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- EMDB-27963: Mycobacterial respiratory complex I with both quinone positions m... -

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Basic information

Entry
Database: EMDB / ID: EMD-27963
TitleMycobacterial respiratory complex I with both quinone positions modelled
Map data
Sample
  • Complex: Mycobacterial respiratory complex I, consensus map
    • Protein or peptide: x 15 types
  • Ligand: x 7 types
Function / homology
Function and homology information


NADH dehydrogenase (quinone) / 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 / phosphorelay signal transduction system / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport ...NADH dehydrogenase (quinone) / 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 / phosphorelay signal transduction system / 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
NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Soluble ligand binding domain / SLBB 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 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Soluble ligand binding domain / SLBB 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-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 / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / 4Fe-4S dicluster domain / CheY-like superfamily / 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 N / NADH-quinone oxidoreductase, M subunit / NADH-quinone oxidoreductase, L subunit / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase chain e ...NADH-quinone oxidoreductase subunit N / NADH-quinone oxidoreductase, M subunit / NADH-quinone oxidoreductase, L subunit / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase chain e / NADH-quinone oxidoreductase subunit D / NADH-quinone oxidoreductase subunit C / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit A / Two-component system response regulator
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLiang Y / Rubinstein JL
Funding support Canada, 4 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT162186 Canada
Canadian Institutes of Health Research (CIHR)PJT451412 Canada
Canadian Institutes of Health Research (CIHR)PJT173353 Canada
Canada Research Chairs Canada
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure of mycobacterial respiratory complex I.
Authors: Yingke Liang / Alicia Plourde / Stephanie A Bueler / Jun Liu / Peter Brzezinski / Siavash Vahidi / John L Rubinstein /
Abstract: Oxidative phosphorylation, the combined activity of the electron transport chain (ETC) and adenosine triphosphate synthase, has emerged as a valuable target for the treatment of infection by and ...Oxidative phosphorylation, the combined activity of the electron transport chain (ETC) and adenosine triphosphate synthase, has emerged as a valuable target for the treatment of infection by and other mycobacteria. The mycobacterial ETC is highly branched with multiple dehydrogenases transferring electrons to a membrane-bound pool of menaquinone and multiple oxidases transferring electrons from the pool. The proton-pumping type I nicotinamide adenine dinucleotide (NADH) dehydrogenase (Complex I) is found in low abundance in the plasma membranes of mycobacteria in typical in vitro culture conditions and is often considered dispensable. We found that growth of in carbon-limited conditions greatly increased the abundance of Complex I and allowed isolation of a rotenone-sensitive preparation of the enzyme. Determination of the structure of the complex by cryoEM revealed the "orphan" two-component response regulator protein MSMEG_2064 as a subunit of the assembly. MSMEG_2064 in the complex occupies a site similar to the proposed redox-sensing subunit NDUFA9 in eukaryotic Complex I. An apparent purine nucleoside triphosphate within the NuoG subunit resembles the GTP-derived molybdenum cofactor in homologous formate dehydrogenase enzymes. The membrane region of the complex binds acyl phosphatidylinositol dimannoside, a characteristic three-tailed lipid from the mycobacterial membrane. The structure also shows menaquinone, which is preferentially used over ubiquinone by gram-positive bacteria, in two different positions along the quinone channel, comparable to ubiquinone in other structures and suggesting a conserved quinone binding mechanism.
#1: Journal: Biorxiv / Year: 2022
Title: Structure of mycobacterial respiratory Complex I
Authors: Liang Y / Plourde A / Bueler SA / Liu J / Brzezinski P / Vahidi S / Rubinstein JL
History
DepositionAug 26, 2022-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateApr 5, 2023-
Current statusApr 5, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27963.png

Downloads & links

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Map

FileDownload / File: emd_27963.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.18021 Å
Density
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-0.6017861 - 8.819921
Average (Standard dev.)0.036085602 (±0.18185923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 453.19986 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27963_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27963_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : Mycobacterial respiratory complex I, consensus map

EntireName: Mycobacterial respiratory complex I, consensus map
Components
  • Complex: Mycobacterial respiratory complex I, consensus map
    • Protein or peptide: Two-component system response regulatorTwo-component regulatory system
    • Protein or peptide: NADH-quinone oxidoreductase subunit BNADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit ANADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit CNADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit DNADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit ENADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit GNADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit FNADH 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 JNADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit KNADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase, L subunitNADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase subunit NNADH dehydrogenase (quinone)
    • Protein or peptide: NADH-quinone oxidoreductase, M subunitNADH dehydrogenase (quinone)
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: MENAQUINONE-9Vitamin K2
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: ZINC ION
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: (2R)-3-{[(R)-hydroxy({(1S,2R,3R,4R,5S,6S)-3,4,5-trihydroxy-2-(alpha-D-mannopyranosyloxy)-6-[(6-O-undecanoyl-beta-D-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate

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Supramolecule #1: Mycobacterial respiratory complex I, consensus map

SupramoleculeName: Mycobacterial respiratory complex I, consensus map / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Location in cell: Inner membrane
Molecular weightTheoretical: 560 KDa

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Macromolecule #1: Two-component system response regulator

MacromoleculeName: Two-component system response regulator / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 14.119161 KDa
SequenceString:
MAGSAPLRIL VYSDNPRTRE QVRLALGKRI HPELPEIEYV DVATAPMAIS QMDAGGFDLA ILDGEATPAG GMGVAKQVKD EIDDCPPIL VLTGRADDAW LAKWSRAEAA VPHPIDPIRL SDAVVSLLRA PAQ

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Macromolecule #2: NADH-quinone oxidoreductase subunit B

MacromoleculeName: NADH-quinone oxidoreductase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 20.123703 KDa
SequenceString:
MGLEERLPGG ILLSTVETVA GYVRKGSLWP ATFGLACCAI EMMSTAGPRF DIARFGMERF SATPRQADLM IVAGRVSQKM APVLRQIYD QMVEPKWVLA MGVCASSGGM FNNYAVVQGV DHVVPVDIYL PGCPPRPEML LHAILKLHDK IQQMPLGVNR E EAIREAEQ AALAVPPTIE LKGLLR

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Macromolecule #3: NADH-quinone oxidoreductase subunit A

MacromoleculeName: NADH-quinone oxidoreductase subunit A / 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: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 13.628287 KDa
SequenceString:
MALYTPILIL GAIAAVFAVV SVGIALVIGP RRFNRSKLEA YECGIDPLPP VAAGLTGQRI PIRYYLIAML FIVFDIEIVF LYPWAVAFD SLGLFAVIEM LLFMLTVFVA YAYVWRRGGL NWD

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Macromolecule #4: NADH-quinone oxidoreductase subunit C

MacromoleculeName: NADH-quinone oxidoreductase subunit C / 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: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 26.610689 KDa
SequenceString: MSTSNGSANG TNGVGLPRGD EPEIIAVRRG MFGNRDTGDT SGYGRLVRPV ALPGSTPRPY GGYFDAVMDR LAEVLGEERY AMSIERVVV YRDQLTIEVS RVQLPAVASV LRDDPDLRFE LCLGVSGVHY PEDTGRELHA VYPLMSITHN RRIQLEVAAP D ADPHIPSL ...String:
MSTSNGSANG TNGVGLPRGD EPEIIAVRRG MFGNRDTGDT SGYGRLVRPV ALPGSTPRPY GGYFDAVMDR LAEVLGEERY AMSIERVVV YRDQLTIEVS RVQLPAVASV LRDDPDLRFE LCLGVSGVHY PEDTGRELHA VYPLMSITHN RRIQLEVAAP D ADPHIPSL YAVYPTTDWH ERETYDFFGI IFDGHPSLTR IEMPDDWEGH PQRKDYPLGG IPVEYHGAQI PPPDQRRSYS

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Macromolecule #5: NADH-quinone oxidoreductase subunit D

MacromoleculeName: NADH-quinone oxidoreductase subunit D / 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: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 48.55675 KDa
SequenceString: MSTSTVPPDG GEKVVVVGGN DWHEVVAAAR AGAAAQAGER IVVNMGPQHP STHGVLRLIL EIEGEIITEA RCGIGYLHTG IEKNLEYRN WTQGVTFVTR MDYLSPFFNE TAYCLGVEKL LGITDDIPER ASVIRVMLME LNRISSHLVA LATGGMELGA M SAMFYGFR ...String:
MSTSTVPPDG GEKVVVVGGN DWHEVVAAAR AGAAAQAGER IVVNMGPQHP STHGVLRLIL EIEGEIITEA RCGIGYLHTG IEKNLEYRN WTQGVTFVTR MDYLSPFFNE TAYCLGVEKL LGITDDIPER ASVIRVMLME LNRISSHLVA LATGGMELGA M SAMFYGFR EREEILRVFE SITGLRMNHA YIRPGGLAAD LPDDAITQVR RLVEILPKRL KDLEDLLNEN YIWKARTVGV GY LDLTGCM ALGITGPILR STGLPHDLRK AQPYCGYENY EFDVITDDRC DSYGRYIIRV KEMHESVKIV EQCLARLKPG PVM ISDKKL AWPADLKLGP DGLGNSPEHI AKIMGRSMEG LIHHFKLVTE GIRVPPGQVY VAVESPRGEL GVHMVSDGGT RPYR VHYRD PSFTNLQAVA ATCEGGMVAD AIAAVASIDP VMGGVDR

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Macromolecule #6: NADH-quinone oxidoreductase subunit E

MacromoleculeName: NADH-quinone oxidoreductase subunit E / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH dehydrogenase (quinone)
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 25.746746 KDa
SequenceString: MSEVFLELGQ RPDEAGPPIS GPATYPDDVT ESLRADAEQI IARYPDARSA LLPLLHLVQA QDGYLTPAGI GFCAAQLGLT EAEVTAVAT FYSMYRRTPT GDYLVGVCTN TLCAIMGGDA ILEALEDHLG VHPGQTTPDG RVTLEHVECN AACDYAPVVM V NWEFYDNQ ...String:
MSEVFLELGQ RPDEAGPPIS GPATYPDDVT ESLRADAEQI IARYPDARSA LLPLLHLVQA QDGYLTPAGI GFCAAQLGLT EAEVTAVAT FYSMYRRTPT GDYLVGVCTN TLCAIMGGDA ILEALEDHLG VHPGQTTPDG RVTLEHVECN AACDYAPVVM V NWEFYDNQ TPSSARDLVD GLRSGSPPPP TRGSLCTFRE TARTLAGLTD PNAPGGAPGA ATLAGLRLAR ERGMTAPTPP QT NGSAS

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Macromolecule #7: NADH-quinone oxidoreductase subunit G

MacromoleculeName: NADH-quinone oxidoreductase subunit G / 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: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 83.894773 KDa
SequenceString: MTLAEPTKDT PPVEMVSLTI DDHEISVPKG TLLIRAAELM GIQIPRFCDH PLLDPVGACR QCLVEVEGQR KPMASCTTTV MPDMVVRTQ FTSEAADKAQ RGVMELLLIN HPLDCPICDK GGECPLQNQA MSNGRPETRF EDVKRTFPKP ISISSQVLLD R ERCVLCAR ...String:
MTLAEPTKDT PPVEMVSLTI DDHEISVPKG TLLIRAAELM GIQIPRFCDH PLLDPVGACR QCLVEVEGQR KPMASCTTTV MPDMVVRTQ FTSEAADKAQ RGVMELLLIN HPLDCPICDK GGECPLQNQA MSNGRPETRF EDVKRTFPKP ISISSQVLLD R ERCVLCAR CTRFSSQIAG DPFIDLMERG ALQQVGIGQD KPFQSYFSGN TVQICPVGAL TGTAYRFRAR PFDLVSSPSV CE HCASGCA QRTDHRRGKV LRRLAGDEPE VNEEWNCDKG RWAFTYATVG DRITTPMLRD GGVLRPASWS EALTVAAAGL LTA AGSTGV LVGGRCTVED AYAYAKFARM VLNTNDVDFR ARPHSAEEAE FLAAHVAGQT MGLRYAELEN APTVLLAGFE PEEE SPIVF LRLRKGVRKN GVQVVAVAPW ASRGLTKLAG TVVPTVPGDE PAALDGMHDD DRLRRPGAVI LVGERLATSP GALSA AVRL AAATGARLAW IPRRAGERGA IEAGALPNLL PGGRPVDDAD ARAEVARAWY ISALPEAPGR DTAAILSTAA SGHLAA LLV GGVELGDLPD PELAVAAVRT TPFVVSLELR ESAVTELADV VFPVAPVVEK AGSFLNWEGR PRPFAPSLKT NAIPDLR VL HYLADEIGVD LALPTAEAAD AELAQLGTWG GARPPAPTAP PTARPEAGSG QAVLASWRML LDAGRLQDGE PHLAGTAV R PVARMSAATA AGIGASDGAP VTVSTERGAV TLPLAVTDMP DGVVWLPMNS PGSAVHQRLG VTAGAVVSIG AGA

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Macromolecule #8: NADH-quinone oxidoreductase subunit F

MacromoleculeName: NADH-quinone oxidoreductase subunit F / 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: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 47.831078 KDa
SequenceString: MTPLTPVLSR FWDEPEPWTL ETYRRHDGYQ GLQRALSMGP DDVIAFVKDS GLRGRGGAGF PTGTKWSFIP QERGDQPAGG PAAKPHYLV INADESEPGT CKDIPLLLTT PHFLVEGAII AAYAIRARHA FIYVRGEVLP VLRRLQAAVA EAYAAGYLGT D IMGSGFDL ...String:
MTPLTPVLSR FWDEPEPWTL ETYRRHDGYQ GLQRALSMGP DDVIAFVKDS GLRGRGGAGF PTGTKWSFIP QERGDQPAGG PAAKPHYLV INADESEPGT CKDIPLLLTT PHFLVEGAII AAYAIRARHA FIYVRGEVLP VLRRLQAAVA EAYAAGYLGT D IMGSGFDL DLIVHAGAGA YICGEETALL DSLEGRRGQP RLRPPFPAVA GLYACPTVVN NVESIASVPP IMVNGVDWFR SM GSEKSPG FTLYSLSGHV TRPGQYEAPL GITLRELLEY AGGVRAGHQL KFWTPGGSST PLLTAEHLDV PLDYEGMASV GSM LGTKAL QIFDETTCVV RAVRRWTQFY AHESCGKCTP CREGTYWLAQ IYARLENGAG TEADIDKLLD ISDNIFGKSF CALG DGAAS PIMSSIKHFR DEYVAHLDGG CPFDPHASTL MATEGAGV

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Macromolecule #9: NADH-quinone oxidoreductase subunit I

MacromoleculeName: NADH-quinone oxidoreductase subunit I / 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: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 19.86051 KDa
SequenceString:
MPKFLDALAG FAVTLGSMFK KPITEGYPEK PGPVAPRYHG RHQLNRYPDG LEKCIGCELC AWACPADAIY VEGADNTADE RYSPGERYG RVYQINYLRC IGCGLCIEAC PTRALTMTTE YEMADDNRAD LIWGKDKLLA PLQEGMQAPP HDMAPGKTDD D YYLGNVTP ITPVPSGTED AR

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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: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 44.477293 KDa
SequenceString: MTHPDPTLFG HDPWWLMLAK AVAIFVFLLL TVLSAILIER KLLGRMQMRF GPNRVGPAGL LQSLADGIKL ALKEGLVPAG VDKPIYLLA PVISVIPAFV AFSVIPLGGA VSVFGHRTPL QLTDLPVAVL FILAATSIGV YGIVLAGWAS GSTYPLLGGL R SSAQVVSY ...String:
MTHPDPTLFG HDPWWLMLAK AVAIFVFLLL TVLSAILIER KLLGRMQMRF GPNRVGPAGL LQSLADGIKL ALKEGLVPAG VDKPIYLLA PVISVIPAFV AFSVIPLGGA VSVFGHRTPL QLTDLPVAVL FILAATSIGV YGIVLAGWAS GSTYPLLGGL R SSAQVVSY EIAMGLSFVA VFLYAGTMST SGIVAAQDRT WFVFLLLPSF LVYVVSMVGE TNRAPFDLPE AEGELVGGFH TE YSSLKFA MFMLAEYVNM TTVSALATTM FLGGWHAPFP FNLIDGANSG WWPLLWFTAK VWTFMFLYFW LRATLPRLRY DQF MALGWK VLIPVSLLWI MVVAITRSLR QHGEGTWAAW LLTAAVVVVV ALIWGLATSL RRRTVQPPPP QSTGAYPVPP LPSV GTKET ADA

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Macromolecule #11: NADH-quinone oxidoreductase subunit J

MacromoleculeName: NADH-quinone oxidoreductase subunit J / 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: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 26.398791 KDa
SequenceString: MNSDLMLLAA EGARTSTSEA VVFWVVGTVA LVGAIGVVAA RKAVYSAVFL ACTMISLAVL YIAQDAPFLG VVQIVVYTGA VMMLFLFVL MLIGVDLTES LVETIKGHRI AALIAGAGFG ILVIAGIGNV SVAGFSGLAA ANSGGNVEGL AALIFTRYLW A FELTSALL ...String:
MNSDLMLLAA EGARTSTSEA VVFWVVGTVA LVGAIGVVAA RKAVYSAVFL ACTMISLAVL YIAQDAPFLG VVQIVVYTGA VMMLFLFVL MLIGVDLTES LVETIKGHRI AALIAGAGFG ILVIAGIGNV SVAGFSGLAA ANSGGNVEGL AALIFTRYLW A FELTSALL ITAALGAMVL AHRERFERRK TQRELAIERF QTGGHPTPLP NPGVYARHNS VDVPARLPDG SESPLSVSTI LP HRTVGSA TNGKR

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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: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 10.876923 KDa
SequenceString:
MNPDNYLYLS ALLFTIGAAG VLLRRNAIVM FMCVELMLNA ANLAFVNFSR MHGQLDGQVV AFFTMVVAAC EVVVGLAIIM AIFRTRRSA SVDDANLLKH

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Macromolecule #13: NADH-quinone oxidoreductase, L subunit

MacromoleculeName: NADH-quinone oxidoreductase, L subunit / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH dehydrogenase (quinone)
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 65.446609 KDa
SequenceString: MITDWLPVWL LIALPAAGAT ILLLAGRRSD RWGHLLGCAM SLAAFAVGTV LFAGMLGRSG EERAVHEALF SWVPVGGLQV DFGLQLDQL SVCFVLLITG VGSLIHIYSI GYMAEDPDRR RFFAYLNLFL AAMLLLVLAD NYLGLYAGWE GVGLASYLLI G FWSHKPSA ...String:
MITDWLPVWL LIALPAAGAT ILLLAGRRSD RWGHLLGCAM SLAAFAVGTV LFAGMLGRSG EERAVHEALF SWVPVGGLQV DFGLQLDQL SVCFVLLITG VGSLIHIYSI GYMAEDPDRR RFFAYLNLFL AAMLLLVLAD NYLGLYAGWE GVGLASYLLI G FWSHKPSA ATAAKKAFVV NRVGDMGLAI ALMIMFATIG SISFAGVFAA APGLSEATLS AIGLLLLLGA CGKSAQVPLQ SW LGDAMEG PTPVSALIHA ATMVTAGVYL IVRSGPIFDL APTAQTGVVI VGAVTLLFGA IIGCAKDDIK KALAASTMSQ IGY MVLAAG LGPAGYAFAI MHLLTHGFFK AGLFLGAGSV MHAMNDEVNM RRYGGLRKVL PVTFATFGLG YLAIIGVPPL AGFF SKDGI IEAALGAGGA RGVILGGAAI LGAGITAFYM TRVMLMTFFG EKRWAANSHP HEAPAVMTWP MILLAVGSVV SGGAL AIGG TLSHWLEPVV GTHEAHHAVP VWVVTAIVLA VVAVGIAVAY RMYARQAVPE EVPEGSALTV AARRDLYGDA FNEAVF MRG GQTLTAAMVT VDDKAVDGTA GGLAALVSRT SDALRQVQTG FARSYALSML GGSALVVAAI LAVQLW

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Macromolecule #14: NADH-quinone oxidoreductase subunit N

MacromoleculeName: NADH-quinone oxidoreductase subunit N / 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: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 54.013266 KDa
SequenceString: MITPSIEYGL LSPMLIVFGV AIAGVLIEAL APRQSRYPLQ VTLALGGLIA TVVAVVFVAR GLSGTPGRPA VLGAVVLDAP AVFLQGTIA LVGILGIMLI AERQKATVSA GEARGLEDFT PQASAVAGSV AEQLATKTGV MQTEVFPLTM FAIGGMLLFP A ADDLLTMF ...String:
MITPSIEYGL LSPMLIVFGV AIAGVLIEAL APRQSRYPLQ VTLALGGLIA TVVAVVFVAR GLSGTPGRPA VLGAVVLDAP AVFLQGTIA LVGILGIMLI AERQKATVSA GEARGLEDFT PQASAVAGSV AEQLATKTGV MQTEVFPLTM FAIGGMLLFP A ADDLLTMF VALEVLSLPL YLLCGLARRR RLLSQEAALK YFLLGAFSSA FFIYGAAMLY GSAGTLDLSG IAESVAAGSG NT SLALLGV ALLLVGVLFK VGAVPFHSWI PDVYQGAPTS ITAFMAAATK IAAFGAMLRI FYVAVPALRD DWRPVLWAIA ILT MVVGTV TAVTQTDVKR MLAYSAVAHS GFILTGVIAA NPAGVSSTLF YLFAYGFSTL GAFAVVGLIR NAAGDEETSM AQWA GLGRR YPIVGVVFSL FLLAFAGIPL TSGFVSKFAV FKAAGEGGAI PLVIIGVIAS AVAAYFYVRV IVLMFFTEPP DDAPE LVVP SGLSTAVVTV TAAVTFALGA LPQPLLDLAN SAETFLH

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Macromolecule #15: NADH-quinone oxidoreductase, M subunit

MacromoleculeName: NADH-quinone oxidoreductase, M subunit / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH dehydrogenase (quinone)
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 56.338316 KDa
SequenceString: MVSTFPWLTV LWAVPVVGAA VVILLPAAQQ VLAKWLALAV SVLTLAVTAV VAIGFDPAAA QYQFVESHRW IPSFGTGYIL GVDGIALAL VVLTAVLVPL LIIAGWNDAS RQTGLAGRSV QAYLALTLAV EGMVLMSLVA LDILLFYVFF EAMLIPMYFL I GGFGGENR ...String:
MVSTFPWLTV LWAVPVVGAA VVILLPAAQQ VLAKWLALAV SVLTLAVTAV VAIGFDPAAA QYQFVESHRW IPSFGTGYIL GVDGIALAL VVLTAVLVPL LIIAGWNDAS RQTGLAGRSV QAYLALTLAV EGMVLMSLVA LDILLFYVFF EAMLIPMYFL I GGFGGENR SRAAVKFLLY NLFGGLIMLA AVIGLYVVTA GSDAFAAGTF DFREIVAAVS SGEFAVNPAI MNFLFLGFMF AF AVKAPLW PFHRWLPDAA VEATPASAVL MMAVMDKVGT FGMLRYCLQL FPDASTYFRP VVITLAAIGI VYGAVLAIGQ TDV MRLIAY TSISHFGFII LGIFVMTSQG QSGSTLYMIN HGISTAALFL IAGFLVSRRG SRLIDSYGGV QKVAPVLAGT FLVA GLATL SLPGLAPFIS EFLVLIGTFT RYPVVAVFAA TALVLSAVYI LWTYQRMMTG PVRDGIGDGD RPVRDLVPRE LVVVA PLLA LLLVLGIYPK PALDVINPAV EHTLTTIGQT DPEPTVPPTI AEGAR

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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 / Iron–sulfur cluster

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Macromolecule #17: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 17 / Number of copies: 2 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9 / Vitamin K2

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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 / Iron–sulfur cluster

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Macromolecule #19: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 19 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

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Macromolecule #20: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 20 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #21: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 21 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

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Macromolecule #22: (2R)-3-{[(R)-hydroxy({(1S,2R,3R,4R,5S,6S)-3,4,5-trihydroxy-2-(alp...

MacromoleculeName: (2R)-3-{[(R)-hydroxy({(1S,2R,3R,4R,5S,6S)-3,4,5-trihydroxy-2-(alpha-D-mannopyranosyloxy)-6-[(6-O-undecanoyl-beta-D-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate
type: ligand / ID: 22 / Number of copies: 1 / Formula: XP2
Molecular weightTheoretical: 1.121243 KDa
Chemical component information

ChemComp-XP2:
(2R)-3-{[(R)-hydroxy({(1S,2R,3R,4R,5S,6S)-3,4,5-trihydroxy-2-(alpha-D-mannopyranosyloxy)-6-[(6-O-undecanoyl-beta-D-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate

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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

Concentration2 mg/mL
BufferpH: 6
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 36.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 357064
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 61177
FSC plot (resolution estimation)

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