[English] 日本語
Yorodumi
- EMDB-19963: III2IV respiratory supercomplex from Saccharomyces cerevisiae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19963
TitleIII2IV respiratory supercomplex from Saccharomyces cerevisiae
Map data
Sample
  • Complex: III2-IV respiratory supercomplex
    • Protein or peptide: x 22 types
  • Ligand: x 14 types
KeywordsRespiration / supercomplex / MEMBRANE PROTEIN
Function / homology
Function and homology information


: / Complex III assembly / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / mitochondrial respirasome assembly / Mitochondrial protein degradation / : ...: / Complex III assembly / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / : / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / nuclear periphery / proton transmembrane transport / mitochondrial membrane / metalloendopeptidase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / membrane / metal ion binding / cytosol
Similarity search - Function
Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily ...Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / 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 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 b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / 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 c1, transmembrane anchor, C-terminal / Cytochrome c/quinol oxidase subunit II / : / Cytochrome b / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / : / 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. / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / 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 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.
Similarity search - Domain/homology
Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7, mitochondrial / Cytochrome b / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 6, mitochondrial / Cytochrome c oxidase subunit 4, mitochondrial / Cytochrome c oxidase subunit 8, mitochondrial ...Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7, mitochondrial / Cytochrome b / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 6, mitochondrial / Cytochrome c oxidase subunit 4, mitochondrial / Cytochrome c oxidase subunit 8, mitochondrial / Cytochrome c1, heme protein, mitochondrial / Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 8, mitochondrial / Cytochrome c oxidase subunit 7, mitochondrial / Cytochrome b-c1 complex subunit 9, mitochondrial / Cytochrome c oxidase subunit 13, mitochondrial / Cytochrome b-c1 complex subunit 10, mitochondrial / Cytochrome c oxidase subunit 12, mitochondrial / Cytochrome c oxidase subunit 26, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsWu F / Di Trani JM / Rubinstein JL / Brzezinski P / Moe A
Funding support Sweden, Canada, 3 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
Canadian Institutes of Health Research (CIHR)PJT191893 Canada
CitationJournal: Nat Commun / Year: 2024
Title: Electron transfer in the respiratory chain at low salinity.
Authors: Ana Paula Lobez / Fei Wu / Justin M Di Trani / John L Rubinstein / Mikael Oliveberg / Peter Brzezinski / Agnes Moe /
Abstract: Recent studies have established that cellular electrostatic interactions are more influential than assumed previously. Here, we use cryo-EM and perform steady-state kinetic studies to investigate ...Recent studies have established that cellular electrostatic interactions are more influential than assumed previously. Here, we use cryo-EM and perform steady-state kinetic studies to investigate electrostatic interactions between cytochrome (cyt.) c and the complex (C) III-IV supercomplex from Saccharomyces cerevisiae at low salinity. The kinetic studies show a sharp transition with a Hill coefficient ≥2, which together with the cryo-EM data at 2.4 Å resolution indicate multiple cyt. c molecules bound along the supercomplex surface. Negatively charged loops of CIII subunits Qcr6 and Qcr9 become structured to interact with cyt. c. In addition, the higher resolution allows us to identify water molecules in proton pathways of CIV and, to the best of our knowledge, previously unresolved cardiolipin molecules. In conclusion, the lowered electrostatic screening renders engagement of multiple cyt. c molecules that are directed by electrostatically structured CIII loops to conduct electron transfer between CIII and CIV.
History
DepositionMar 27, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19963.png

Downloads & links

-
Map

FileDownload / File: emd_19963.map.gz / Format: CCP4 / Size: 846.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 606 pix.
= 512.918 Å		0.85 Å/pix.
x 604 pix.
= 511.226 Å		0.85 Å/pix.
x 606 pix.
= 512.918 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.8464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-0.9931986 - 5.9896693
Average (Standard dev.)0.026874615 (±0.08503735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1-3-4
Dimensions604606606
Spacing606604606
CellA: 512.9184 Å / B: 511.22562 Å / C: 512.9184 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : III2-IV respiratory supercomplex

EntireName: III2-IV respiratory supercomplex
Components
  • Complex: III2-IV respiratory supercomplex
    • Protein or peptide: Cytochrome b-c1 complex subunit 1, mitochondrial
    • 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: Cytochrome b-c1 complex subunit 6, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 7, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 8, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 9, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 10, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 1
    • Protein or peptide: Cytochrome c oxidase subunit 2
    • Protein or peptide: Cytochrome c oxidase subunit 3
    • Protein or peptide: Cytochrome c oxidase subunit 4, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 6, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 7, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 8, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 9, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 12, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 13, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 26, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 5A, mitochondrial
  • Ligand: CARDIOLIPIN
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
  • 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: HEME C
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: COPPER (II) ION
  • Ligand: HEME-A
  • Ligand: CALCIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: DINUCLEAR COPPER ION
  • Ligand: ZINC ION
  • Ligand: water

+
Supramolecule #1: III2-IV respiratory supercomplex

SupramoleculeName: III2-IV respiratory supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#22
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

+
Macromolecule #1: Cytochrome b-c1 complex subunit 1, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 1, mitochondrial / 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: Cytochrome b-c1 complex subunit 1, mitochondrial

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

MacromoleculeName: Cytochrome b-c1 complex subunit 2, mitochondrial / type: protein_or_peptide / ID: 2 / 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: Cytochrome b-c1 complex subunit 2, mitochondrial

+
Macromolecule #3: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
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

+
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: 27.678215 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

UniProtKB: Cytochrome c1, heme protein, mitochondrial

+
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: Cytochrome b-c1 complex subunit Rieske, mitochondrial

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

MacromoleculeName: Cytochrome b-c1 complex subunit 6, mitochondrial / type: protein_or_peptide / ID: 6 / 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: Cytochrome b-c1 complex subunit 6, mitochondrial

+
Macromolecule #7: Cytochrome b-c1 complex subunit 7, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 7, mitochondrial / type: protein_or_peptide / ID: 7 / 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: Cytochrome b-c1 complex subunit 7, mitochondrial

+
Macromolecule #8: Cytochrome b-c1 complex subunit 8, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 8, mitochondrial / type: protein_or_peptide / ID: 8 / 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: Cytochrome b-c1 complex subunit 8, mitochondrial

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

MacromoleculeName: Cytochrome b-c1 complex subunit 9, mitochondrial / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 6.535484 KDa
SequenceString:
SFSSLYKTFF KRNAVFVGTI FAGAFVFQTV FDTAITSWYE NHNKGKLWKD VKARIAA

UniProtKB: Cytochrome b-c1 complex subunit 9, mitochondrial

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

MacromoleculeName: Cytochrome b-c1 complex subunit 10, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.471717 KDa
SequenceString:
AYTSHLSSKT GLHFGRLSLR SLTAYAPNLM LWGGASMLGL FVFTEGWPKF QDTLYKKIPL LGPTLEDHTP PEDKPN

UniProtKB: Cytochrome b-c1 complex subunit 10, mitochondrial

+
Macromolecule #11: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 58.832586 KDa
SequenceString: MVQRWLYSTN AKDIAVLYFM LAIFSGMAGT AMSLIIRLEL AAPGSQYLHG NSQLFNVLVV GHAVLMIFFL VMPALIGGFG NYLLPLMIG ATDTAFPRIN NIAFWVLPMG LVCLVTSTLV ESGAGTGWTV YPPLSSIQAH SGPSVDLAIF ALHLTSISSL L GAINFIVT ...String:
MVQRWLYSTN AKDIAVLYFM LAIFSGMAGT AMSLIIRLEL AAPGSQYLHG NSQLFNVLVV GHAVLMIFFL VMPALIGGFG NYLLPLMIG ATDTAFPRIN NIAFWVLPMG LVCLVTSTLV ESGAGTGWTV YPPLSSIQAH SGPSVDLAIF ALHLTSISSL L GAINFIVT TLNMRTNGMT MHKLPLFVWS IFITAFLLLL SLPVLSAGIT MLLLDRNFNT SFFEVSGGGD PILYEHLFWF FG HPEVYIL IIPGFGIISH VVSTYSKKPV FGEISMVYAM ASIGLLGFLV WSHHMYIVGL DADTRAYFTS ATMIIAIPTG IKI FSWLAT IHGGSIRLAT PMLYAIAFLF LFTMGGLTGV ALANASLDVA FHDTYYVVGH FHYVLSMGAI FSLFAGYYYW SPQI LGLNY NEKLAQIQFW LIFIGANVIF FPMHFLGING MPRRIPDYPD AFAGWNYVAS IGSFIATLSL FLFIYILYDQ LVNGL NNKV NNKSVIYNKA PDFVESNTIF NLNTVKSSSI EFLLTSPPAV HSFNTPAVQS

UniProtKB: Cytochrome c oxidase subunit 1

+
Macromolecule #12: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 26.779816 KDa
SequenceString: DVPTPYACYF QDSATPNQEG ILELHDNIMF YLLVILGLVS WMLYTIVMTY SKNPIAYKYI KHGQTIEVIW TIFPAVILLI IAFPSFILL YLCDEVISPA MTIKAIGYQW YWKYEYSDFI NDSGETVEFE SYVIPDELLE EGQLRLLDTD TSMVVPVDTH I RFVVTAAD ...String:
DVPTPYACYF QDSATPNQEG ILELHDNIMF YLLVILGLVS WMLYTIVMTY SKNPIAYKYI KHGQTIEVIW TIFPAVILLI IAFPSFILL YLCDEVISPA MTIKAIGYQW YWKYEYSDFI NDSGETVEFE SYVIPDELLE EGQLRLLDTD TSMVVPVDTH I RFVVTAAD VIHDFAIPSL GIKVDATPGR LNQVSALIQR EGVFYGACSE LCGTGHANMP IKIEAVSLPK FLEWLNEQ

UniProtKB: Cytochrome c oxidase subunit 2

+
Macromolecule #13: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 30.383582 KDa
SequenceString: MTHLERSRHQ QHPFHMVMPS PWPIVVSFAL LSLALSTALT MHGYIGNMNM VYLALFVLLT SSILWFRDIV AEATYLGDHT MAVRKGINL GFLMFVLSEV LIFAGLFWAY FHSAMSPDVT LGACWPPVGI EAVQPTELPL LNTIILLSSG ATVTYSHHAL I AGNRNKAL ...String:
MTHLERSRHQ QHPFHMVMPS PWPIVVSFAL LSLALSTALT MHGYIGNMNM VYLALFVLLT SSILWFRDIV AEATYLGDHT MAVRKGINL GFLMFVLSEV LIFAGLFWAY FHSAMSPDVT LGACWPPVGI EAVQPTELPL LNTIILLSSG ATVTYSHHAL I AGNRNKAL SGLLITFWLI VIFVTCQYIE YTNAAFTISD GVYGSVFYAG TGLHFLHMVM LAAMLGVNYW RMRNYHLTAG HH VGYETTI IYTHVLDVIW LFLYVVFYWW GV

UniProtKB: Cytochrome c oxidase subunit 3

+
Macromolecule #14: Cytochrome c oxidase subunit 4, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 4, mitochondrial / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 12.94768 KDa
SequenceString:
VVKTAQNLAE VNGPETLIGP GAKEGTVPTD LDQETGLARL ELLGKLEGID VFDTKPLDSS RKGTMKDPII IESYDDYRYV GCTGSPAGS HTIMWLKPTV NEVARCWECG SVYKLNPVGV P

UniProtKB: Cytochrome c oxidase subunit 4, mitochondrial

+
Macromolecule #15: Cytochrome c oxidase subunit 6, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 6, mitochondrial / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 12.056452 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
DEETFEEFTA RYEKEFDEAY DLFEVQRVLN NCFSYDLVPA PAVIEKALRA ARRVNDLPTA IRVFEALKYK VENEDQYKAY LDELKDVRQ ELGVPLKEEL FPS

UniProtKB: Cytochrome c oxidase subunit 6, mitochondrial

+
Macromolecule #16: Cytochrome c oxidase subunit 7, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7, mitochondrial / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 6.811154 KDa
SequenceString:
ANKVIQLQKI FQSSTKPLWW RHPRSALYLY PFYAIFAVAV VTPLLYIPNA IRGIKAKKA

UniProtKB: Cytochrome c oxidase subunit 7, mitochondrial

+
Macromolecule #17: Cytochrome c oxidase subunit 8, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 8, mitochondrial / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 5.737735 KDa
SequenceString:
VHFKDGVYEN IPFKVKGRKT PYALSHFGFF AIGFAVPFVA CYVQLKKSGA F

UniProtKB: Cytochrome c oxidase subunit 8, mitochondrial

+
Macromolecule #18: Cytochrome c oxidase subunit 9, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 9, mitochondrial / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 6.471684 KDa
SequenceString:
TIAPITGTIK RRVIMDIVLG FSLGGVMASY WWWGFHMDKI NKREKFYAEL AERKK

UniProtKB: Cytochrome c oxidase subunit 9, mitochondrial

+
Macromolecule #19: Cytochrome c oxidase subunit 12, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 12, mitochondrial / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.909022 KDa
SequenceString:
SPLHTVGFDA RFPQQNQTKH CWQSYVDYHK CVNMKGEDFA PCKVFWKTYN ALCPLDWIEK WDDQREKGIF AGDIN

UniProtKB: Cytochrome c oxidase subunit 12, mitochondrial

+
Macromolecule #20: Cytochrome c oxidase subunit 13, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 13, mitochondrial / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.116012 KDa
SequenceString:
LPPNALKPAF GPPDKVAAQK FKESLMATEK HAKDTSNMWV KISVWVALPA IALTAVNTYF VEKEHAEHRE HLKHVPDSEW PRDYEFMNI RSKPFFWGDG DKTLFWNPVV NRHI

UniProtKB: Cytochrome c oxidase subunit 13, mitochondrial

+
Macromolecule #21: Cytochrome c oxidase subunit 26, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 26, mitochondrial / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 5.088929 KDa
SequenceString:
GRIGESWVIT EGRRLIPEIF QWSAVLSVCL GWPGAVYFFS KARKA

UniProtKB: Cytochrome c oxidase subunit 26, mitochondrial

+
Macromolecule #22: Cytochrome c oxidase subunit 5A, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 5A, mitochondrial / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.891784 KDa
SequenceString:
AQTHALSNAA VMDLQSRWEN MPSTEQQDIV SKLSERQKLP WAQLTEPEKQ AVWYISYGEW GPRRPVLNKG DSSFIAKGVA AGLLFSVGL FAVVRMAGGQ DAKTMNKEWQ LKSDEYLKSK NANPWGGYSQ VQSK

UniProtKB: Cytochrome c oxidase subunit 5A, mitochondrial

+
Macromolecule #23: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 23 / Number of copies: 11 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

+
Macromolecule #24: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 24 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #25: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 25 / Number of copies: 26 / Formula: PEF
Molecular weightTheoretical: 691.959 Da
Chemical component information

ChemComp-PEF:
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

+
Macromolecule #26: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / type: ligand / ID: 26 / Number of copies: 6 / Formula: PCF
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PCF:
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

+
Macromolecule #27: 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: 27 / 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

+
Macromolecule #28: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 28 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

+
Macromolecule #29: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 29 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

+
Macromolecule #30: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 30 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

+
Macromolecule #31: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 31 / Number of copies: 2 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

+
Macromolecule #32: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 32 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #33: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 33 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #34: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 34 / Number of copies: 1 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

+
Macromolecule #35: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 35 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #36: water

MacromoleculeName: water / type: ligand / ID: 36 / Number of copies: 11 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6hu9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 196457
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • 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

-
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

Read more