[English] 日本語
Yorodumi
- EMDB-65585: Cryo-EM structure of complex IV on the bovine heart submitochondr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65585
TitleCryo-EM structure of complex IV on the bovine heart submitochondrial particles, IV-A
Map data
Sample
  • Complex: Complex IV on the bovine heart submitochondrial particles
    • Protein or peptide: x 14 types
  • Ligand: x 9 types
Keywordsrespiratory chain complex / supercomplex / submitochondrial particles / MOTOR PROTEIN / OXIDOREDUCTASE
Function / homology
Function and homology information


Complex IV assembly / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation ...Complex IV assembly / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / ATP synthesis coupled electron transport / enzyme regulator activity / proton transmembrane transport / aerobic respiration / central nervous system development / respiratory electron transport chain / mitochondrial membrane / oxidoreductase activity / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / metal ion binding
Similarity search - Function
NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa ...NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome C oxidase chain VIIB / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, 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 VIb superfamily / 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 2, C-terminal / Cytochrome oxidase c subunit VIb / 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 Vb / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / 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 / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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 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. / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxin
Similarity search - Domain/homology
Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial ...Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit FA4
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsNakano A / Masuya T / Akisada S / Ishikawa-Fukuda M / Mitsuoka K / Miyoshi H / Murai M / Yokoyama K
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H02453 Japan
Japan Society for the Promotion of Science (JSPS)25K01958 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Nat Commun / Year: 2026
Title: Structures of respiratory supercomplexes and ATP synthase oligomers in mammalian mitochondrial inner membrane.
Authors: Atsuki Nakano / Takahiro Masuya / Shinsuke Akisada / Moe Ishikawa-Fukuda / Kaoru Mitsuoka / Hideto Miyoshi / Masatoshi Murai / Ken Yokoyama /
Abstract: Understanding the functional mechanisms of membrane protein complexes requires structural analysis within their native membrane environment. Here, we applied cryo-electron microscopy to determine the ...Understanding the functional mechanisms of membrane protein complexes requires structural analysis within their native membrane environment. Here, we applied cryo-electron microscopy to determine the structures of FF ATP synthase and respiratory supercomplexes (SCs) on sub-mitochondrial particles (SMPs) isolated from bovine heart mitochondria. Most FF complexes were observed as dimers stabilized by the regulatory factor IF₁, and a tetrameric assembly comprising two FF-IF₁ dimers arranged linearly was also identified. This finding indicates that the tetrameric units of FF are present in the mitochondrial inner membrane and contribute to shaping cristae tips in mammalian mitochondria. F domain maps resolve the e-subunit- c₈-ring interface and show no discrete density for a tightly bound lipid within the c₈-ring. In addition to the previously reported SCs compositions CI₁CIII₂CIV₁ and CI₁CIII₂CIV₂, our analysis identified an additional assembly with the composition CI₁CIII₂CIV₃, as well as a CI₂CIII₂CIV₆ mega-complex. This approach enables rapid structural determination of FF ATP synthase and SCs from minimal membrane fractions, providing a foundation for elucidating the molecular basis of metabolic disorders and mitochondrial diseases at the level of higher-order architecture.
History
DepositionJul 28, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_65585.png

Downloads & links

-
Map

FileDownload / File: emd_65585.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 600 pix.
= 654. Å		1.09 Å/pix.
x 600 pix.
= 654. Å		1.09 Å/pix.
x 600 pix.
= 654. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.56985325 - 1.0761553
Average (Standard dev.)-0.00009742596 (±0.018998837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 654.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_65585_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_65585_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_65585_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_65585_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Complex IV on the bovine heart submitochondrial particles

EntireName: Complex IV on the bovine heart submitochondrial particles
Components
  • Complex: Complex IV on the bovine heart submitochondrial particles
    • 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 isoform 1, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 5A, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 5B, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 6A2, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 6B1
    • Protein or peptide: Cytochrome c oxidase subunit 6C
    • Protein or peptide: Cytochrome c oxidase subunit 7A1, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 7B, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 7C, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 8B, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit NDUFA4
  • Ligand: HEME-A
  • Ligand: COPPER (II) ION
  • Ligand: MAGNESIUM ION
  • Ligand: PEROXIDE ION
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: DINUCLEAR COPPER ION
  • Ligand: SODIUM ION
  • Ligand: ZINC ION
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE

+
Supramolecule #1: Complex IV on the bovine heart submitochondrial particles

SupramoleculeName: Complex IV on the bovine heart submitochondrial particles
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 200 KDa

+
Macromolecule #1: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 57.093852 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString: (FME)FINRWLFST NHKDIGTLYL LFGAWAGMVG TALSLLIRAE LGQPGTLLGD DQIYNVVVTA HAFVMIFFMV MPIMIG GFG NWLVPLMIGA PDMAFPRMNN MSFWLLPPSF LLLLASSMVE AGAGTGWTVY PPLAGNLAHA GASVDLTIFS LHLAGVS SI LGAINFITTI ...String:
(FME)FINRWLFST NHKDIGTLYL LFGAWAGMVG TALSLLIRAE LGQPGTLLGD DQIYNVVVTA HAFVMIFFMV MPIMIG GFG NWLVPLMIGA PDMAFPRMNN MSFWLLPPSF LLLLASSMVE AGAGTGWTVY PPLAGNLAHA GASVDLTIFS LHLAGVS SI LGAINFITTI INMKPPAMSQ YQTPLFVWSV MITAVLLLLS LPVLAAGITM LLTDRNLNTT FFDPAGGGDP ILYQHLFW F FGHPEVYILI LPGFGMISHI VTYYSGKKEP FGYMGMVWAM MSIGFLGFIV WAHHMFTVGM DVDTRAYFTS ATMIIAIPT GVKVFSWLAT LHGGNIKWSP AMMWALGFIF LFTVGGLTGI VLANSSLDIV LHDTYYVVAH FHYVLSMGAV FAIMGGFVHW FPLFSGYTL NDTWAKIHFA IMFVGVNMTF FPQHFLGLSG MPRRYSDYPD AYTMWNTISS MGSFISLTAV MLMVFIIWEA F ASKREVLT VDLTTTNLEW LNGCPPPYHT FEEPTYVNLK

UniProtKB: Cytochrome c oxidase subunit 1

+
Macromolecule #2: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 25.909197 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString: AYPMQLGFQD ATSPIMEELL HFHDHTLMIV FLISSLVLYI ISLMLTTKLT HTSTMDAQEV ETIWTILPAI ILILIALPSL RILYMMDEI NNPSLTVKTM GHQWYWSYEY TDYEDLSFDS YMIPTSELKP GELRLLEVDN RVVLPMEMTI RMLVSSEDVL H SWAVPSLG ...String:
AYPMQLGFQD ATSPIMEELL HFHDHTLMIV FLISSLVLYI ISLMLTTKLT HTSTMDAQEV ETIWTILPAI ILILIALPSL RILYMMDEI NNPSLTVKTM GHQWYWSYEY TDYEDLSFDS YMIPTSELKP GELRLLEVDN RVVLPMEMTI RMLVSSEDVL H SWAVPSLG LKTDAIPGRL NQTTLMSSRP GLYYGQCSEI CGSNHSFMPI VLELVPLKYF EKWSASML

UniProtKB: Cytochrome c oxidase subunit 2

+
Macromolecule #3: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 29.443051 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString: QTHAYHMVNP SPWPLTGALS ALLMTSGLTM WFHFNSMTLL MIGLTTNMLT MYQWWRDVIR ESTFQGHHTP AVQKGLRYGM ILFIISEVL FFTGFFWAFY HSSLAPTPEL GGCWPPTGIH PLNPLEVPLL NTSVLLASGV SITWAHHSLM EGDRKHMLQA L FITITLGV ...String:
QTHAYHMVNP SPWPLTGALS ALLMTSGLTM WFHFNSMTLL MIGLTTNMLT MYQWWRDVIR ESTFQGHHTP AVQKGLRYGM ILFIISEVL FFTGFFWAFY HSSLAPTPEL GGCWPPTGIH PLNPLEVPLL NTSVLLASGV SITWAHHSLM EGDRKHMLQA L FITITLGV YFTLLQASEY YEAPFTISDG VYGSTFFVAT GFHGLHVIIG STFLIVCFFR QLKFHFTSNH HFGFEAAAWY WH FVDVVWL FLYVSIYWW

UniProtKB: Cytochrome c oxidase subunit 3

+
Macromolecule #4: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 16.038386 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString:
YALPSYVDRR DYPLPDVAHV KNLSASQKAL KEKEKASWSS LSIDEKVELY RLKFKESFAE MNRSTNEWKT VVGAAMFFIG FTALLLIWE KHYVYGPIPH TFEEEWVAKQ TKRMLDMKVA PIQGFSAKWD YDKNEWK

UniProtKB: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

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

MacromoleculeName: Cytochrome c oxidase subunit 5A, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 11.717335 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString:
TDEEFDARWV TYFNKPDIDA WELRKGMNTL VGYDLVPEPK IIDAALRACR RLNDFASAVR ILEVVKDKAG PHKEIYPYVI QELRPTLNE LGISTPEELG LDK

UniProtKB: Cytochrome c oxidase subunit 5A, mitochondrial

+
Macromolecule #6: Cytochrome c oxidase subunit 5B, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 5B, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 9.937226 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString:
GGGVPTDEEQ ATGLEREVML AARKGQDPYN ILAPKATSGT KEDPNLVPSI TNKRIVGCIC EEDNSTVIWF WLHKGEAQRC PSCGTHYKL VP

UniProtKB: Cytochrome c oxidase subunit 5B, mitochondrial

+
Macromolecule #7: Cytochrome c oxidase subunit 6A2, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 6A2, mitochondrial / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 8.368521 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString:
GARTWRFLTF GLALPSVALC TLNSWLHSGH RERPAFIPYH HLRIRTKPFS WGDGNHTFFH NPRVNPLPTG YE

UniProtKB: Cytochrome c oxidase subunit 6A2, mitochondrial

+
Macromolecule #8: Cytochrome c oxidase subunit 6B1

MacromoleculeName: Cytochrome c oxidase subunit 6B1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 9.610806 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString:
QAKIKNYQTA PFDSRFPNQN QTRNCWQNYL DFHRCEKAMT AKGGDVSVCE WYRRVYKSLC PISWVSTWDD RRAEGTFPGK I

UniProtKB: Cytochrome c oxidase subunit 6B1

+
Macromolecule #9: Cytochrome c oxidase subunit 6C

MacromoleculeName: Cytochrome c oxidase subunit 6C / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 8.177621 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString:
ALAKPQMRGL LARRLRFHIV GAFMVSLGFA TFYKFAVAEK RKKAYADFYR NYDSMKDFEE MRKAGIFQSA

UniProtKB: Cytochrome c oxidase subunit 6C

+
Macromolecule #10: Cytochrome c oxidase subunit 7A1, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7A1, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 6.189105 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString:
FENRVAEKQK LFQEDNGLPV HLKGGATDNI LYRVTMTLCL GGTLYSLYCL GWASF

UniProtKB: Cytochrome c oxidase subunit 7A1, mitochondrial

+
Macromolecule #11: Cytochrome c oxidase subunit 7B, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7B, mitochondrial / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 5.442168 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString:
APDFHDKYGN AVLASGATFC VAVWVYMATQ IGIEWNPSPV GRVTPKEWR

UniProtKB: Cytochrome c oxidase subunit 7B, mitochondrial

+
Macromolecule #12: Cytochrome c oxidase subunit 7C, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7C, mitochondrial / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 5.094992 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString:
YEEGPGKNIP FSVENKWRLL AMMTLFFGSG FAAPFFIVRH QLLK

UniProtKB: Cytochrome c oxidase subunit 7C, mitochondrial

+
Macromolecule #13: Cytochrome c oxidase subunit 8B, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 8B, mitochondrial / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 4.393086 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString:
ITAKPAKTPT SPKEQAIGLS VTFLSFLLPA GWVLYHLDNY

UniProtKB: Cytochrome c oxidase subunit 8B, mitochondrial

+
Macromolecule #14: Cytochrome c oxidase subunit NDUFA4

MacromoleculeName: Cytochrome c oxidase subunit NDUFA4 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 9.2055 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString:
LRQIIGQAKR HPSLIPLFIF IGAGGTGAAL YVTRLALFNP DVSWDRKNNP EPWNKLGPND QYKFYSVNVD YSKLKKEGPD F

UniProtKB: Cytochrome c oxidase subunit FA4

+
Macromolecule #15: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 15 / Number of copies: 2 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

+
Macromolecule #16: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 16 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

+
Macromolecule #17: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 17 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #18: PEROXIDE ION

MacromoleculeName: PEROXIDE ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: PER
Molecular weightTheoretical: 31.999 Da
Chemical component information

ChemComp-PER:
PEROXIDE ION

+
Macromolecule #19: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 19 / Number of copies: 2 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM

+
Macromolecule #20: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 20 / Number of copies: 1 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

+
Macromolecule #21: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 21 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

+
Macromolecule #22: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 22 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #23: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)...

MacromoleculeName: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
type: ligand / ID: 23 / Number of copies: 1 / Formula: PEK
Molecular weightTheoretical: 768.055 Da
Chemical component information

ChemComp-PEK:
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 30421492
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 227858
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7qsk


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9w2z:
Cryo-EM structure of complex IV on the bovine heart submitochondrial particles, IV-A

+
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