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- EMDB-50526: Respiratory supercomplex CIII2-CIV2 from alphaproteobacterium -

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Basic information

Entry
Database: EMDB / ID: EMD-50526
TitleRespiratory supercomplex CIII2-CIV2 from alphaproteobacterium
Map dataThis postprocessed .mrc file has been trimmed to a smaller box size of 375 pixels. This differs from that of the half-maps which has an untrimmed box size of 600 pixels and rescaled to 1.048 A/pix.
Sample
  • Complex: Respiratory supercomplex CIII2-CIV2 from alphaproteobacterium
    • Complex: Alphaproteobacterial respiratory complex III (ubiquinone-cytochrome c oxidoreductase, cytochrome bc1)
      • Protein or peptide: x 3 types
    • Complex: Alphaproteobacterial respiratory complex IV (Cytochrome c oxidase, aa3-type)
      • Protein or peptide: x 4 types
    • Complex: Transmembrane-anchored cytochrome c (c552)
      • Protein or peptide: x 1 types
  • Ligand: x 15 types
KeywordsSupercomplex / multi-subunit membrane protein complex / electron transport chain / native purification / ELECTRON TRANSPORT
Function / homology
Function and homology information


aerobic electron transport chain / respiratory chain complex IV / cytochrome-c oxidase / respiratory chain complex III / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport ...aerobic electron transport chain / respiratory chain complex IV / cytochrome-c oxidase / respiratory chain complex III / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / copper ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome c oxidase, subunit I bacterial type / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome c, class IA/ IB / Cytochrome c oxidase subunit I domain ...Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome c oxidase, subunit I bacterial type / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome c, class IA/ IB / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / 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 / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Cytochrome b / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Rieske iron-sulphur protein, C-terminal / Cytochrome c / 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 / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin
Similarity search - Domain/homology
Aa3 type cytochrome c oxidase subunit IV / Cytochrome c, class I / Cytochrome c oxidase subunit 1 / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome b / Cytochrome c1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesParacoccus denitrificans PD1222 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.31 Å
AuthorsYaikhomba M / Hirst J / Croll TI / Spikes TE / Agip ANA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 and MC_UU_00028/1 United Kingdom
CitationJournal: To Be Published
Title: Minimal supercomplexes in alphaproteobacteria reveal conserved structural mechanisms for efficient respiration
Authors: Yaikhomba M / Hirst J / Croll TI / Spikes TE
History
DepositionJun 4, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50526.png

Downloads & links

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Map

FileDownload / File: emd_50526.map.gz / Format: CCP4 / Size: 201.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis postprocessed .mrc file has been trimmed to a smaller box size of 375 pixels. This differs from that of the half-maps which has an untrimmed box size of 600 pixels and rescaled to 1.048 A/pix.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 375 pix.
= 393. Å		1.05 Å/pix.
x 375 pix.
= 393. Å		1.05 Å/pix.
x 375 pix.
= 393. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.028444044 - 0.076803245
Average (Standard dev.)-0.00019913552 (±0.0030814873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions375375375
Spacing375375375
CellA=B=C: 393.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50526_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the 2 half maps obtained from...

Fileemd_50526_half_map_1.map
AnnotationOne of the 2 half maps obtained from the 3D refinement procedure. The pixel size (1.07) here is the nominal one. The box size of this half map, 600 pixels, is not trimmed.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the 2 half maps obtained from...

Fileemd_50526_half_map_2.map
AnnotationOne of the 2 half maps obtained from the 3D refinement procedure. The pixel size (1.07) here is the nominal one. The box size of this half map, 600 pixels, is not trimmed.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Respiratory supercomplex CIII2-CIV2 from alphaproteobacterium

EntireName: Respiratory supercomplex CIII2-CIV2 from alphaproteobacterium
Components
  • Complex: Respiratory supercomplex CIII2-CIV2 from alphaproteobacterium
    • Complex: Alphaproteobacterial respiratory complex III (ubiquinone-cytochrome c oxidoreductase, cytochrome bc1)
      • Protein or peptide: Cytochrome b
      • Protein or peptide: Cytochrome c1
      • Protein or peptide: Ubiquinol-cytochrome c reductase iron-sulfur subunit
    • Complex: Alphaproteobacterial respiratory complex IV (Cytochrome c oxidase, aa3-type)
      • Protein or peptide: Cytochrome c oxidase subunit 1
      • Protein or peptide: Cytochrome c oxidase subunit 2
      • Protein or peptide: cytochrome-c oxidase
      • Protein or peptide: Aa3 type cytochrome c oxidase subunit IV
    • Complex: Transmembrane-anchored cytochrome c (c552)
      • Protein or peptide: Cytochrome c, class I
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: UBIQUINONE-10
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CALCIUM ION
  • Ligand: HEME C
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: CARDIOLIPIN
  • Ligand: HEME-A
  • Ligand: COPPER (II) ION
  • Ligand: MANGANESE (II) ION
  • Ligand: DINUCLEAR COPPER ION
  • Ligand: ZINC ION

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Supramolecule #1: Respiratory supercomplex CIII2-CIV2 from alphaproteobacterium

SupramoleculeName: Respiratory supercomplex CIII2-CIV2 from alphaproteobacterium
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

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Supramolecule #2: Alphaproteobacterial respiratory complex III (ubiquinone-cytochro...

SupramoleculeName: Alphaproteobacterial respiratory complex III (ubiquinone-cytochrome c oxidoreductase, cytochrome bc1)
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

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Supramolecule #3: Alphaproteobacterial respiratory complex IV (Cytochrome c oxidase...

SupramoleculeName: Alphaproteobacterial respiratory complex IV (Cytochrome c oxidase, aa3-type)
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#7
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

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Supramolecule #4: Transmembrane-anchored cytochrome c (c552)

SupramoleculeName: Transmembrane-anchored cytochrome c (c552) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

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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: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 50.154727 KDa
SequenceString: MAGIPHDHYE PKTGFERWLH RRLPIVSLVY DTLMIPTPKN LNWWWIWGIV LAFCLVLQIA TGIVLVMHYT PHVDLAFASV EHIMRDVNG GYMLRYLHAN GASLFFLAVY IHIFRGLYYG SYKAPREVTW IVGMLIYLMM MGTAFMGYVL PWGQMSFWGA T VITGLFGA ...String:
MAGIPHDHYE PKTGFERWLH RRLPIVSLVY DTLMIPTPKN LNWWWIWGIV LAFCLVLQIA TGIVLVMHYT PHVDLAFASV EHIMRDVNG GYMLRYLHAN GASLFFLAVY IHIFRGLYYG SYKAPREVTW IVGMLIYLMM MGTAFMGYVL PWGQMSFWGA T VITGLFGA IPGVGEAIQT WLLGGPAVDN PTLNRFFSLH YLLPFVIAAL VVVHIWAFHT TGNNNPTGVE VRRGSKEEAK KD TLPFWPY FVIKDLFALA VVLVVFFAIV GFMPNYLGHP DNYIEANPLV TPAHIVPEWY FLPFYAILRA FTADVWVVML VNW LSFGII DAKFFGVIAM FGAILVMALV PWLDTSRVRS GQYRPLFKWW FWLLAVDFVV LMWVGAMPAE GIYPYIALAG SAYW FAYFL IILPLLGIIE KPDAMPQTIE EDFNAHYGPE THPAE

UniProtKB: Cytochrome b

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Macromolecule #2: Cytochrome c1

MacromoleculeName: Cytochrome c1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 46.904332 KDa
SequenceString: MTLRNASLTA VAALTVALAG GAVAQDASTA PGTTAPAGSS YHTNEAAPAA ADTAPAAEAA DEPAAEEAEA GEAEVTEEPA ATETPAEEP AADEPAATEE PDAEAEPAAE EAQATTEEAP AEEPAAEEPA AEEPAEEPAA DAPAEEAAAE EAPAEPEAAA E EPAAEEPE ...String:
MTLRNASLTA VAALTVALAG GAVAQDASTA PGTTAPAGSS YHTNEAAPAA ADTAPAAEAA DEPAAEEAEA GEAEVTEEPA ATETPAEEP AADEPAATEE PDAEAEPAAE EAQATTEEAP AEEPAAEEPA AEEPAEEPAA DAPAEEAAAE EAPAEPEAAA E EPAAEEPE ATEEEAPAEE AAAEEAPAEE VVEDEAAADH GDAAAQEAGD SHAAAHIEDI SFSFEGPFGK FDQHQLQRGL QV YTEVCSA CHGLRYVPLR TLADEGGPQL PEDQVRAYAA NFDITDPETE EDRPRVPTDH FPTVSGEGMG PDLSLMAKAR AGF HGPYGT GLSQLFNGIG GPEYIHAVLT GYDGEEKEEA GAVLYHNAAF AGNWIQMAAP LSDDQVTYED GTPATVDQMA TDVA AFLMW TAEPKMMDRK QVGFVSVIFL IVLAALLYLT NKKLWQPIKH PRKPE

UniProtKB: Cytochrome c1

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Macromolecule #3: Ubiquinol-cytochrome c reductase iron-sulfur subunit

MacromoleculeName: Ubiquinol-cytochrome c reductase iron-sulfur subunit / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 20.889236 KDa
SequenceString: MEIKPVSHAD EHAGDHGATR RDFLYYATAG AGTVAAGAAA WTLVNQMNPS ADVQALASIQ VDVSGVETGT QLTVKWLGKP VFIRRRTED EIQAGREVDL GQLIDRSAQN SNKPDAPATD ENRTMDEAGE WLVMIGVCTH LGCVPIGDGA GDFGGWFCPC H GSHYDTSG ...String:
MEIKPVSHAD EHAGDHGATR RDFLYYATAG AGTVAAGAAA WTLVNQMNPS ADVQALASIQ VDVSGVETGT QLTVKWLGKP VFIRRRTED EIQAGREVDL GQLIDRSAQN SNKPDAPATD ENRTMDEAGE WLVMIGVCTH LGCVPIGDGA GDFGGWFCPC H GSHYDTSG RIRRGPAPQN LHIPVAEFLD DTTIKLG

UniProtKB: Ubiquinol-cytochrome c reductase iron-sulfur subunit

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Macromolecule #4: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 62.486645 KDa
SequenceString: MADAAVHGHG DHHDTRGFFT RWFMSTNHKD IGILYLFTAG IVGLISVCFT VYMRMELQHP GVQYMCLEGA RLIADASAEC TPNGHLWNV MITYHGVLMM FFVVIPALFG GFGNYFMPLH IGAPDMAFPR LNNLSYWMYV CGVALGVASL LAPGGNDQMG S GVGWVLYP ...String:
MADAAVHGHG DHHDTRGFFT RWFMSTNHKD IGILYLFTAG IVGLISVCFT VYMRMELQHP GVQYMCLEGA RLIADASAEC TPNGHLWNV MITYHGVLMM FFVVIPALFG GFGNYFMPLH IGAPDMAFPR LNNLSYWMYV CGVALGVASL LAPGGNDQMG S GVGWVLYP PLSTTEAGYS MDLAIFAVHV SGASSILGAI NIITTFLNMR APGMTLFKVP LFAWSVFITA WLILLSLPVL AG AITMLLM DRNFGTQFFD PAGGGDPVLY QHILWFFGHP EVYIIILPGF GIISHVISTF AKKPIFGYLP MVLAMAAIGI LGF VVWAHH MYTAGMSLTQ QAYFMLATMT IAVPTGIKVF SWIATMWGGS IEFKTPMLWA FGFLFLFTVG GVTGVVLSQA PLDR VYHDT YYVVAHFHYV MSLGAVFGIF AGVYYWIGKM SGRQYPEWAG QLHFWMMFIG SNLIFFPQHF LGRQGMPRRY IDYPV EFAY WNNISSIGAY ISFASFLFFI GIVFYTLFAG KRVNVPNYWN EHADTLEWTL PSPPPEHTFE TLPKREDWDR AHAH

UniProtKB: Cytochrome c oxidase subunit 1

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Macromolecule #5: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 32.563643 KDa
SequenceString: MMAIATKRRG VAAVMSLGVA TMTAVPALAQ DVLGDLPVIG KPVNGGMNFQ PASSPLAHDQ QWLDHFVLYI ITAVTIFVCL LLLICIVRF NRRANPVPAR FTHNTPIEVI WTLVPVLILV AIGAFSLPIL FRSQEMPNDP DLVIKAIGHQ WYWSYEYPND G VAFDALML ...String:
MMAIATKRRG VAAVMSLGVA TMTAVPALAQ DVLGDLPVIG KPVNGGMNFQ PASSPLAHDQ QWLDHFVLYI ITAVTIFVCL LLLICIVRF NRRANPVPAR FTHNTPIEVI WTLVPVLILV AIGAFSLPIL FRSQEMPNDP DLVIKAIGHQ WYWSYEYPND G VAFDALML EKEALADAGY SEDEYLLATD NPVVVPVGKK VLVQVTATDV IHAWTIPAFA VKQDAVPGRI AQLWFSVDQE GV YFGQCSE LCGINHAYMP IVVKAVSQEK YEAWLAGAKE EFAADASDYL PASPVKLASA E

UniProtKB: Cytochrome c oxidase subunit 2

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Macromolecule #6: cytochrome-c oxidase

MacromoleculeName: cytochrome-c oxidase / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 30.833162 KDa
SequenceString: MAHVKNHDYQ ILPPSIWPFF GAIGAFVMLT GAVAWMKGIT FFGLPVEGPW MFLIGLVGVL YVMFGWWADV VNEGETGEHT PVVRIGLQY GFILFIMSEV MFFVAWFWAF IKNALYPMGP DSPIKDGVWP PEGIVTFDPW HLPLINTLIL LLSGVAVTWA H HAFVHEGD ...String:
MAHVKNHDYQ ILPPSIWPFF GAIGAFVMLT GAVAWMKGIT FFGLPVEGPW MFLIGLVGVL YVMFGWWADV VNEGETGEHT PVVRIGLQY GFILFIMSEV MFFVAWFWAF IKNALYPMGP DSPIKDGVWP PEGIVTFDPW HLPLINTLIL LLSGVAVTWA H HAFVHEGD RKTTINGLIV AVILGVCFTG LQAYEYSHAA FGLADTVYAG AFYMATGFHG AHVIIGTIFL FVCLIRLLKG QM TQKQHVG FEAAAWYWHF VDVVWLFLFV VIYIWGR

UniProtKB: Cytochrome c oxidase subunit 3

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Macromolecule #7: Aa3 type cytochrome c oxidase subunit IV

MacromoleculeName: Aa3 type cytochrome c oxidase subunit IV / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 7.351497 KDa
SequenceString:
MGYPCARRIA SFTDRIMASH HEITDHKHGE MDIRHQQATF AGFIKGATWV SILSIAVLVF LALANS

UniProtKB: Aa3 type cytochrome c oxidase subunit IV

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Macromolecule #8: Cytochrome c, class I

MacromoleculeName: Cytochrome c, class I / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 18.177406 KDa
SequenceString:
MFDTMTVTKA AGALIGSLLF LLLMSWAASG IFHVGTSGHG AEGEEHAQAY TIPVESAGGA EGEAVDEGPD FATVLASADP AAGEKVFGK CKACHKLDGN DGVGPHLNGV VGRTVAGVDG FNYSDPMKAH GGDWTPEALQ EFLTNPKAVV KGTKMAFAGL P KIEDRANL IAYLEGQQ

UniProtKB: Cytochrome c, class I

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Macromolecule #9: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 9 / Number of copies: 12 / 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 #10: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 10 / Number of copies: 4 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

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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: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 12 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #13: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 13 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #14: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 14 / Number of copies: 13 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

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

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Macromolecule #15: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13...

MacromoleculeName: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol
type: ligand / ID: 15 / Number of copies: 11 / Formula: DU0
Molecular weightTheoretical: 516.752 Da
Chemical component information

ChemComp-DU0:
2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol

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Macromolecule #16: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 16 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #17: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 17 / Number of copies: 10 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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Macromolecule #18: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 18 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #19: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 19 / Number of copies: 4 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

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Macromolecule #20: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 20 / Number of copies: 2 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #21: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 21 / Number of copies: 2 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #22: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 22 / Number of copies: 2 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

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Macromolecule #23: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 23 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration2.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 55.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10322
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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