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- EMDB-39323: Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF23... -

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Basic information

Entry
Database: EMDB / ID: EMD-39323
TitleCryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF23694-bound state
Map data
Sample
  • Complex: Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF23694-bound state
    • Protein or peptide: x 10 types
  • Ligand: x 8 types
KeywordsComplex / mitochondria / ELECTRON TRANSPORT / MEMBRANE PROTEIN
Function / homology
Function and homology information


: / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / cellular respiration / respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / proton transmembrane transport / aerobic respiration ...: / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / cellular respiration / respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / proton transmembrane transport / aerobic respiration / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome b / : / Cytochrome c1 / Cytochrome C1 family ...Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome b / : / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Cytochrome b / quinol--cytochrome-c reductase / : / : / : / : / : / : / Cytochrome b-c1 complex subunit 9, mitochondrial / Cytochrome b-c1 complex subunit 10, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsYe Y / Li ZW / Yang GF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Am Chem Soc / Year: 2024
Title: Cryo-EM Structures Reveal the Unique Binding Modes of Metyltetraprole in Yeast and Porcine Cytochrome Complex Enabling Rational Design of Inhibitors.
Authors: Yu-Xia Wang / Ying Ye / Zhi-Wen Li / Guang-Rui Cui / Xing-Xing Shi / Ying Dong / Jia-Jia Jiang / Jia-Yue Sun / Ze-Wei Guan / Nan Zhang / Qiong-You Wu / Fan Wang / Xiao-Lei Zhu / Guang-Fu Yang /
Abstract: Cytochrome (complex III) represents a significant target for the discovery of both drugs and fungicides. Metyltetraprole (MET) is commonly classified as a quinone site inhibitor (QI) that combats ...Cytochrome (complex III) represents a significant target for the discovery of both drugs and fungicides. Metyltetraprole (MET) is commonly classified as a quinone site inhibitor (QI) that combats the G143A mutated isolate, which confers high resistance to strobilurin fungicides such as pyraclostrobin (PYR). The binding mode and antiresistance mechanism of MET remain unclear. Here, we determined the high-resolution structures of inhibitor-bound complex III (MET, 2.52 Å; PYR, 2.42 Å) and inhibitor-bound porcine complex III (MET, 2.53 Å; PYR, 2,37 Å) by cryo-electron microscopy. The distinct binding modes of MET and PYR were observed for the first time. Notably, the MET exhibited different binding modes in the two species. In , the binding site of MET was the same as PYR, serving as a -type inhibitor of the Q site. However, in porcine, MET acted as a dual-target inhibitor of both Q and Q. Based on the structural insights, a novel inhibitor (YF23694) was discovered and demonstrated excellent fungicidal activity against downy mildew and powdery mildew fungi. This work provides a new starting point for the design of the next generation of inhibitors to overcome the resistance.
History
DepositionFeb 29, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39323.png

Downloads & links

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Map

FileDownload / File: emd_39323.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 320 pix.
= 307.2 Å		0.96 Å/pix.
x 320 pix.
= 307.2 Å		0.96 Å/pix.
x 320 pix.
= 307.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.7736042 - 4.682308
Average (Standard dev.)0.0006024898 (±0.13431564)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 307.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39323_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

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Half map: #1

Fileemd_39323_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF23...

EntireName: Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF23694-bound state
Components
  • Complex: Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF23694-bound state
    • Protein or peptide: COR1 isoform 1
    • Protein or peptide: Cytochrome b-c1 complex subunit 2, mitochondrial
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome c1, heme protein, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
    • Protein or peptide: QCR6 isoform 1
    • Protein or peptide: Cytochrome b-c1 complex subunit 7
    • Protein or peptide: Cytochrome b-c1 complex subunit 8
    • Protein or peptide: Cytochrome b-c1 complex subunit 9, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 10, mitochondrial
  • Ligand: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
  • Ligand: (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate
  • Ligand: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate
  • Ligand: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
  • Ligand: 1-[2-[(4,6-dimethyl-1,3-benzothiazol-2-yl)sulfanylmethyl]-3-methyl-phenyl]-4-methyl-1,2,3,4-tetrazol-5-one
  • Ligand: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate

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Supramolecule #1: Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF23...

SupramoleculeName: Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF23694-bound state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2, #4-#5, #7-#8, #6, #9-#10
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: COR1 isoform 1

MacromoleculeName: COR1 isoform 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 47.45927 KDa
SequenceString: AEVTQLSNGI VVATEHNPSA HTASVGVVFG SGAANENPYN NGVSNLWKNI FLSKENSAVA AKEGLALSSN ISRDFQSYIV SSLPGSTDK SLDFLNQSFI QQKANLLSSS NFEATKKSVL KQVQDFEEND HPNRVLEHLH STAFQNTPLS LPTRGTLESL E NLVVADLE ...String:
AEVTQLSNGI VVATEHNPSA HTASVGVVFG SGAANENPYN NGVSNLWKNI FLSKENSAVA AKEGLALSSN ISRDFQSYIV SSLPGSTDK SLDFLNQSFI QQKANLLSSS NFEATKKSVL KQVQDFEEND HPNRVLEHLH STAFQNTPLS LPTRGTLESL E NLVVADLE SFANNHFLNS NAVVVGTGNI KHEDLVNSIE SKNLSLQTGT KPVLKKKAAF LGSEVRLRDD TLPKAWISLA VE GEPVNSP NYFVAKLAAQ IFGSYNAFEP ASRLQGIKLL DNIQEYQLCD NFNHFSLSYK DSGLWGFSTA TRNVTMIDDL IHF TLKQWN RLTISVTDTE VERAKSLLKL QLGQLYESGN PVNDANLLGA EVLIKGSKLS LGEAFKKIDA ITVKDVKAWA GKRL WDQDI AIAGTGQIEG LLDYMRIRSD MSMMRW

UniProtKB: UNIPROTKB: A0A6A5Q3X1

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Macromolecule #2: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 43.68659 KDa
SequenceString: MAFRKSNVYL SLVNSYIIDS PQPSSINYWW NMGSLLGLCL VIQIVTGIFM AMHYSSNIEL AFSSVEHIMR DVHNGYILRY LHANGASFF FMVMFMHMAK GLYYGSYRSP RVTLWNVGVI IFILTIATAF LGYCCVYGQM SHWGATVITN LFSAIPFVGN D IVSWLWGG ...String:
MAFRKSNVYL SLVNSYIIDS PQPSSINYWW NMGSLLGLCL VIQIVTGIFM AMHYSSNIEL AFSSVEHIMR DVHNGYILRY LHANGASFF FMVMFMHMAK GLYYGSYRSP RVTLWNVGVI IFILTIATAF LGYCCVYGQM SHWGATVITN LFSAIPFVGN D IVSWLWGG FSVSNPTIQR FFALHYLVPF IIAAMVIMHL MALHIHGSSN PLGITGNLDR IPMHSYFIFK DLVTVFLFML IL ALFVFYS PNTLGHPDNY IPGNPLVTPA SIVPEWYLLP FYAILRSIPD KLLGVITMFA AILVLLVLPF TDRSVVRGNT FKV LSKFFF FIFVFNFVLL GQIGACHVEV PYVLMGQIAT FIYFAYFLII VPVISTIENV LFYIGRVNK

UniProtKB: Cytochrome b

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Macromolecule #3: Cytochrome b-c1 complex subunit 2, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 2, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 38.751918 KDa
SequenceString: LTVSARDAPT KISTLAVKVH GGSRYATKDG VAHLLNRFNF QNTNTRSALK LVRESELLGG TFKSTLDREY ITLKATFLKD DLPYYVNAL ADVLYKTAFK PHELTESVLP AARYDYAVAE QCPVKSAEDQ LYAITFRKGL GNPLLYDGVE RVSLQDIKDF A DKVYTKEN ...String:
LTVSARDAPT KISTLAVKVH GGSRYATKDG VAHLLNRFNF QNTNTRSALK LVRESELLGG TFKSTLDREY ITLKATFLKD DLPYYVNAL ADVLYKTAFK PHELTESVLP AARYDYAVAE QCPVKSAEDQ LYAITFRKGL GNPLLYDGVE RVSLQDIKDF A DKVYTKEN LEVSGENVVE ADLKRFVDES LLSTLPAGKS LVSKSEPKFF LGEENRVRFI GDSVAAIGIP VNKASLAQYE VL ANYLTSA LSELSGLISS AKLDKFTDGG LFTLFVRDQD SAVVSSNIKK IVADLKKGKD LSPAINYTKL KNAVQNESVS SPI ELNFDA VKDFKLGKFN YVAVGDVSNL PYLDEL

UniProtKB: UNIPROTKB: A0A6A5Q625

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Macromolecule #4: Cytochrome c1, heme protein, mitochondrial

MacromoleculeName: Cytochrome c1, heme protein, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 27.807395 KDa
SequenceString: MTAAEHGLHA PAYAWSHNGP FETFDHASIR RGYQVYREVC AACHSLDRVA WRTLVGVSHT NEEVRNMAEE FEYDDEPDEQ GNPKKRPGK LSDYIPGPYP NEQAARAANQ GALPPDLSLI VKARHGGCDY IFSLLTGYPD EPPAGVALPP GSNYNPYFPG G SIAMARVL ...String:
MTAAEHGLHA PAYAWSHNGP FETFDHASIR RGYQVYREVC AACHSLDRVA WRTLVGVSHT NEEVRNMAEE FEYDDEPDEQ GNPKKRPGK LSDYIPGPYP NEQAARAANQ GALPPDLSLI VKARHGGCDY IFSLLTGYPD EPPAGVALPP GSNYNPYFPG G SIAMARVL FDDMVEYEDG TPATTSQMAK DVTTFLNWCA EPEHDERKRL GLKTVIILSS LYLLSIWVKK FKWAGIKTRK FV FNPPKPR K

UniProtKB: quinol--cytochrome-c reductase

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Macromolecule #5: Cytochrome b-c1 complex subunit Rieske, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 20.122955 KDa
SequenceString:
KSTYRTPNFD DVLKENNDAD KGRSYAYFMV GAMGLLSSAG AKSTVETFIS SMTATADVLA MAKVEVNLAA IPLGKNVVVK WQGKPVFIR HRTPHEIQEA NSVDMSALKD PQTDADRVKD PQWLIMLGIC THLGCVPIGE AGDFGGWFCP CHGSHYDISG R IRKGPAPL NLEIPAYEFD GDKVIVG

UniProtKB: UNIPROTKB: A0A8H8ULJ0

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Macromolecule #6: Cytochrome b-c1 complex subunit 8

MacromoleculeName: Cytochrome b-c1 complex subunit 8 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 10.856314 KDa
SequenceString:
GPPSGKTYMG WWGHMGGPKQ KGITSYAVSP YAQKPLQGIF HNAVFNSFRR FKSQFLYVLI PAGIYWYWWK NGNEYNEFLY SKAGREELE RVNV

UniProtKB: UNIPROTKB: A0A6A5PU80

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Macromolecule #7: QCR6 isoform 1

MacromoleculeName: QCR6 isoform 1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.983905 KDa
SequenceString:
EVTDQLEDLR EHFKNTEEGK ALVHHYEECA ERVKIQQQQP GYADLEHKED CVEEFFHLQH YLDTATAPRL FDKLK

UniProtKB: UNIPROTKB: A0A8H8ULB7

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Macromolecule #8: Cytochrome b-c1 complex subunit 7

MacromoleculeName: Cytochrome b-c1 complex subunit 7 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.452557 KDa
SequenceString:
PQSFTSIARI GDYILKSPVL SKLCVPVANQ FINLAGYKKL GLKFDDLIAE ENPIMQTALR RLPEDESYAR AYRIIRAHQT ELTHHLLPR NEWIKAQEDV PYLLPYILEA EAAAKEKDEL DNIEVSK

UniProtKB: UNIPROTKB: A0A6A5Q2H4

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Macromolecule #9: Cytochrome b-c1 complex subunit 9, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 9, mitochondrial / type: protein_or_peptide / ID: 9
Details: The sequence of organism Saccharomyces cerevisiae is not available, replaced by P22289 temporarily.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 6.301232 KDa
SequenceString:
SSLYKTFFKR NAVFVGTIFA GAFVFQTVFD TAITSWYENH NKGKLWKDVK ARIAA

UniProtKB: Cytochrome b-c1 complex subunit 9, mitochondrial

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Macromolecule #10: Cytochrome b-c1 complex subunit 10, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 10, mitochondrial / type: protein_or_peptide / ID: 10
Details: The sequence of organism Saccharomyces cerevisiae is not available, replaced by P37299 temporarily.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 5.879958 KDa
SequenceString:
KTGLHFGRLS LRSLTAYAPN LMLWGGASML GLFVFTEGWP KFQDTLYKKI PL

UniProtKB: Cytochrome b-c1 complex subunit 10, mitochondrial

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Macromolecule #11: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate

MacromoleculeName: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
type: ligand / ID: 11 / Number of copies: 2 / Formula: 6PH
Molecular weightTheoretical: 592.785 Da
Chemical component information

ChemComp-6PH:
(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate

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Macromolecule #12: (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16...

MacromoleculeName: (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate
type: ligand / ID: 12 / Number of copies: 2 / Formula: CN3
Molecular weightTheoretical: 834.862 Da
Chemical component information

ChemComp-CN3:
(2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate

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Macromolecule #13: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoy...

MacromoleculeName: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
type: ligand / ID: 13 / Number of copies: 2 / Formula: 9PE
Molecular weightTheoretical: 593.773 Da
Chemical component information

ChemComp-9PE:
(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate / phospholipid*YM

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Macromolecule #14: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 14 / Number of copies: 6 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #15: (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-penta...

MacromoleculeName: (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate
type: ligand / ID: 15 / Number of copies: 1 / Formula: CN5
Molecular weightTheoretical: 634.631 Da
Chemical component information

ChemComp-CN5:
(5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate

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Macromolecule #16: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)...

MacromoleculeName: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
type: ligand / ID: 16 / Number of copies: 2 / Formula: UQ6
Molecular weightTheoretical: 592.891 Da
Chemical component information

ChemComp-UQ6:
5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL

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Macromolecule #17: 1-[2-[(4,6-dimethyl-1,3-benzothiazol-2-yl)sulfanylmethyl]-3-methy...

MacromoleculeName: 1-[2-[(4,6-dimethyl-1,3-benzothiazol-2-yl)sulfanylmethyl]-3-methyl-phenyl]-4-methyl-1,2,3,4-tetrazol-5-one
type: ligand / ID: 17 / Number of copies: 2 / Formula: A1D6O
Molecular weightTheoretical: 397.517 Da

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Macromolecule #18: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradeca...

MacromoleculeName: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
type: ligand / ID: 18 / Number of copies: 2 / Formula: 8PE
Molecular weightTheoretical: 691.959 Da
Chemical component information

ChemComp-8PE:
(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate / phospholipid*YM

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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

Concentration0.5 mg/mL
BufferpH: 7.4 / Details: PBS, 0.1% DDM
GridModel: Quantifoil R1.2/1.3 / Support film - Material: GRAPHENE OXIDE
VitrificationCryogen name: NITROGEN
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 1650 / Average electron dose: 49.48 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 658118
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120260
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ymx


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8yin:
Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF23694-bound state

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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