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- EMDB-12703: Murine supercomplex CIII2CIV in the mature unlocked conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-12703
TitleMurine supercomplex CIII2CIV in the mature unlocked conformation
Map datamurine full supercomplex CIII2CIV in the unlocked conformation
Sample
  • Complex: Murine full supercomplex CIII2CIV in the unlocked conformation
    • Protein or peptide: x 24 types
  • Ligand: x 13 types
Function / homology
Function and homology information


subthalamus development / pons development / TP53 Regulates Metabolic Genes / Respiratory electron transport / cerebellar Purkinje cell layer development / pyramidal neuron development / respiratory chain complex IV assembly / response to mercury ion / thalamus development / Cytoprotection by HMOX1 ...subthalamus development / pons development / TP53 Regulates Metabolic Genes / Respiratory electron transport / cerebellar Purkinje cell layer development / pyramidal neuron development / respiratory chain complex IV assembly / response to mercury ion / thalamus development / Cytoprotection by HMOX1 / respiratory chain complex IV / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / response to alkaloid / cytochrome-c oxidase / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / response to copper ion / response to glucagon / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / hypothalamus development / midbrain development / response to cobalamin / response to hyperoxia / ATP synthesis coupled electron transport / animal organ regeneration / enzyme regulator activity / response to cadmium ion / response to electrical stimulus / respiratory electron transport chain / lactation / cerebellum development / response to hormone / response to activity / central nervous system development / hippocampus development / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / response to toxic substance / response to calcium ion / myelin sheath / response to ethanol / mitochondrial inner membrane / response to oxidative stress / response to hypoxia / oxidoreductase activity / response to xenobiotic stimulus / copper ion binding / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / protein-containing complex / mitochondrion / proteolysis / nucleoplasm / membrane / metal ion binding / cytosol
Similarity search - Function
Cytochrome c oxidase subunit VIIa-related, mitochondrial / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / 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 VIIa-related, mitochondrial / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / 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 / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / 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 / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / : / Cytochrome b-c1 complex, subunit 6 / 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 b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / 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 b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome c oxidase subunit III-like superfamily / 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 oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome b / : / : / Cytochrome c/quinol oxidase subunit II / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / 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. / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Cytochrome c oxidase subunit I
Similarity search - Domain/homology
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 7C, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 8B, 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 7C, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 9 / Cox7a2l protein / Cytochrome c oxidase subunit 6C / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse) / Mouse (mice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsVercellino I / Sazanov LA
Funding support Austria, 1 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission754411 Austria
CitationJournal: Nature / Year: 2021
Title: Structure and assembly of the mammalian mitochondrial supercomplex CIIICIV.
Authors: Irene Vercellino / Leonid A Sazanov /
Abstract: The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes, whose precise role is ...The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes, whose precise role is debated. Supercomplexes CIIICIV (refs. ), CICIII (ref. ) and CICIIICIV (respirasome) exist in mammals, but in contrast to CICIII and the respirasome, to date the only known eukaryotic structures of CIIICIV come from Saccharomyces cerevisiae and plants, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIIICIV and its assembly intermediates, in different conformations. We describe the assembly of CIIICIV from the CIII precursor to the final CIIICIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. ) deep into CIII, while its C terminus is integrated into CIV. Our structures (which include CICIII and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIIICIV and has no role in the assembly of the respirasome. We show that CIII is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII, explaining the presence of one copy of CIV in CIIICIV in mammals. Finally, we show that CIII and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIIICIV in fine tuning the efficiency of electron transfer in the electron transport chain.
History
DepositionApr 1, 2021-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
UpdateOct 27, 2021-
Current statusOct 27, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7o3c
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12703.png

Downloads & links

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Map

FileDownload / File: emd_12703.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmurine full supercomplex CIII2CIV in the unlocked conformation
Voxel sizeX=Y=Z: 1.064 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.021125618 - 0.271028
Average (Standard dev.)0.007197164 (±0.020066923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions217206122
Spacing122217206
CellA: 129.808 Å / B: 230.888 Å / C: 219.184 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0641.0641.064
M x/y/z122217206
origin x/y/z0.0000.0000.000
length x/y/z129.808230.888219.184
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ122217206
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS206217122
D min/max/mean-0.0210.2710.007

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Supplemental data

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Sample components

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Entire : Murine full supercomplex CIII2CIV in the unlocked conformation

EntireName: Murine full supercomplex CIII2CIV in the unlocked conformation
Components
  • Complex: Murine full supercomplex CIII2CIV in the unlocked conformation
    • 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 7
    • Protein or peptide: Cytochrome b-c1 complex subunit 8
    • Protein or peptide: Cytochrome b-c1 complex subunit 6, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 9
    • Protein or peptide: Cytochrome b-c1 complex subunit 10
    • Protein or peptide: Cytochrome b-c1 complex subunit 9
    • Protein or peptide: Cox7a2l protein
    • 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 7B, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 7C, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 8B, mitochondrial
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: CARDIOLIPIN
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: HEME C
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: COPPER (II) ION
  • Ligand: SODIUM IONSodium
  • Ligand: HEME-A
  • Ligand: MAGNESIUM ION
  • Ligand: DINUCLEAR COPPER ION
  • Ligand: ZINC ION
  • Ligand: TRISTEAROYLGLYCEROLStearin

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Supramolecule #1: Murine full supercomplex CIII2CIV in the unlocked conformation

SupramoleculeName: Murine full supercomplex CIII2CIV in the unlocked conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#24
Details: Dimer of Complex III, monomer of complex IV, bridged by SCAF1
Source (natural)Organism: Mus musculus (house mouse) / Strain: CD1 / Organ: heart / Tissue: cardiac muscle / Organelle: mitochondria / Location in cell: inner mitochondrial membrane
Molecular weightExperimental: 700 KDa

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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: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 49.355301 KDa
SequenceString: TATFAQALQS VPETQVSILD NGLRVASEQS SHATCTVGVW IDAGSRYETE KNNGAGYFLE HLAFKGTKNR PGNALEKEVE SIGAHLNAY STREHTAYLI KALSKDLPKV VELLADIVQN SSLEDSQIEK ERDVILREMQ ENDASMQNVV FDYLHATAFQ G TPLAQAVE ...String:
TATFAQALQS VPETQVSILD NGLRVASEQS SHATCTVGVW IDAGSRYETE KNNGAGYFLE HLAFKGTKNR PGNALEKEVE SIGAHLNAY STREHTAYLI KALSKDLPKV VELLADIVQN SSLEDSQIEK ERDVILREMQ ENDASMQNVV FDYLHATAFQ G TPLAQAVE GPSENVRRLS RTDLTDYLNR HYKAPRMVLA AAGGVEHQQL LDLAQKHLSS VSRVYEEDAV PGLTPCRFTG SE IRHRDDA LPLAHVAIAV EGPGWANPDN VTLQVANAII GHYDCTYGGG VHLSSPLASV AVANKLCQSF QTFNISYSDT GLL GAHFVC DAMSIDDMVF FLQGQWMRLC TSATESEVTR GKNILRNALV SHLDGTTPVC EDIGRSLLTY GRRIPLAEWE SRIQ EVDAQ MLRDICSKYF YDQCPAVAGY GPIEQLPDYN RIRSGMFWLR F

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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: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 46.641773 KDa
SequenceString: SLKVAPKVKT SAAPGGVPLQ PQDLEFTKLP NGLVIASLEN YAPLSRIGLF VKAGSRYEDS NNLGTSHLLR LASSLTTKGA SSFKITRGI EAVGGKLSVT ATRENMAYTV EGIRSDIEIL MEFLLNVTTA PEFRRWEVAA LRSQLKIDKA VAFQNSQTRI I ENLHDVAY ...String:
SLKVAPKVKT SAAPGGVPLQ PQDLEFTKLP NGLVIASLEN YAPLSRIGLF VKAGSRYEDS NNLGTSHLLR LASSLTTKGA SSFKITRGI EAVGGKLSVT ATRENMAYTV EGIRSDIEIL MEFLLNVTTA PEFRRWEVAA LRSQLKIDKA VAFQNSQTRI I ENLHDVAY KNALANPLYC PDYRMGKITS EELHYFVQNH FTSARMALVG LGVSHSVLKQ VAEQFLNMRG GLGLAGAKAK YR GGEIREQ NGDNLVHAAI VAESAAIGNA EANAFSVLQH LLGAGPHIKR GNNTTSLLSQ SVAKGSHQPF DVSAFNASYS DSG LFGIYT ISQAAAAGEV INAAYNQVKA VAQGNLSSAD VQAAKNKLKA GYLMSVETSE GFLSEIGSQA LAAGSYMPPS TVLQ QIDSV ADADVVKAAK KFVSGKKSMA ASGNLGHTPF LDEL

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Macromolecule #3: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 43.240305 KDa
SequenceString: MTNMRKTHPL FKIINHSFID LPAPSNISSW WNFGSLLGVC LMVQIITGLF LAMHYTSDTM TAFSSVTHIC RDVNYGWLIR YMHANGASM FFICLFLHVG RGLYYGSYTF METWNIGVLL LFAVMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTT L VEWIWGGF ...String:
MTNMRKTHPL FKIINHSFID LPAPSNISSW WNFGSLLGVC LMVQIITGLF LAMHYTSDTM TAFSSVTHIC RDVNYGWLIR YMHANGASM FFICLFLHVG RGLYYGSYTF METWNIGVLL LFAVMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTT L VEWIWGGF SVDKATLTRF FAFHFILPFI IAALAIVHLL FLHETGSNNP TGLNSDADKI PFHPYYTIKD ILGILIMFLI LM TLVLFFP DMLGDPDNYM PANPLNTPPH IKPEWYFLFA YAILRSIPNK LGGVLALILS ILILALMPFL HTSKQRSLMF RPI TQILYW ILVANLLILT WIGGQPVEHP FIIIGQLASI SYFSIILILM PISGIIEDKM LKLYP

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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: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 27.312188 KDa
SequenceString: SDLELHPPSY PWSHRGLLSS LDHTSIRRGF QVYKQVCSSC HSMDYVAYRH LVGVCYTEEE AKALAEEVEV QDGPNDDGEM FMRPGKLSD YFPKPYPNPE AARAANNGAL PPDLSYIVRA RHGGEDYVFS LLTGYCEPPT GVSLREGLYF NPYFPGQAIG M APPIYTEV ...String:
SDLELHPPSY PWSHRGLLSS LDHTSIRRGF QVYKQVCSSC HSMDYVAYRH LVGVCYTEEE AKALAEEVEV QDGPNDDGEM FMRPGKLSD YFPKPYPNPE AARAANNGAL PPDLSYIVRA RHGGEDYVFS LLTGYCEPPT GVSLREGLYF NPYFPGQAIG M APPIYTEV LEYDDGTPAT MSQVAKDVAT FLRWASEPEH DHRKRMGLKM LLMMGLLLPL TYAMKRHKWS VLKSRKLAYR PP K

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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: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 21.524398 KDa
SequenceString: SHTDVKVPDF SDYRRAEVLD STKSSKESSE ARKGFSYLVT ATTTVGVAYA AKNVVSQFVS SMSASADVLA MSKIEIKLSD IPEGKNMAF KWRGKPLFVR HRTKKEIDQE AAVEVSQLRD PQHDLDRVKK PEWVILIGVC THLGCVPIAN AGDFGGYYCP C HGSHYDAS ...String:
SHTDVKVPDF SDYRRAEVLD STKSSKESSE ARKGFSYLVT ATTTVGVAYA AKNVVSQFVS SMSASADVLA MSKIEIKLSD IPEGKNMAF KWRGKPLFVR HRTKKEIDQE AAVEVSQLRD PQHDLDRVKK PEWVILIGVC THLGCVPIAN AGDFGGYYCP C HGSHYDAS GRIRKGPAPL NLEVPAYEFT SDDVVVVG

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Macromolecule #6: Cytochrome b-c1 complex subunit 7

MacromoleculeName: Cytochrome b-c1 complex subunit 7 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 13.456336 KDa
SequenceString:
AGRSAVSASS KWLDGFRKWY YNAAGFNKLG LMRDDTLHET EDVKEAIRRL PEDLYNDRMF RIKRALDLTM RHQILPKDQW TKYEEDKFY LEPYLKEVIR ERKEREEWAK K

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Macromolecule #7: Cytochrome b-c1 complex subunit 8

MacromoleculeName: Cytochrome b-c1 complex subunit 8 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 9.652051 KDa
SequenceString:
GREFGNLARI RHVISYSLSP FEQRAFPSYF SKGIPNVLRR TRERILRVAP PFVVVYLIYT WGNQEFEQSK RKNPAMYEND K

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Macromolecule #8: Cytochrome b-c1 complex subunit 6, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 6, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 9.002015 KDa
SequenceString:
GDPKEEEEEE LVDPLTTVRE HCEQLEKCVK ARERLELCDN RVSSRSQTEE DCTEELFDFL HARDHCVAHK LFKNLK

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Macromolecule #9: Cytochrome b-c1 complex subunit 9

MacromoleculeName: Cytochrome b-c1 complex subunit 9 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 7.32633 KDa
SequenceString:
SSPTIPSRLY SLLFRRTSTF ALTIAVGALF FERAFDQGAD AIYEHINEGK LWKHIKHKYE NKE

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Macromolecule #10: Cytochrome b-c1 complex subunit 10

MacromoleculeName: Cytochrome b-c1 complex subunit 10 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 6.546627 KDa
SequenceString:
MLSRFLGPRY RELARNWIPT AGMWGTVGAV GLVWATDWRL ILDWVPYING KFKKDD

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Macromolecule #11: Cytochrome b-c1 complex subunit 9

MacromoleculeName: Cytochrome b-c1 complex subunit 9 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 7.900234 KDa
SequenceString:
MLSVAARSGP FAPVLSATSR GVAGALRPLL QGAVPAASEP PVLDVKRPFL CRESLSGQAA ARPLVATVGL NVPASVRF

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Macromolecule #12: Cox7a2l protein

MacromoleculeName: Cox7a2l protein / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 12.575581 KDa
SequenceString:
MYYKFSSFTQ KLAGAWASEA YTPQGLKPVS TEAPPIIFAT PTKLTSSVTA YDYSGKNKVP ELQKFFQKAD GVPIHLKRGL PDQMLYRTT MALTLGGTIY CLIALYMASQ PRNK

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Macromolecule #13: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 56.945641 KDa
SequenceString: MFINRWLFST NHKDIGTLYL LFGAWAGMVG TALSILIRAE LGQPGALLGD DQIYNVIVTA HAFVMIFFMV MPMMIGGFGN WLVPLMIGA PDMAFPRMNN MSFWLLPPSF LLLLASSMVE AGAGTGWTVY PPLAGNLAHA GASVDLTIFS LHLAGVSSIL G AINFITTI ...String:
MFINRWLFST NHKDIGTLYL LFGAWAGMVG TALSILIRAE LGQPGALLGD DQIYNVIVTA HAFVMIFFMV MPMMIGGFGN WLVPLMIGA PDMAFPRMNN MSFWLLPPSF LLLLASSMVE AGAGTGWTVY PPLAGNLAHA GASVDLTIFS LHLAGVSSIL G AINFITTI INMKPPAMTQ YQTPLFVWSV LITAVLLLLS LPVLAAGITM LLTDRNLNTT FFDPAGGGDP ILYQHLFWFF GH PEVYILI LPGFGIISHV VTYYSGKKEP FGYMGMVWAM MSIGFLGFIV WAHHMFTVGL DVDTRAYFTS ATMIIAIPTG VKV FSWLAT LHGGNIKWSP AMLWALGFIF LFTVGGLTGI VLSNSSLDIV LHDTYYVVAH FHYVLSMGAV FAIMAGFVHW FPLF SGFTL DDTWAKAHFA IMFVGVNMTF FPQHFLGLSG MPRRYSDYPD AYTTWNTVSS MGSFISLTAV LIMIFMIWEA FASKR EVMS VSYASTNLEW LHGCPPPYHT FEEPTYVKVK

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Macromolecule #14: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 25.993318 KDa
SequenceString: MAYPFQLGLQ DATSPIMEEL MNFHDHTLMI VFLISSLVLY IISLMLTTKL THTSTMDAQE VETIWTILPA VILIMIALPS LRILYMMDE INNPVLTVKT MGHQWYWSYE YTDYEDLCFD SYMIPTNDLK PGELRLLEVD NRVVLPMELP IRMLISSEDV L HSWAVPSL ...String:
MAYPFQLGLQ DATSPIMEEL MNFHDHTLMI VFLISSLVLY IISLMLTTKL THTSTMDAQE VETIWTILPA VILIMIALPS LRILYMMDE INNPVLTVKT MGHQWYWSYE YTDYEDLCFD SYMIPTNDLK PGELRLLEVD NRVVLPMELP IRMLISSEDV L HSWAVPSL GLKTDAIPGR LNQATVTSNR PGLFYGQCSE ICGSNHSFMP IVLEMVPLKY FENWSASMI

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Macromolecule #15: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 29.948689 KDa
SequenceString: MTHQTHAYHM VNPSPWPLTG AFSALLLTSG LVMWFHYNSI TLLTLGLLTN ILTMYQWWRD VIREGTYQGH HTPIVQKGLR YGMILFIVS EVFFFAGFFW AFYHSSLVPT HDLGGCWPPT GISPLNPLEV PLLNTSVLLA SGVSITWAHH SLMEGKRNHM N QALLITIM ...String:
MTHQTHAYHM VNPSPWPLTG AFSALLLTSG LVMWFHYNSI TLLTLGLLTN ILTMYQWWRD VIREGTYQGH HTPIVQKGLR YGMILFIVS EVFFFAGFFW AFYHSSLVPT HDLGGCWPPT GISPLNPLEV PLLNTSVLLA SGVSITWAHH SLMEGKRNHM N QALLITIM LGLYFTILQA SEYFETSFSI SDGIYGSTFF MATGFHGLHV IIGSTFLIVC LLRQLKFHFT SKHHFGFEAA AW YWHFVDV VWLFLYVSIY WWGS

+
Macromolecule #16: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 17.225596 KDa
SequenceString:
AHGSVVKSED YAFPTYADRR DYPLPDVAHV TMLSASQKAL KEKEKADWSS LSRDEKVQLY RIQFNESFAE MNRGTNEWKT VVGMAMFFI GFTALVLIWE KSYVYGPIPH TFDRDWVAMQ TKRMLDMKAN PIQGFSAKWD YDKNEWKK

+
Macromolecule #17: Cytochrome c oxidase subunit 5A, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 5A, mitochondrial / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 12.453081 KDa
SequenceString:
SHGSHETDEE FDARWVTYFN KPDIDAWELR KGMNTLVGYD LVPEPKIIDA ALRACRRLND FASAVRILEV VKDKAGPHKE IYPYVIQEL RPTLNELGIS TPEELGLDKV

+
Macromolecule #18: Cytochrome c oxidase subunit 5B, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 5B, mitochondrial / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 10.862376 KDa
SequenceString:
MASGGGVPTD EEQATGLERE IMIAAQKGLD PYNMLPPKAA SGTKEDPNLV PSISNKRIVG CICEEDNCTV IWFWLHKGES QRCPNCGTH YKLVPHQMAH

+
Macromolecule #19: Cytochrome c oxidase subunit 6A2, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 6A2, mitochondrial / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 9.437691 KDa
SequenceString:
ASAAKGDHGG AGANTWRLLT FVLALPGVAL CSLNCWMHAG HHERPEFIPY HHLRIRTKPF AWGDGNHTLF HNPHVNPLPT GYEHP

+
Macromolecule #20: Cytochrome c oxidase subunit 6B1

MacromoleculeName: Cytochrome c oxidase subunit 6B1 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 9.95527 KDa
SequenceString:
AEDIKTKIKN YKTAPFDSRF PNQNQTKNCW QNYLDFHRCE KAMTAKGGDV SVCEWYRRVY KSLCPVSWVS AWDDRIAEGT FPGKI

+
Macromolecule #21: Cytochrome c oxidase subunit 6C

MacromoleculeName: Cytochrome c oxidase subunit 6C / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 8.352825 KDa
SequenceString:
SSGALLPKPQ MRGLLAKRLR VHIAGAFIVA LGVAAAYKFG VAEPRKKAYA EFYRNYDSMK DFEEMRKAGI FQSAK

+
Macromolecule #22: Cytochrome c oxidase subunit 7B, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7B, mitochondrial / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 6.317091 KDa
SequenceString:
SHQKRAPSFH DKYGNAILAG GAIFCVSTWT YTATQIGIEW NMSPVGRVTP KEWRDQ

+
Macromolecule #23: Cytochrome c oxidase subunit 7C, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7C, mitochondrial / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 5.451369 KDa
SequenceString:
SHYEEGPGKN LPFSVENKWR LLAMMTVYFG SGFAAPFFIV RHQLLKK

+
Macromolecule #24: Cytochrome c oxidase subunit 8B, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 8B, mitochondrial / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice) / Organ: heart
Molecular weightTheoretical: 4.66041 KDa
SequenceString:
VSAKPAKTPT SAVEQAVGIS AIVVGFMVPA GWVLAHLESY KKSSAA

+
Macromolecule #25: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 25 / Number of copies: 15 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

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

+
Macromolecule #26: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 26 / Number of copies: 7 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

+
Macromolecule #27: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 27 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

+
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 / 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 / Iron–sulfur cluster

+
Macromolecule #30: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 30 / Number of copies: 3 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

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

+
Macromolecule #31: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 31 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION / Copper

+
Macromolecule #32: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 32 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

+
Macromolecule #33: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 33 / Number of copies: 2 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A / Heme A

+
Macromolecule #34: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 34 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #35: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 35 / Number of copies: 1 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

+
Macromolecule #36: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 36 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #37: TRISTEAROYLGLYCEROL

MacromoleculeName: TRISTEAROYLGLYCEROL / type: ligand / ID: 37 / Number of copies: 1 / Formula: TGL
Molecular weightTheoretical: 891.48 Da
Chemical component information

ChemComp-TGL:
TRISTEAROYLGLYCEROL / Stearin

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4 mg/mL
BufferpH: 7.7
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
200.0 mMNaClSodium chloridesodium chloride
2.0 mMC10H16N2O8EDTAEthylenediaminetetraacetic acid
0.2 %C32H58N2O7SCHAPS

Details: CHAPS was added only upon freezing
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.7 µm / Calibrated defocus min: 0.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 7245 / Average exposure time: 1.17 sec. / Average electron dose: 90.66 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1500000
Details: multiple rounds of picking and classification performed, first with Relion LoG and then with Topaz, to extract the best particles from the non-pure starting material
CTF correctionSoftware:
Namedetails
Gctfused for per-particle defocus
CTFFINDused for initial CTF estimation
RELION (ver. 3.1)used for CTF refinement
Startup model#0 - Type of model: PDB ENTRY
#0 - PDB model - PDB ID:

1ntz


#0 - Details: PDB 1NTZ for CIII and 5IY5 for CIV / #1 - Type of model: PDB ENTRY
#1 - PDB model - PDB ID:

5iy5

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 27000 / Software - Name: RELION (ver. 3.1)
Details: the particles were not evenly distributed in the classes. the two good classes, corresponding to the two conformations of CIIICIV, had each c.a. 15k particles.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 16228
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model(PDB ID:

1ntz

,

3l75

,

5iy5

,

5z62

)
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 80 / Target criteria: MAXIMAL LIKELYHOOD
Output model

PDB-7o3c:
Murine supercomplex CIII2CIV in the mature unlocked conformation

+
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