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- EMDB-15322: Complex III2 from Yarrowia lipolytica,antimycin A bound, int-position -

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Basic information

Entry
Database: EMDB / ID: EMD-15322
TitleComplex III2 from Yarrowia lipolytica,antimycin A bound, int-position
Map data
Sample
  • Organelle or cellular component: Complex III2, with antmiycin A, int-position
    • Protein or peptide: x 10 types
  • Ligand: x 9 types
Keywordsoxidoreductase / electron transport chain / inhibitor / MEMBRANE PROTEIN
Function / homology
Function and homology information


mitochondrial processing peptidase complex / mitochondrial processing peptidase / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista ...mitochondrial processing peptidase complex / mitochondrial processing peptidase / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / nuclear periphery / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / 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 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain ...Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / 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 / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur 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
Similarity search - Domain/homology
YALI0F24673p / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 7 / YALI0C12210p / Complex III subunit 9 / quinol--cytochrome-c reductase / mitochondrial processing peptidase / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWieferig JP / Kuhlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: IUCrJ / Year: 2023
Title: Analysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III by cryo-EM.
Authors: Jan Philip Wieferig / Werner Kühlbrandt /
Abstract: Movement of the Rieske domain of the iron-sulfur protein is essential for intramolecular electron transfer within complex III (CIII) of the respiratory chain as it bridges a gap in the cofactor chain ...Movement of the Rieske domain of the iron-sulfur protein is essential for intramolecular electron transfer within complex III (CIII) of the respiratory chain as it bridges a gap in the cofactor chain towards the electron acceptor cytochrome c. We present cryo-EM structures of CIII from Yarrowia lipolytica at resolutions up to 2.0 Å under different conditions, with different redox states of the cofactors of the high-potential chain. All possible permutations of three primary positions were observed, indicating that the two halves of the dimeric complex act independently. Addition of the substrate analogue decylubiquinone to CIII with a reduced high-potential chain increased the occupancy of the Q site. The extent of Rieske domain interactions through hydrogen bonds to the cytochrome b and cytochrome c subunits varied depending on the redox state and substrate. In the absence of quinols, the reduced Rieske domain interacted more closely with cytochrome b and cytochrome c than in the oxidized state. Upon addition of the inhibitor antimycin A, the heterogeneity of the cd-helix and ef-loop increased, which may be indicative of a long-range effect on the Rieske domain.
History
DepositionJul 4, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15322.png

Downloads & links

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Map

FileDownload / File: emd_15322.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 299.16 Å		0.83 Å/pix.
x 360 pix.
= 299.16 Å		0.83 Å/pix.
x 360 pix.
= 299.16 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.013865968 - 0.057650354
Average (Standard dev.)0.00034604903 (±0.002585331)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 299.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_15322_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_15322_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex III2, with antmiycin A, int-position

EntireName: Complex III2, with antmiycin A, int-position
Components
  • Organelle or cellular component: Complex III2, with antmiycin A, int-position
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 7
    • Protein or peptide: YALI0F24673p
    • Protein or peptide: YALI0A14806p
    • Protein or peptide: Cytochrome b-c1 complex subunit 2, mitochondrial
    • Protein or peptide: YALI0A17468p
    • Protein or peptide: Cytochrome b-c1 complex subunit 8
    • Protein or peptide: Complex III subunit 9
    • Protein or peptide: YALI0C12210p
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: CARDIOLIPIN
  • Ligand: [(2R,3S,6S,7R,8R)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 3-methylbutanoate
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: HEME C

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Supramolecule #1: Complex III2, with antmiycin A, int-position

SupramoleculeName: Complex III2, with antmiycin A, int-position / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Yarrowia lipolytica (yeast)

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Macromolecule #1: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150
Molecular weightTheoretical: 43.409406 KDa
SequenceString: MALRKKNSLL NMANSYVLDS PQPSNLNYFW NFGSLLALCL VIQLATGITL AMHYTSHASL AFDSVEHIMR DVNFGWFIRY AHANTASFF FICIYAHMGR NIYYGSYKTP RVLPWSIGVI IFLLLIITAF MGYVLVFGQM SLWGATVICN LVSAIPWLGE D IVHFLWGG ...String:
MALRKKNSLL NMANSYVLDS PQPSNLNYFW NFGSLLALCL VIQLATGITL AMHYTSHASL AFDSVEHIMR DVNFGWFIRY AHANTASFF FICIYAHMGR NIYYGSYKTP RVLPWSIGVI IFLLLIITAF MGYVLVFGQM SLWGATVICN LVSAIPWLGE D IVHFLWGG FSVGNPTLQR FFALHYLMPF VLAVFALLHL IALHTAGSSN PLGITSNVDK LSMHPYYSFK DLITVFAFLL MF TLFVFFS PDKLGHPDNY IPANPMVTPA SIVPEWYLLP FYAILRAIPD KLGGVIAMVA AILILLILPI VDRSIIRGNA FKP ISKLLF GFFICNFLLL GVLGQVHIEP PFIVLGQICT IFYFSYFLIL LPMVSTIENI FFYIGSLRK

UniProtKB: Cytochrome b

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

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150
Molecular weightTheoretical: 24.563213 KDa
SequenceString: MSLLRTAAQA VKAPKAYTPL VAAKAFAQTR SVSSQPIGGK STYKIPDFTP YLKKDRNTDA NRLFSYFMIG SFGMLSAAGA KATVQDFLS NMSASADVLA MAKVEVKLGA IPLGKNVIIK WRGKPIFIRH RTSEEIEEAN EVNVATLRDP QTDDERVQKP E WLVMIGVC ...String:
MSLLRTAAQA VKAPKAYTPL VAAKAFAQTR SVSSQPIGGK STYKIPDFTP YLKKDRNTDA NRLFSYFMIG SFGMLSAAGA KATVQDFLS NMSASADVLA MAKVEVKLGA IPLGKNVIIK WRGKPIFIRH RTSEEIEEAN EVNVATLRDP QTDDERVQKP E WLVMIGVC THLGCVPIGE AGDFGGWFCP CHGSHYDISG RIRRGPAPLN LEIPEYDFAD AETLVIG

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

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Macromolecule #3: Cytochrome b-c1 complex subunit 7

MacromoleculeName: Cytochrome b-c1 complex subunit 7 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150
Molecular weightTheoretical: 14.675995 KDa
SequenceString:
MASITSVVKT SELILKSPLL SKIVVPLAKT YVKFSGYRQL GFKMNDLIIE ETPNMQLALR RLPPTESYDR VYRLIRATQF SLSHKLATG NDITKPEEDD HYLIPYILDV EAEAFEKDAL DNLEVVKRK

UniProtKB: Cytochrome b-c1 complex subunit 7

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Macromolecule #4: YALI0F24673p

MacromoleculeName: YALI0F24673p / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150
Molecular weightTheoretical: 15.789444 KDa
SequenceString:
MSYFLTLASE VAESLLPTVA FASEEEKEQD EPVEVESDDD ESEEKEDDDE EEDEDDDDDD DDDEVPDPAI ALHEAAAEGP CHDFKHHFD ECVERVTKAQ EAEDYDHAEY KEDCVEEFFH LQHCINDNTA DKLFRVLK

UniProtKB: YALI0F24673p

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Macromolecule #5: YALI0A14806p

MacromoleculeName: YALI0A14806p / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150
Molecular weightTheoretical: 52.846945 KDa
SequenceString: MNSLLRLPAL KRGVFTMSKR GLATTVSPKT RTSNLKNGLT IASESNPLVQ TATVGVWIDA GSRNENAYNN GTAHFFEHLA FKGTDKRSQ HQLELDIENM GGHLNAYTSR ESTVYYAKSF KDDVPKSVEI LADILQHSKL AESAIDRERE VITRELEEVN K QYEEVVFD ...String:
MNSLLRLPAL KRGVFTMSKR GLATTVSPKT RTSNLKNGLT IASESNPLVQ TATVGVWIDA GSRNENAYNN GTAHFFEHLA FKGTDKRSQ HQLELDIENM GGHLNAYTSR ESTVYYAKSF KDDVPKSVEI LADILQHSKL AESAIDRERE VITRELEEVN K QYEEVVFD HLHATAFMNQ PLGRTILGPR ENIQTITNTE LRKFITENYT ADRMVLVGAG AVDHDALVEL AEKYFSHLPS SQ SPVPLGT PRSSGEDANQ NPIPNFVGSE VRLRDDTMPV AHIAIAVEGV SWTSEDYYTA LVAQAIIGNY DRAVGTSRHQ GSR LSNIVS ENNLANSFQS FSTSYSDTGL WGIYLTSENT TQIDDLVHFT LKEWNRLSTS VSNLQVERAK SQLKAGLLLS LDGT TYVAE DIGRQLTTLG RRVTPAEVEA KLEAVTEHDV RAWAQKTLYD KDIALVGLGP IEGLYDYNRI RNDMSMMRW

UniProtKB: mitochondrial processing peptidase

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Macromolecule #6: Cytochrome b-c1 complex subunit 2, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 2, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150
Molecular weightTheoretical: 44.27784 KDa
SequenceString: MTRGVPRLAV AARHFSTAEA AGVKVAAQDG QSPISDLSVV LRGGSRYATV PGVSHILEKF AFQNTVPKSA LRFVRELELF GGKLYTHTT REHIVLRTQF LKQDLPYFVD AFANVLKETK FQQFELTERV APVAELDLLK RESDPAFTAL EAAHEVAFRT G LGNSVYAQ ...String:
MTRGVPRLAV AARHFSTAEA AGVKVAAQDG QSPISDLSVV LRGGSRYATV PGVSHILEKF AFQNTVPKSA LRFVRELELF GGKLYTHTT REHIVLRTQF LKQDLPYFVD AFANVLKETK FQQFELTERV APVAELDLLK RESDPAFTAL EAAHEVAFRT G LGNSVYAQ GYSPVTLEDV KEFARQVYAK QNVAVVGNNV VPADLQQLVG TAFADLQEGS KVTQAGTTTL HGGEARVRTS TG NALTIAL PIAEPKPVYH ALASFLGGPA SMPWSVGASP LAQATVGTHT SVKATYHNYG DAGLFAITIK GDSPAEISQV AHK AVQALK DTGAEVTEEQ AARAYAKSKF AAAEAFENPD SSASVIGMEL LSGVSRIAPE NVQKFTPAEL SEAAAQLSAS AKPV VAAVG QVHALPFADE LF

UniProtKB: Cytochrome b-c1 complex subunit 2, mitochondrial

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Macromolecule #7: YALI0A17468p

MacromoleculeName: YALI0A17468p / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150
Molecular weightTheoretical: 36.555605 KDa
SequenceString: MRRRRIGVWP ENRRVSRLWV SLSPRSCVTC PVPTNQNPPI NNHHTPILTQ MFKAIPLRQA LLGISSAVCA GATTTYYYTT KAEAMTAAE HGLHPAEYPW PQNGMLSTFD HASLRRGYQV YKEVCAACHS LDRIAWRNLV GVTHTTDEAK AFAEELEYDD E PDDEGNPR ...String:
MRRRRIGVWP ENRRVSRLWV SLSPRSCVTC PVPTNQNPPI NNHHTPILTQ MFKAIPLRQA LLGISSAVCA GATTTYYYTT KAEAMTAAE HGLHPAEYPW PQNGMLSTFD HASLRRGYQV YKEVCAACHS LDRIAWRNLV GVTHTTDEAK AFAEELEYDD E PDDEGNPR KRPGKLADYI PGPYPNEQAA RAANQGALPP DLSLIAKARH GGADYIFALL TGYPDEPPAG VVLAPGMNYN PY FPGGGIG MARTLFDGVV EYEDGTPATT SQMAKDVAAF LTWAAEPEHD ERKKLGLKAI IVISAMLGLS VYIKKFKWSP IKN RKFIYN PPKN

UniProtKB: quinol--cytochrome-c reductase

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Macromolecule #8: Cytochrome b-c1 complex subunit 8

MacromoleculeName: Cytochrome b-c1 complex subunit 8 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150
Molecular weightTheoretical: 10.46397 KDa
SequenceString:
MGGNGHYMGW WGHMGSPPQK GIAGYTISPF AARPFAGVVH AAIFNTFRRT KNQALFVILP VSFFYYVWTQ ASEKNEWLYT KAGRHELAK ALAE

UniProtKB: Cytochrome b-c1 complex subunit 8

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Macromolecule #9: Complex III subunit 9

MacromoleculeName: Complex III subunit 9 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150
Molecular weightTheoretical: 8.038856 KDa
SequenceString:
MAWATTFYNV FVKRNSAFVA TILASAFVFD MTFETAIDNF WDRINAGKQW KDIRHKYIEA AGDDDEDDE

UniProtKB: Complex III subunit 9

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Macromolecule #10: YALI0C12210p

MacromoleculeName: YALI0C12210p / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150
Molecular weightTheoretical: 9.114678 KDa
SequenceString:
MICGEGDYVK KPSYKIVPHF LGFNIPTVSK WIPIFGIWGA AAGIGALFLI EGVPRTRQDI LSKIPIIGEH WIREIPASDN PF

UniProtKB: YALI0C12210p

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Macromolecule #11: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 11 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #12: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 12 / Number of copies: 4 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #13: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 13 / Number of copies: 4 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #14: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 14 / Number of copies: 10 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #15: [(2R,3S,6S,7R,8R)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino...

MacromoleculeName: [(2R,3S,6S,7R,8R)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 3-methylbutanoate
type: ligand / ID: 15 / Number of copies: 2 / Formula: AWB
Molecular weightTheoretical: 548.625 Da
Chemical component information

ChemComp-AWB:
[(2R,3S,6S,7R,8R)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 3-methylbutanoate

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Macromolecule #16: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 16 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #17: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 17 / Number of copies: 2 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #18: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 18 / Number of copies: 2 / Formula: XP4
Molecular weightTheoretical: 591.777 Da
Chemical component information

ChemComp-XP4:
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE / DMPA, phospholipid*YM

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Macromolecule #19: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 19 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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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

BufferpH: 8
GridModel: Quantifoil R2/2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 41754
Initial angle assignmentType: OTHER / Software - Name: RELION
Final angle assignmentType: OTHER / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Software - Name: RELION
FSC plot (resolution estimation)

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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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