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- EMDB-42229: High resolution in-situ structure of complex IV in respiratory su... -

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Basic information

Entry
Database: EMDB / ID: EMD-42229
TitleHigh resolution in-situ structure of complex IV in respiratory supercomplex
Map dataIn-situ complex IV
Sample
  • Organelle or cellular component: In-situ cryo-EM structure of respiratory supercomplex by directly imaging mitochondria
    • Protein or peptide: x 14 types
  • Ligand: x 12 types
Keywordsin-situ cryo-EM structure / mammalian / mitochondria / respiratory supercomplex / proton pumping / membrane protein / electron transport
Function / homology
Function and homology information


Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / Respiratory electron transport / mitochondrial respiratory chain complex IV / regulation of oxidative phosphorylation / Mitochondrial protein degradation / cytochrome-c oxidase ...Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / Respiratory electron transport / mitochondrial respiratory chain complex IV / regulation of oxidative phosphorylation / Mitochondrial protein degradation / cytochrome-c oxidase / mitochondrial respirasome / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / positive regulation of vasoconstriction / central nervous system development / mitochondrial inner membrane / oxidoreductase activity / 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 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs ...NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit VIIa superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome c oxidase subunit VIc / Cytochrome C oxidase chain VIIB / : / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa 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 VIa / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase subunit Va / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb, zinc binding region signature. / 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 I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / 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 oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / 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 / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 4 / Cytochrome c oxidase subunit 6C / Mitochondrial NDUFA4 / Cytochrome c oxidase subunit / Cytochrome c oxidase subunit 8 / Cytochrome c oxidase polypeptide Va / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 7C, mitochondrial ...Cytochrome c oxidase subunit / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 4 / Cytochrome c oxidase subunit 6C / Mitochondrial NDUFA4 / Cytochrome c oxidase subunit / Cytochrome c oxidase subunit 8 / Cytochrome c oxidase polypeptide Va / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 7A1, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZheng W / Zhu J / Zhang K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM142959 United States
CitationJournal: Nature / Year: 2024
Title: High-resolution in situ structures of mammalian respiratory supercomplexes.
Authors: Wan Zheng / Pengxin Chai / Jiapeng Zhu / Kai Zhang /
Abstract: Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in ...Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: IIIIIV, IIIIIV, IIIIIV and IIIIIV, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context.
History
DepositionOct 5, 2023-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42229.png

Downloads & links

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Map

FileDownload / File: emd_42229.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn-situ complex IV
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.42 Å/pix.
x 512 pix.
= 212.992 Å		0.42 Å/pix.
x 512 pix.
= 212.992 Å		0.42 Å/pix.
x 512 pix.
= 212.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.416 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.025
Minimum - Maximum-1.1543552 - 1.6971585
Average (Standard dev.)0.00062522915 (±0.04914768)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 212.992 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: In-situ complex IV

Fileemd_42229_half_map_1.map
AnnotationIn-situ complex IV
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: In-situ complex IV

Fileemd_42229_half_map_2.map
AnnotationIn-situ complex IV
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : In-situ cryo-EM structure of respiratory supercomplex by directly...

EntireName: In-situ cryo-EM structure of respiratory supercomplex by directly imaging mitochondria
Components
  • Organelle or cellular component: In-situ cryo-EM structure of respiratory supercomplex by directly imaging mitochondria
    • 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
    • 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
    • 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
    • Protein or peptide: Cytochrome c oxidase subunit 7C, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 8
    • Protein or peptide: Cytochrome c oxidase subunit NDUFA4
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: HEME-A
  • Ligand: COPPER (II) ION
  • Ligand: MAGNESIUM ION
  • Ligand: SODIUM IONSodium
  • Ligand: CARDIOLIPIN
  • Ligand: DINUCLEAR COPPER ION
  • Ligand: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE
  • 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
  • Ligand: PHOSPHATE IONPhosphate
  • Ligand: water

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Supramolecule #1: In-situ cryo-EM structure of respiratory supercomplex by directly...

SupramoleculeName: In-situ cryo-EM structure of respiratory supercomplex by directly imaging mitochondria
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Sus scrofa (pig)

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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
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 56.992711 KDa
SequenceString: MFVNRWLYST NHKDIGTLYL LFGAWAGMVG TALSLLIRAE LGQPGTLLGD DQIYNVIVTA HAFVMIFFMV MPIMIGGFGN WLVPLMIGA PDMAFPRMNN MSFWLLPPSF LLLLASSMVE AGAGTGWTVY PPLAGNLAHA GASVDLTIFS LHLAGVSSIL G AINFITTI ...String:
MFVNRWLYST NHKDIGTLYL LFGAWAGMVG TALSLLIRAE LGQPGTLLGD DQIYNVIVTA HAFVMIFFMV MPIMIGGFGN WLVPLMIGA PDMAFPRMNN MSFWLLPPSF LLLLASSMVE AGAGTGWTVY PPLAGNLAHA GASVDLTIFS LHLAGVSSIL G AINFITTI INMKPPAMSQ YQTPLFVWSV LITAVLLLLS LPVLAAGITM LLTDRNLNTT FFDPAGGGDP ILYQHLFWFF GH PEVYILI LPGFGMISHI VTYYSGKKEP FGYMGMVWAM MSIGFLGFIV WAHHMFTVGM DVDTRAYFTS ATMIIAIPTG VKV FSWLAT LHGGNIKWSP AMLWALGFIF LFTVGGLTGI VLANSSLDIV LHDTYYVVAH FHYVLSMGAV FAIMGGFVHW FPLF SGYTL NQAWAKIHFV IMFVGVNMTF FPQHFLGLSG MPRRYSDYPD AYTAWNTISS MGSFISLTAV MLMIFIIWEA FASKR EVSA VELTSTNLEW LHGCPPPYHT FEEPTYINLK

UniProtKB: Cytochrome c oxidase subunit 1

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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
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 26.288627 KDa
SequenceString: (FME)AYPFQLGFQ DATSPIMEEL LHFHDHTLMI VFLISSLVLY IISLMLTTKL THTSTMDAQE VETIWTILPA IILILI ALP SLRILYMMDE INNPALTVKT MGHQWYWSYE YTDYEDLTFD SYMIPTSDLK PGEMRLLEVD NRVVLPMEMT IRMLVSS ED VLHSWAVPSL ...String:
(FME)AYPFQLGFQ DATSPIMEEL LHFHDHTLMI VFLISSLVLY IISLMLTTKL THTSTMDAQE VETIWTILPA IILILI ALP SLRILYMMDE INNPALTVKT MGHQWYWSYE YTDYEDLTFD SYMIPTSDLK PGEMRLLEVD NRVVLPMEMT IRMLVSS ED VLHSWAVPSL GLKTDAIPGR LNQTTLMSTR PGLYYGQCSE ICGSNHSFMP IVLELVPLKY FEKWSTSMLT G

UniProtKB: Cytochrome c oxidase subunit 2

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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
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 29.753361 KDa
SequenceString: MTHQTHAYHM VNPSPWPLTG ALSALLMTSG LTMWFHFNSM LLLSLGLLTN TLTMYQWWRD IIRESTFQGH HTSVVQKGLR YGMILFIIS EVLFFTGFFW AFYHSSLAPT PELGGCWPPT GIHPLNPLEV PLLNTSILLA SGVSITWAHH SLMEGDRKHM I QALSITIA ...String:
MTHQTHAYHM VNPSPWPLTG ALSALLMTSG LTMWFHFNSM LLLSLGLLTN TLTMYQWWRD IIRESTFQGH HTSVVQKGLR YGMILFIIS EVLFFTGFFW AFYHSSLAPT PELGGCWPPT GIHPLNPLEV PLLNTSILLA SGVSITWAHH SLMEGDRKHM I QALSITIA LGVYFTLLQA SEYYEAPFTI SDGVYGSTFF VATGFHGLHV IIGSTFLAVC LLRQLKFHFT SNHHFGFEAA AW YWHFVDV VWLFLYVSIY WWGS

UniProtKB: Cytochrome c oxidase subunit 3

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Macromolecule #4: Cytochrome c oxidase subunit 4

MacromoleculeName: Cytochrome c oxidase subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 19.670664 KDa
SequenceString:
MLATRVFNLI GRRAISTSVC VRAHGSVVKS EDYALPVYVD RRDYPLPDVA HVKNLSASQK ALKEKEKASW SSLSMDEKVE LYRLKFNES FAEMNRSTNE WKTIVGTALF FIGFTALLLI WEKHYVYGPI PHTFEEEWVA KQTKRMLDMK VAPIQGFSAK W DYDKNEWK K

UniProtKB: Cytochrome c oxidase subunit 4

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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: Sus scrofa (pig)
Molecular weightTheoretical: 16.771195 KDa
SequenceString:
MLGAAVRRCS VAAAAVARAS PRGLLHPTPT PGPAAAIQSI RCYSHGSHET DEEFDARWVT YFNKPDIDAW ELRKGMNTLV GYDLVPEPK IIDAALRACR RLNDFASAVR ILEVVKDKAG PHKEIYPYVI QELRPTLNEL GISTPEELGL DKV

UniProtKB: Cytochrome c oxidase polypeptide Va

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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: Sus scrofa (pig)
Molecular weightTheoretical: 13.801783 KDa
SequenceString:
MASRLLRGAG ALAAQTLRAR GPNGVAVVRS MASGGGVPTD EEQATGLERE VMMAARKGLD PYNILAPKAA SGTKEDPNLV PSITNKRIV GCICEEDNST VIWFWVHKGE TQRCPSCGTH YKLVSHQLAH

UniProtKB: Cytochrome c oxidase subunit 5B, mitochondrial

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Macromolecule #7: Cytochrome c oxidase subunit 6A2

MacromoleculeName: Cytochrome c oxidase subunit 6A2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 10.87637 KDa
SequenceString:
MALPLRSLSR GLASAAKGDH GGTGARTWRF LTFGLALPSV ALCTLNSWLH SGHHHRPEFI PYHHLRIRTK PYSWGDGNHT LFHNPRVNP LPTGYEQP

UniProtKB: Cytochrome c oxidase subunit

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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: Sus scrofa (pig)
Molecular weightTheoretical: 10.204456 KDa
SequenceString:
MAEDIQTKIK NYQTAPFDSR FPNQNQTRNC WQNYLDFHRC EKAMTAKGGD VSVCEWYRRV YKSFCPISWV SAWDDRRAEG TFPGKI

UniProtKB: Cytochrome c oxidase subunit

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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: Sus scrofa (pig)
Molecular weightTheoretical: 8.617122 KDa
SequenceString:
MATSSLTKPQ MRGLLAKRLR FHIVGAFIVS LGVATFYKFA VAEPRKKAYA DFYRNYDSMK DFEEMRKAGI FQSAK

UniProtKB: Cytochrome c oxidase subunit 6C

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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: Sus scrofa (pig)
Molecular weightTheoretical: 9.028479 KDa
SequenceString:
MRALRVSQAL VRSFSSTARN RLENRVAEKQ KIFQADNDLP VHLKGGATDN ILYRVTMTLC LGGTVYSLYC LGWASFPHKK

UniProtKB: Cytochrome c oxidase subunit 7A1, mitochondrial

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Macromolecule #11: Cytochrome c oxidase subunit 7B

MacromoleculeName: Cytochrome c oxidase subunit 7B / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 9.169476 KDa
SequenceString:
MFPLAKNALS RLRVRNIQQT MARQNHQKRA PDFHDKYGNA ILASGATFCV AVWAYTATQI GIEWNLSPVG RVTPKEWREE

UniProtKB: Cytochrome c oxidase subunit 7B, mitochondrial

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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: Sus scrofa (pig)
Molecular weightTheoretical: 7.358661 KDa
SequenceString:
MLGQSIRRFT TSVVRRSHYE EGPGKNLPFS VENKWRLLAM MTLYFGSGFA APFFIVRHQL LKK

UniProtKB: Cytochrome c oxidase subunit 7C, mitochondrial

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Macromolecule #13: Cytochrome c oxidase subunit 8

MacromoleculeName: Cytochrome c oxidase subunit 8 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 7.615939 KDa
SequenceString:
MLRLAPTVRL LQAPLGGWVV PKAHIYAKPA RTPTSPTEQA IGLSVTFLSF LIPAGWVLSH LDHYKRSSAA

UniProtKB: Cytochrome c oxidase subunit 8

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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: Sus scrofa (pig)
Molecular weightTheoretical: 9.322771 KDa
SequenceString:
MLRQIITQAK KHPSLIPLFV FIGAGGTGAA LYVTRLALFN PDVCWDRKNN PEPWNKLGPN DQYKFFAVNV DYSKLKKEGP DF

UniProtKB: Mitochondrial NDUFA4

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Macromolecule #15: (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: 15 / Number of copies: 15 / 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 / Phosphatidylglycerol

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Macromolecule #16: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 16 / Number of copies: 2 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A / Heme A

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Macromolecule #17: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 17 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION / Copper

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Macromolecule #18: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #19: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 19 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #20: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 20 / Number of copies: 3 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #21: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 21 / Number of copies: 1 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

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Macromolecule #22: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)MET...

MacromoleculeName: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE
type: ligand / ID: 22 / Number of copies: 1 / Formula: PSC
Molecular weightTheoretical: 759.068 Da
Chemical component information

ChemComp-PSC:
(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE / phospholipid*YM / Phosphatidylcholine

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Macromolecule #23: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 23 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #24: (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: 24 / Number of copies: 2 / 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 / Phosphatidylethanolamine

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Macromolecule #25: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 25 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION / Phosphate

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Macromolecule #26: water

MacromoleculeName: water / type: ligand / ID: 26 / Number of copies: 804 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.3 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56000

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