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- EMDB-14632: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Re... -

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Basic information

Entry
Database: EMDB / ID: EMD-14632
TitleComplex I from E. coli, LMNG-purified, under Turnover at pH 6, Resting stateRespiratory complex I
Map data
Sample
  • Complex: Complex IRespiratory complex I
    • Protein or peptide: x 13 types
  • Ligand: x 7 types
Function / homology
Function and homology information


NADH dehydrogenase complex / oxidoreductase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / respiratory chain complex I / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport ...NADH dehydrogenase complex / oxidoreductase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / respiratory chain complex I / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / 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
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 / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I ...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 / 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-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, F subunit / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / 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. / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / 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 / NuoE domain / NADH:ubiquinone oxidoreductase / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH-quinone oxidoreductase subunit E, N-terminal / 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. / Aspartate decarboxylase-like domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / 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 L / NADH-quinone oxidoreductase subunit C/D / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit E / NADH-quinone oxidoreductase subunit A / NADH-quinone oxidoreductase subunit M ...NADH-quinone oxidoreductase subunit L / NADH-quinone oxidoreductase subunit C/D / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit E / NADH-quinone oxidoreductase subunit A / NADH-quinone oxidoreductase subunit M / NADH-quinone oxidoreductase subunit N / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 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
DepositionMar 28, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateOct 5, 2022-
Current statusOct 5, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14632.png

Downloads & links

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Map

FileDownload / File: emd_14632.map.gz / Format: CCP4 / Size: 24.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 231 pix.
= 244.86 Å		1.06 Å/pix.
x 194 pix.
= 205.64 Å		1.06 Å/pix.
x 144 pix.
= 152.64 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: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.035797678 - 0.538314
Average (Standard dev.)0.0042774365 (±0.02034352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions194144231
Spacing144194231
CellA: 152.63998 Å / B: 205.63998 Å / C: 244.85999 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: MD focused map

Fileemd_14632_additional_1.map
AnnotationMD focused map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: PA focused map

Fileemd_14632_additional_2.map
AnnotationPA focused map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex I

EntireName: Complex IRespiratory complex I
Components
  • Complex: Complex IRespiratory complex I
    • Protein or peptide: NADH-quinone oxidoreductase subunit FNADH dehydrogenase (quinone)
    • Protein or peptide: NADH dehydrogenase I subunit E
    • Protein or peptide: NADH-quinone oxidoreductaseNADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit C/DNADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit BNADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit INADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit HNADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit ANADH dehydrogenase (quinone)
    • Protein or peptide: NADH dehydrogenase subunit L
    • Protein or peptide: NADH dehydrogenase I subunit M
    • Protein or peptide: NADH-quinone oxidoreductase subunit NNADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit KNADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit JNADH dehydrogenase (quinone)
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: CALCIUM IONCalcium
  • Ligand: EICOSANEIcosane
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine

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Supramolecule #1: Complex I

SupramoleculeName: Complex I / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MC4100

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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 (E. coli)
Molecular weightTheoretical: 49.352332 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 IQPNLLKERW

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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 (E. coli)
Molecular weightTheoretical: 18.614049 KDa
SequenceString:
MHENQQPQTE AFELSAAERE AIEHEMHHYE DPRAASIEAL KIVQKQRGWV PDGAIHAIAD VLGIPASDVE GVATFYSQIF RQPVGRHVI RYCDSVVCHI NGYQGIQAAL EKKLNIKPGQ TTFDGRFTLL PTCCLGNCDK GPNMMIDEDT HAHLTPEAIP E LLERYK

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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 (E. coli)
Molecular weightTheoretical: 100.419211 KDa
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

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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 (E. coli)
Molecular weightTheoretical: 68.321945 KDa
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

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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 (E. coli)
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

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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
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.562771 KDa
SequenceString:
MTLKELLVGF GTQVRSIWMI GLHAFAKRET RMYPEEPVYL PPRYRGRIVL TRDPDGEERC VACNLCAVAC PVGCISLQKA ETKDGRWYP EFFRINFSRC IFCGLCEEAC PTTAIQLTPD FEMGEYKRQD LVYEKEDLLI SGPGKYPEYN FYRMAGMAID G KDKGEAEN EAKPIDVKSL LP

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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
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

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Macromolecule #8: NADH-quinone oxidoreductase subunit A

MacromoleculeName: NADH-quinone oxidoreductase subunit A / 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: 16.474283 KDa
SequenceString:
MSMSTSTEVI AHHWAFAIFL IVAIGLCCLM LVGGWFLGGR ARARSKNVPF ESGIDSVGSA RLRLSAKFYL VAMFFVIFDV EALYLFAWS TSIRESGWVG FVEAAIFIFV LLAGLVYLVR IGALDWTPAR SRRERMNPET NSIANRQR

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Macromolecule #9: NADH dehydrogenase subunit L

MacromoleculeName: NADH dehydrogenase subunit L / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: ec: 1.6.5.11
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 66.483609 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 SAPGRLLGTW WYNAWGFDWL YDKVFVKPFL GIAWLL KRD PLNSMMNIPA VLSRFAGKGL LLSENGYLRW YVASMSIGAV VVLALLMVLR

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Macromolecule #10: NADH dehydrogenase I subunit M

MacromoleculeName: NADH dehydrogenase I subunit M / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 56.56009 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 TTTRP

+
Macromolecule #11: NADH-quinone oxidoreductase subunit N

MacromoleculeName: NADH-quinone oxidoreductase subunit N / 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: 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

+
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 (E. coli)
Molecular weightTheoretical: 10.852961 KDa
SequenceString:
MIPLQHGLIL AAILFVLGLT GLVIRRNLLF MLIGLEIMIN ASALAFVVAG SYWGQTDGQV MYILAISLAA AEASIGLALL LQLHRRRQN LNIDSVSEMR G

+
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 (E. coli) / Strain: IAI39 / ExPEC
Molecular weightTheoretical: 19.889551 KDa
SequenceString:
MEFAFYICGL IAILATLRVI THTNPVHALL YLIISLLAIS GVFFSLGAYF AGALEIIVYA GAIMVLFVFV VMMLNLGGSE IEQERQWLK PQVWIGPAIL SAIMLVVIVY AILGVNDQGI DGTPISAKAV GITLFGPYVL AVELASMLLL AGLVVAFHVG R EERAGEVL SNRKDDSAKR KTEEHA

+
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 / Iron–sulfur cluster

+
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 / Flavin mononucleotide

+
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 / Nicotinamide adenine dinucleotide

+
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 / Iron–sulfur cluster

+
Macromolecule #18: CALCIUM ION

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

+
Macromolecule #19: EICOSANE

MacromoleculeName: EICOSANE / type: ligand / ID: 19 / Number of copies: 5 / Formula: LFA
Molecular weightTheoretical: 282.547 Da
Chemical component information

ChemComp-LFA:
EICOSANE / Icosane

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Macromolecule #20: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 20 / Number of copies: 11 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

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

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.25 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
20.0 mMC6H13NO4SMES
2.0 mMCaCl2calcium chloride
250.0 mMNaClSodium chloridesodium chloride
0.01 %C47H88O22LMNG
0.25 mg/mlC40H80NO8PE. coli lipid extract
0.1 %C32H58N2O7SCHAPS
2.0 mMC21H27N7O14P2NADHNicotinamide adenine dinucleotide
0.8 mMC19H30O4DQ
GridModel: Quantifoil R0.6/1 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.9 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 11316 / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 4483166
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4hea

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 189796
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

4hea

,

3rko

)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: ML
Output model

PDB-7zci:
Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Resting state

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