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- EMDB-30944: Cryo-EM structure of hybrid respiratory supercomplex consisting o... -

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Basic information

Entry
Database: EMDB / ID: EMD-30944
TitleCryo-EM structure of hybrid respiratory supercomplex consisting of Mycobacterium tuberculosis complexIII and Mycobacterium smegmatis complexIV in the presence of Q203
Map data
Sample
  • Complex: hybrid respiratory supercomplex consisting of Mycobacterium tuberculosis complexIII and Mycobacterium smegmatis complexIV in the presence of Q203
    • Protein or peptide: x 10 types
  • Ligand: x 12 types
Function / homology
Function and homology information


aerobic electron transport chain / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / respirasome / respiratory electron transport chain / peptidoglycan-based cell wall / monooxygenase activity ...aerobic electron transport chain / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / respirasome / respiratory electron transport chain / peptidoglycan-based cell wall / monooxygenase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding / copper ion binding / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / QcrA subunit, N-terminal / QcrA subunit N-terminal region / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase subunit IV, actinobacteria / Cytochrome c oxidase subunit IV / Cytochrome b(N-terminal)/b6/petB / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c oxidase subunit III ...Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / QcrA subunit, N-terminal / QcrA subunit N-terminal region / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase subunit IV, actinobacteria / Cytochrome c oxidase subunit IV / Cytochrome b(N-terminal)/b6/petB / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Cytochrome C oxidase subunit II, periplasmic domain / Rieske iron-sulphur protein / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome c / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Probable cytochrome c oxidase subunit 3 / Cytochrome c oxidase polypeptide 4 / cytochrome-c oxidase / Uncharacterized protein MSMEG_4692/MSMEI_4575 / Uncharacterized protein / Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 complex cytochrome c subunit / Cytochrome bc1 complex cytochrome b subunit
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 51 (bacteria) / Mycobacterium smegmatis MC2 51 (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsZhou S / Wang W / Gao Y / Gong H / Rao Z
Funding support China, 5 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030201 China
Chinese Academy of SciencesXDB37020203 China
Chinese Academy of Sciences2017YFC0840300 China
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)813300237 China
CitationJournal: Elife / Year: 2021
Title: Structure of cytochrome in complex with Q203 and TB47, two anti-TB drug candidates.
Authors: Shan Zhou / Weiwei Wang / Xiaoting Zhou / Yuying Zhang / Yuezheng Lai / Yanting Tang / Jinxu Xu / Dongmei Li / Jianping Lin / Xiaolin Yang / Ting Ran / Hongming Chen / Luke W Guddat / Quan ...Authors: Shan Zhou / Weiwei Wang / Xiaoting Zhou / Yuying Zhang / Yuezheng Lai / Yanting Tang / Jinxu Xu / Dongmei Li / Jianping Lin / Xiaolin Yang / Ting Ran / Hongming Chen / Luke W Guddat / Quan Wang / Yan Gao / Zihe Rao / Hongri Gong /
Abstract: Pathogenic mycobacteria pose a sustained threat to global human health. Recently, cytochrome complexes have gained interest as targets for antibiotic drug development. However, there is currently no ...Pathogenic mycobacteria pose a sustained threat to global human health. Recently, cytochrome complexes have gained interest as targets for antibiotic drug development. However, there is currently no structural information for the cytochrome complex from these pathogenic mycobacteria. Here, we report the structures of cytochrome alone (2.68 Å resolution) and in complex with clinical drug candidates Q203 (2.67 Å resolution) and TB47 (2.93 Å resolution) determined by single-particle cryo-electron microscopy. cytochrome forms a dimeric assembly with endogenous menaquinone/menaquinol bound at the quinone/quinol-binding pockets. We observe Q203 and TB47 bound at the quinol-binding site and stabilized by hydrogen bonds with the side chains of Thr and Glu, residues that are conserved across pathogenic mycobacteria. These high-resolution images provide a basis for the design of new mycobacterial cytochrome inhibitors that could be developed into broad-spectrum drugs to treat mycobacterial infections.
History
DepositionFeb 3, 2021-
Header (metadata) releaseOct 27, 2021-
Map releaseOct 27, 2021-
UpdateJul 27, 2022-
Current statusJul 27, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7e1w
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30944.png

Downloads & links

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Map

FileDownload / File: emd_30944.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.4
Minimum - Maximum-1.2059138 - 2.828317
Average (Standard dev.)-0.00063818006 (±0.062727965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z419.840419.840419.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-1.2062.828-0.001

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Supplemental data

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Sample components

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Entire : hybrid respiratory supercomplex consisting of Mycobacterium tuber...

EntireName: hybrid respiratory supercomplex consisting of Mycobacterium tuberculosis complexIII and Mycobacterium smegmatis complexIV in the presence of Q203
Components
  • Complex: hybrid respiratory supercomplex consisting of Mycobacterium tuberculosis complexIII and Mycobacterium smegmatis complexIV in the presence of Q203
    • Protein or peptide: Cytochrome c oxidase subunit 2
    • Protein or peptide: Cytochrome c oxidase subunit 1
    • Protein or peptide: Cytochrome c oxidase subunit 3
    • Protein or peptide: Cytochrome c oxidase polypeptide 4
    • Protein or peptide: Cytochrome c oxidase subunit CtaJ
    • Protein or peptide: Uncharacterized protein MSMEG_4692/MSMEI_4575
    • Protein or peptide: Prokaryotic respiratory supercomplex associate factor 1 PRSAF1
    • Protein or peptide: Cytochrome bc1 complex cytochrome b subunit
    • Protein or peptide: Cytochrome bc1 complex Rieske iron-sulfur subunit
    • Protein or peptide: Cytochrome bc1 complex cytochrome c subunit
  • Ligand: COPPER (II) ION
  • Ligand: CARDIOLIPIN
  • Ligand: PALMITIC ACID
  • Ligand: HEME-A
  • Ligand: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: MENAQUINONE-9Vitamin K2
  • Ligand: 6-chloranyl-2-ethyl-N-[[4-[4-[4-(trifluoromethyloxy)phenyl]piperidin-1-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate
  • Ligand: HEME C
  • Ligand: water

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Supramolecule #1: hybrid respiratory supercomplex consisting of Mycobacterium tuber...

SupramoleculeName: hybrid respiratory supercomplex consisting of Mycobacterium tuberculosis complexIII and Mycobacterium smegmatis complexIV in the presence of Q203
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Mycolicibacterium smegmatis MC2 51 (bacteria)
Molecular weightExperimental: 800 KDa

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Macromolecule #1: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 38.077465 KDa
SequenceString: MTPRGFRVVA LSIVLGGSAL LLSGCSWSDA LALGWPTGIT PEAKLNRELW IGSVIASFAV GAIVWGLIFW TSAFHRKKAT DTELPRQFG YNMPLELTLT VIPFLIISVL FYFTVVVQER MMHKDPNPEV VIDVTAFQWN WKFGYQKIAF ADGSFDYDGA D PERKEAMT ...String:
MTPRGFRVVA LSIVLGGSAL LLSGCSWSDA LALGWPTGIT PEAKLNRELW IGSVIASFAV GAIVWGLIFW TSAFHRKKAT DTELPRQFG YNMPLELTLT VIPFLIISVL FYFTVVVQER MMHKDPNPEV VIDVTAFQWN WKFGYQKIAF ADGSFDYDGA D PERKEAMT SRPEGKDEHG IEKVGPIRGM TPEDRTYLNF DKIETLGTSS EIPVLVLPAG KRIEFVLNSA DVIHGFWVPE FL FKRDVLP EPKANNSDNV FQVSEIQQTG AFVGRCTEMC GTFHAMMNFE VRVVEPNDFK AYIDQRNAGK TNAEALAAIN QPP LAITTE PFESRRGELV PQASK

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Macromolecule #2: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 64.162965 KDa
SequenceString: MVAEAPPIGE LEARRPFPER MGPKGNLIYK LITTTDHKLI GIMYCVVCFA FFLVGGLMAL FMRTELAMPG LQFLSNEQFN QLFTMHGTV MLLFYATPIV FGFANLVLPL QIGAPDVAFP RLNALSFWLF LFGALIAIAG FITPGGAADF GWTAYSPLTD A IHSPGAGG ...String:
MVAEAPPIGE LEARRPFPER MGPKGNLIYK LITTTDHKLI GIMYCVVCFA FFLVGGLMAL FMRTELAMPG LQFLSNEQFN QLFTMHGTV MLLFYATPIV FGFANLVLPL QIGAPDVAFP RLNALSFWLF LFGALIAIAG FITPGGAADF GWTAYSPLTD A IHSPGAGG DLWIMGLAVG GLGTILGGVN MITTVVCMRA PGMTMFRMPI FTWNILVTSI LVLIAFPILT AALFGLAADR HL GAHIYDP ANGGVLLWQH LFWFFGHPEV YIIALPFFGI VSEIFPVFSR KPIFGYTTLI YATLAIAALS VAVWAHHMYA TGA VLLPFF SFMTFLIAVP TGIKFFNWIG TMWKGQLTFE TPMLFSVGFL ITFLLGGLSG VLLASPPLDF HVTDSYFVIA HFHY VLFGT IVFATYAGIY FWFPKMTGRL LDERLGKLHF WLTFIGFHTT FLVQHWLGDE GMPRRYADYL PTDGFTTLNV ISTVG AFIL GVSMLPFVWN VFKSWRYGEP VTVDDPWGYG NSLEWATSCP PPRHNFTELP RIRSERPAFE LHYPHMVERM RAEAHV GRA HHPELETADK SS

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Macromolecule #3: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 22.196883 KDa
SequenceString: MTSAVGTSGT AITSRVHSLN RPNMVSVGTI VWLSSELMFF AGLFAMYFTA RAQAGGAWPP EPTELNLALA VPVTLVLIAS SFTCQMGVF AAERGDVFGL RRWYVITFLM GLFFVLGQGY EYIHLVEHGT TIPGSAYGSV FYLATGFHGL HVIGGLVAFV L LLARTKMS ...String:
MTSAVGTSGT AITSRVHSLN RPNMVSVGTI VWLSSELMFF AGLFAMYFTA RAQAGGAWPP EPTELNLALA VPVTLVLIAS SFTCQMGVF AAERGDVFGL RRWYVITFLM GLFFVLGQGY EYIHLVEHGT TIPGSAYGSV FYLATGFHGL HVIGGLVAFV L LLARTKMS KFTPAQATAA IVVSYYWHFV DIVWIALFAT IYFVR

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Macromolecule #4: Cytochrome c oxidase polypeptide 4

MacromoleculeName: Cytochrome c oxidase polypeptide 4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 15.177424 KDa
SequenceString:
MHIEARLFEI LTAFFALAAV VYAVLTAMFA TGGVEWAGTT ALVLTTGLTL ITGTFFRFVA RRLDTRPEDY EDAEISDGAG ELGFFAPHS WWPILISLSF STAAVGAALW LPWLIAAGVA FVITSVCGLV FEYYWGPEKH

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Macromolecule #5: Cytochrome c oxidase subunit CtaJ

MacromoleculeName: Cytochrome c oxidase subunit CtaJ / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 8.365549 KDa
SequenceString:
MSTALTHGLI GGVPLVLFAV LALIFLTRKG PHPDTYKMSD PWTHAPILWA AEEPREHGHG GHGHDSHGVV IGGGASGKW

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Macromolecule #6: Uncharacterized protein MSMEG_4692/MSMEI_4575

MacromoleculeName: Uncharacterized protein MSMEG_4692/MSMEI_4575 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 15.910971 KDa
SequenceString:
MASGDIATVA NAELDLPYGS ALTSSGRISA VTEPGELSVH YPFPTMDLVV LDDALKYGSR AAKARFAVYI GPLGADTAAT AREILANVP TPENAVLLAV SPDQRAIEVV YGADVKGRGI ESAAPLGVSA AAASFKEGNL IDGLISAVRV MSAGVSPA

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Macromolecule #7: Prokaryotic respiratory supercomplex associate factor 1 PRSAF1

MacromoleculeName: Prokaryotic respiratory supercomplex associate factor 1 PRSAF1
type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 11.329909 KDa
SequenceString:
MSSTQDRSQL DPEEQPVANT EVERHTGVDV EDVPSAEWGW SHMPIGVMHI GGLLSAAFLL VMMRGNHVGH VEDWFLIGFA AVIVALVGR NWWLRRRGWI R

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Macromolecule #8: Cytochrome bc1 complex cytochrome b subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome b subunit / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria) / Strain: H37Rv
Molecular weightTheoretical: 61.077062 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 51 (bacteria)
SequenceString: MSPKLSPPNI GEVLARQAED IDTRYHPSAA LRRQLNKVFP THWSFLLGEI ALYSFVVLLI TGVYLTLFFD PSMVDVTYNG VYQPLRGVE MSRAYQSALD ISFEVRGGLF VRQIHHWAAL MFAAAIMVHL ARIFFTGAFR RPRETNWVIG SLLLILAMFE G YFGYSLPD ...String:
MSPKLSPPNI GEVLARQAED IDTRYHPSAA LRRQLNKVFP THWSFLLGEI ALYSFVVLLI TGVYLTLFFD PSMVDVTYNG VYQPLRGVE MSRAYQSALD ISFEVRGGLF VRQIHHWAAL MFAAAIMVHL ARIFFTGAFR RPRETNWVIG SLLLILAMFE G YFGYSLPD DLLSGLGLRA ALSSITLGMP VIGTWLHWAL FGGDFPGTIL IPRLYALHIL LLPGIILALI GLHLALVWFQ KH TQFPGPG RTEHNVVGVR VMPVFAFKSG AFFAAIVGVL GLMGGLLQIN PIWNLGPYKP SQVSAGSQPD FYMMWTEGLA RIW PPWEFY FWHHTIPAPV WVAVIMGLVF VLLPAYPFLE KRFTGDYAHH NLLQRPRDVP VRTAIGAMAI AFYMVLTLAA MNDI IALKF HISLNATTWI GRIGMVILPP FVYFITYRWC IGLQRSDRSV LEHGVETGII KRLPHGAYIE LHQPLGPVDE HGHPI PLQY QGAPLPKRMN KLGSAGSPGS GSFLFADSAA EDAALREAGH AAEQRALAAL REHQDSIMGS PDGEH

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Macromolecule #9: Cytochrome bc1 complex Rieske iron-sulfur subunit

MacromoleculeName: Cytochrome bc1 complex Rieske iron-sulfur subunit / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria) / Strain: H37Rv
Molecular weightTheoretical: 46.976465 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 51 (bacteria)
SequenceString: MSRADDDAVG VPPTCGGRSD EEERRIVPGP NPQDGAKDGA KATAVPREPD EAALAAMSNQ ELLALGGKLD GVRIAYKEPR WPVEGTKAE KRAERSVAVW LLLGGVFGLA LLLIFLFWPW EFKAADGESD FIYSLTTPLY GLTFGLSILS IAIGAVLYQK R FIPEEISI ...String:
MSRADDDAVG VPPTCGGRSD EEERRIVPGP NPQDGAKDGA KATAVPREPD EAALAAMSNQ ELLALGGKLD GVRIAYKEPR WPVEGTKAE KRAERSVAVW LLLGGVFGLA LLLIFLFWPW EFKAADGESD FIYSLTTPLY GLTFGLSILS IAIGAVLYQK R FIPEEISI QERHDGASRE IDRKTVVANL TDAFEGSTIR RRKLIGLSFG VGMGAFGLGT LVAFAGGLIK NPWKPVVPTA EG KKAVLWT SGWTPRYQGE TIYLARATGT EDGPPFIKMR PEDMDAGGME TVFPWRESDG DGTTVESHHK LQEIAMGIRN PVM LIRIKP SDLGRVVKRK GQESFNFGEF FAFTKVCSHL GCPSSLYEQQ SYRILCPCHQ SQFDALHFAK PIFGPAARAL AQLP ITIDT DGYLVANGDF VEPVGPAFWE RTTT

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Macromolecule #10: Cytochrome bc1 complex cytochrome c subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome c subunit / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria) / Strain: H37Rv
Molecular weightTheoretical: 29.152365 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 51 (bacteria)
SequenceString: LTKLGFTRSG GSKSGRTRRR LRRRLSGGVL LLIALTIAGG LAAVLTPTPQ VAVADESSSA LLRTGKQLFD TSCVSCHGAN LQGVPDHGP SLIGVGEAAV YFQVSTGRMP AMRGEAQAPR KDPIFDEAQI DAIGAYVQAN GGGPTVVRNP DGSIATQSLR G NDLGRGGD ...String:
LTKLGFTRSG GSKSGRTRRR LRRRLSGGVL LLIALTIAGG LAAVLTPTPQ VAVADESSSA LLRTGKQLFD TSCVSCHGAN LQGVPDHGP SLIGVGEAAV YFQVSTGRMP AMRGEAQAPR KDPIFDEAQI DAIGAYVQAN GGGPTVVRNP DGSIATQSLR G NDLGRGGD LFRLNCASCH NFTGKGGALS SGKYAPDLAP ANEQQILTAM LTGPQNMPKF SNRQLSFEAK KDIIAYVKVA TE ARQPGGY LLGGFGPAPE GMAMWIIGMV AAIGLALWIG ARS

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Macromolecule #11: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 11 / Number of copies: 8 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION / Copper

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Macromolecule #12: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 12 / Number of copies: 17 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #13: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 13 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

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Macromolecule #14: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 14 / Number of copies: 4 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A / Heme A

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Macromolecule #15: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)...

MacromoleculeName: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
type: ligand / ID: 15 / Number of copies: 2 / Formula: 9Y0
Molecular weightTheoretical: 717.996 Da
Chemical component information

ChemComp-9Y0:
(2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate

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Macromolecule #16: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 16 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

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Macromolecule #17: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 17 / Number of copies: 8 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9 / Vitamin K2

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Macromolecule #18: 6-chloranyl-2-ethyl-N-[[4-[4-[4-(trifluoromethyloxy)phenyl]piperi...

MacromoleculeName: 6-chloranyl-2-ethyl-N-[[4-[4-[4-(trifluoromethyloxy)phenyl]piperidin-1-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide
type: ligand / ID: 18 / Number of copies: 2 / Formula: HUU
Molecular weightTheoretical: 557.006 Da
Chemical component information

ChemComp-HUU:
6-chloranyl-2-ethyl-N-[[4-[4-[4-(trifluoromethyloxy)phenyl]piperidin-1-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide

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Macromolecule #19: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 19 / 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 #20: (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3...

MacromoleculeName: (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate
type: ligand / ID: 20 / Number of copies: 4 / Formula: 9YF
Molecular weightTheoretical: 853.112 Da
Chemical component information

ChemComp-9YF:
(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate

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Macromolecule #21: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 21 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

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Macromolecule #22: water

MacromoleculeName: water / type: ligand / ID: 22 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 1.8 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106770

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New format data for meta-information of EMDB entries

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