV LFMATSVKAA AFAALLRVAA PPEALALLVA LS VVVGNLA ALAQKEAKRL LAYSSIAHAG YMALALYTGN AQALGFYLLT YVLATGLAFA VLSQISPDRV PLEALRGLYR KDP LLGLAF LVAMLSLLGL PPLAGFWGKY LAFAEAARAG AWGVLVLALV TSAVSAYYYL GLGLAVFARP EETPFRPGPP WARA AVVAA GVLLLALGLL PGLVLPALAA GG

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Macromolecule #15: NADH-quinone oxidoreductase subunit 8

MacromoleculeName: NADH-quinone oxidoreductase subunit 8 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 41.034523 KDa
SequenceString: MTWSYPVDPY WMVALKALLV VVGLLTAFAF MTLIERRLLA RFQVRMGPNR VGPFGLLQPL ADAIKSIFKE DIVVAQADRF LFVLAPLIS VVFALLAFGL IPFGPPGSFF GYQPWVINLD LGILYLFAVS ELAVYGIFLS GWASGSKYSL LGSLRSSASL I SYELGLGL ...String:
MTWSYPVDPY WMVALKALLV VVGLLTAFAF MTLIERRLLA RFQVRMGPNR VGPFGLLQPL ADAIKSIFKE DIVVAQADRF LFVLAPLIS VVFALLAFGL IPFGPPGSFF GYQPWVINLD LGILYLFAVS ELAVYGIFLS GWASGSKYSL LGSLRSSASL I SYELGLGL ALLAPVLLVG SLNLNDIVNW QKEHGWLFLY AFPAFLVYLI ASMAEAARTP FDLPEAEQEL VGGYHTEYSS IK WALFQMA EYIHFITASA LIPTLFLGGW TMPVLEVPYL WMFLKIAFFL FFFIWIRATW FRLRYDQLLR FGWGFLFPLA LLW FLVTAL VVALDLPRTY LLYLSALSFL VLLGAVLYTP KPARKGGGA

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Macromolecule #16: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 16 / Number of copies: 7 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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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

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Macromolecule #18: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 18 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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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

Concentration6.0 mg/mL
BufferpH: 6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III
Detailswith 5 mM NAD+

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-34 / Number grids imaged: 1 / Number real images: 710 / Average exposure time: 2.0 sec. / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.5 µm
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: 91000
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6y11

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 48000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6y11

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6zjl:
Respiratory complex I from Thermus thermophilus, NAD+ dataset, major state

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