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- EMDB-18062: III2-IV1 respiratory supercomplex from S. pombe -

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Basic information

Entry
Database: EMDB / ID: EMD-18062
TitleIII2-IV1 respiratory supercomplex from S. pombe
Map data
Sample
  • Complex: III2-IV1 respiratory supercomplex
    • Protein or peptide: x 23 types
  • Ligand: x 13 types
KeywordsSupercomplex / respiration / MEMBRANE PROTEIN
Function / homology
Function and homology information


Respiratory electron transport / mitochondrial processing peptidase complex / mitochondrial processing peptidase / mitochondrial cytochrome c oxidase assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase / quinol-cytochrome-c reductase ...Respiratory electron transport / mitochondrial processing peptidase complex / mitochondrial processing peptidase / mitochondrial cytochrome c oxidase assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / ATP synthesis coupled electron transport / enzyme regulator activity / proton transmembrane transport / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / structural molecule activity / mitochondrion / metal ion binding
Similarity search - Function
Predicted cytochrome c oxidase subunit VII / Respiratory supercomplex factor 2, mitochondrial / Hypoxia induced protein, domain / Hypoxia induced protein conserved region / HIG1 domain profile. / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / : / Cytochrome b-c1 complex, subunit 6 ...Predicted cytochrome c oxidase subunit VII / Respiratory supercomplex factor 2, mitochondrial / Hypoxia induced protein, domain / Hypoxia induced protein conserved region / HIG1 domain profile. / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / : / 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. / 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 / Peptidase M16, zinc-binding site / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Insulinase family, zinc-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 / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Di-haem cytochrome, transmembrane / Cytochrome C oxidase subunit II, periplasmic domain / Rieske iron-sulphur protein / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] iron-sulphur domain
Similarity search - Domain/homology
Cytochrome c oxidase subunit 7 / Cytochrome b-c1 complex subunit 6 / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 9 / Cytochrome c oxidase subunit 13, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome c oxidase polypeptide 5, mitochondrial / Cytochrome c oxidase subunit 12, mitochondrial / Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome b ...Cytochrome c oxidase subunit 7 / Cytochrome b-c1 complex subunit 6 / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 9 / Cytochrome c oxidase subunit 13, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome c oxidase polypeptide 5, mitochondrial / Cytochrome c oxidase subunit 12, mitochondrial / Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome b / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 2 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome c oxidase subunit 4, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Respiratory supercomplex factor 2 homolog C1565.01 / Cytochrome c oxidase polypeptide VIII, mitochondrial / Cytochrome b-c1 complex subunit 10 / Probable mitochondrial-processing peptidase subunit beta / Cytochrome c oxidase subunit 6, mitochondrial
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMoe A / Brzezinski P
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure and function of the III-IV-cyt supercomplex.
Authors: Agnes Moe / Anna-Roza Dimogkioka / Doron Rapaport / Linda Näsvik Öjemyr / Peter Brzezinski /
Abstract: The respiratory chain in aerobic organisms is composed of a number of membrane-bound protein complexes that link electron transfer to proton translocation across the membrane. In mitochondria, the ...The respiratory chain in aerobic organisms is composed of a number of membrane-bound protein complexes that link electron transfer to proton translocation across the membrane. In mitochondria, the final electron acceptor, complex IV (CIV), receives electrons from dimeric complex III (CIII), via a mobile electron carrier, cytochrome . In the present study, we isolated the CIIICIV supercomplex from the fission yeast and determined its structure with bound cyt. using single-particle electron cryomicroscopy. A respiratory supercomplex factor 2 was found to be bound at CIV distally positioned in the supercomplex. In addition to the redox-active metal sites, we found a metal ion, presumably Zn, coordinated in the CIII subunit Cor1, which is encoded by the same gene () as the mitochondrial-processing peptidase subunit β. Our data show that the isolated CIIICIV supercomplex displays proteolytic activity suggesting a dual role of CIII in . As in the supercomplex from , subunit Cox5 of CIV faces towards one CIII monomer, but in the two complexes are rotated relative to each other by ~45°. This orientation yields equal distances between the cyt. binding sites at CIV and at each of the two CIII monomers. The structure shows cyt. bound at four positions, but only along one of the two symmetrical branches. Overall, this combined structural and functional study reveals the integration of peptidase activity with the CIII respiratory system and indicates a two-dimensional cyt. diffusion mechanism within the CIII-CIV supercomplex.
History
DepositionJul 31, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_18062.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8464 Å
Density
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.34192747 - 0.72714645
Average (Standard dev.)0.00088451646 (±0.021879723)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 433.3568 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3DVA class 0 after heterogeneous refinement, cyt. c...

Fileemd_18062_additional_1.map
Annotation3DVA class 0 after heterogeneous refinement, cyt. c at position (iii) and (iv)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: 3DVA class 1 after heterogeneous refinement, cyt. c...

Fileemd_18062_additional_2.map
Annotation3DVA class 1 after heterogeneous refinement, cyt. c at position (ii) and (iv)
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: 3DVA class 2 after heterogeneous refinement, cyt. c at position (iii)

Fileemd_18062_additional_3.map
Annotation3DVA class 2 after heterogeneous refinement, cyt. c at position (iii)
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: 3DVA class 3 after heterogeneous refinement, cyt. c at position (i)

Fileemd_18062_additional_4.map
Annotation3DVA class 3 after heterogeneous refinement, cyt. c at position (i)
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_18062_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Half map: #1

Fileemd_18062_half_map_2.map
Projections & Slices
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Sample components

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Entire : III2-IV1 respiratory supercomplex

EntireName: III2-IV1 respiratory supercomplex
Components
  • Complex: III2-IV1 respiratory supercomplex
    • Protein or peptide: Probable mitochondrial-processing peptidase subunit beta
    • 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
    • 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 9
    • Protein or peptide: Cytochrome b-c1 complex subunit 10
    • 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 polypeptide 5, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 6, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 7
    • Protein or peptide: Cytochrome c oxidase polypeptide VIII, 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: Respiratory supercomplex factor 2 homolog C1565.01
    • Protein or peptide: Unknown polypeptide
  • Ligand: ZINC ION
  • Ligand: CARDIOLIPIN
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
  • Ligand: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: UBIQUINONE-10Coenzyme Q10
  • Ligand: HEME C
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: HEME-A
  • Ligand: COPPER (II) ION
  • Ligand: CALCIUM IONCalcium
  • Ligand: MAGNESIUM ION
  • Ligand: DINUCLEAR COPPER ION

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Supramolecule #1: III2-IV1 respiratory supercomplex

SupramoleculeName: III2-IV1 respiratory supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#23
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

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Macromolecule #1: Probable mitochondrial-processing peptidase subunit beta

MacromoleculeName: Probable mitochondrial-processing peptidase subunit beta
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 50.802277 KDa
SequenceString: MLRLQNLPKL VRRFATTALP KTETTTLKNG LTVATEHHPY AQTATVLVGV DAGSRAETAK NNGAAHFLEH LAFKGTKNRS QKALELEFE NTGAHLNAYT SREQTVYYAH AFKNAVPNAV AVLADILTNS SISASAVERE RQVILREQEE VDKMADEVVF D HLHATAYQ ...String:
MLRLQNLPKL VRRFATTALP KTETTTLKNG LTVATEHHPY AQTATVLVGV DAGSRAETAK NNGAAHFLEH LAFKGTKNRS QKALELEFE NTGAHLNAYT SREQTVYYAH AFKNAVPNAV AVLADILTNS SISASAVERE RQVILREQEE VDKMADEVVF D HLHATAYQ GHPLGRTILG PKENIESLTR EDLLQYIKDN YRSDRMIISS AGSISHEELV KLAEKYFGHL EPSAEQLSLG AP RGLKPRF VGSEIRARDD DSPTANIAIA VEGMSWKHPD YFTALVMQAI IGNWDRAMGA SPHLSSRLST IVQQHQLANS FMS FSTSYS DTGLWGIYLV TENLGRIDDL VHFTLQNWAR LTVATRAEVE RAKAQLRASL LLSLDSTTAI AEDIGRQLLT TGRR MSPQE VDLRIGQITE KDVARVASEM IWDKDIAVSA VGSIEGLLDY NRIRSSISMN RW

UniProtKB: Probable mitochondrial-processing peptidase subunit beta

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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: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 45.704973 KDa
SequenceString: MKSFTRNLRR FQTPRRNLHG ISYTPKKVEG VSFAGRETPT ATGSLSVVIN AGSRYQPDAG VSHLLEKFAF KTTEERSALR ITRESELLG GQLSTQITRE HIILTARFLN EYLEYYARLL AEVVDATKFL PFQLTEEVLP TARIESELFR EDILRVAMAK L HEKAFHRG ...String:
MKSFTRNLRR FQTPRRNLHG ISYTPKKVEG VSFAGRETPT ATGSLSVVIN AGSRYQPDAG VSHLLEKFAF KTTEERSALR ITRESELLG GQLSTQITRE HIILTARFLN EYLEYYARLL AEVVDATKFL PFQLTEEVLP TARIESELFR EDILRVAMAK L HEKAFHRG IGNEVYLPAS ASPSISEIKD FASKAYVKSN FSVISSGPDV QKASDLCAKY FAVIPDGSPL KSAPTKISSG ES RVYSKGT NYFCLGFPAP AASPELFVLS SILGGDAAVK WSHGNTLLAK AAGTASEYKA TAVADLTPYS DASLLSVVIS GSC PKAIKA TASESFKALK SLSSNIPNDV VKSGIAMAKT KYLSAFEPVT LNAISASSLV SASKGSDAFI SGFDKVTPAS ISKV VSSLL AKPASTVAVG NLDVLPYYDE L

UniProtKB: Cytochrome b-c1 complex subunit 2, mitochondrial

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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: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 43.760602 KDa
SequenceString: MKILKSNPFL ALANNYMIDA PEPSNISYFW NFGSLLACVL VIQIVIGILL ACFYIPNMDL AFLSVERIVR DVNYGFLLRA FHANGASFF FIFLYLHIGR GLYYGSYKYP RTMTWNIGVI IFLLTIITAF LGYCLPANQM SFWGATVITN LLSAVPFIGD D LVHLLWGG ...String:
MKILKSNPFL ALANNYMIDA PEPSNISYFW NFGSLLACVL VIQIVIGILL ACFYIPNMDL AFLSVERIVR DVNYGFLLRA FHANGASFF FIFLYLHIGR GLYYGSYKYP RTMTWNIGVI IFLLTIITAF LGYCLPANQM SFWGATVITN LLSAVPFIGD D LVHLLWGG FSVSNPTLNR FFSLHYLMPF VIAALSVMHL IALHTNGSSN PLGVTANMDR IPMNPYYLIK DLITIFIFLI GI NYMAFYN PYGFMEPDCA LPADPLKTPM SIVPEWYLLP FYAILRAIPN FQLGVIAMLL SILVLLLLPL LDFSAIRGNS FNP FGKFFF WTFVADFVIL AWIGGSHPEN VFITIGAIAT IFYFSYFFIL IPVYTILGNT LIDLNLSSIK R

UniProtKB: Cytochrome b

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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
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 34.383094 KDa
SequenceString: MFQFVKKKNE FLKFARLGSR AFTQNAQKTH SKGSNIALVS SSLLSVGMIA LYYNVYGPSL SAGTPKEEGL HFIQHDWPQS KVLSGFDHA SLRRGFQVYR EVCSACHSLN LIAWRHLVGV THTADEAKQM ASEVEYEDGP DDEGNMFKRP GKLSDFLPPP Y PNVEAARA ...String:
MFQFVKKKNE FLKFARLGSR AFTQNAQKTH SKGSNIALVS SSLLSVGMIA LYYNVYGPSL SAGTPKEEGL HFIQHDWPQS KVLSGFDHA SLRRGFQVYR EVCSACHSLN LIAWRHLVGV THTADEAKQM ASEVEYEDGP DDEGNMFKRP GKLSDFLPPP Y PNVEAARA SNNGAAPPDL SCVVRGRHGG QDYIYSLLTG YTEPPAGVEV PDGMNFNPFF PGTQIAMARP LFDDAVEFED GT PATTAQA AKDVVNFLHW ASEPELDIRK KMGFQVITVL TILTALSMWY KRFKWTPIKN RKIFYQRPIK

UniProtKB: Cytochrome c1, heme protein, mitochondrial

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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
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 24.769352 KDa
SequenceString: MLAKQFISKS LASSLRRLLP VSSTASSLKG SMMTIPKFTS IRTYTDSPEM PDFSEYQTKS TGDRSRVISY AMVGTMGALT AAGAQATVH DFLASWSASA DVLAMSKAEV DLSKIPEGKN LVVKWQGKPV FIRHRTPEEI QEANSVDIST LRDPQADSDR V QKPEWLVM ...String:
MLAKQFISKS LASSLRRLLP VSSTASSLKG SMMTIPKFTS IRTYTDSPEM PDFSEYQTKS TGDRSRVISY AMVGTMGALT AAGAQATVH DFLASWSASA DVLAMSKAEV DLSKIPEGKN LVVKWQGKPV FIRHRTPEEI QEANSVDIST LRDPQADSDR V QKPEWLVM IGVCTHLGCV PIGEAGDYGG WFCPCHGSHY DISGRIRRGP APLNLAIPAY TFEGSKIIIG

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

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Macromolecule #6: Cytochrome b-c1 complex subunit 6

MacromoleculeName: Cytochrome b-c1 complex subunit 6 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 24.340496 KDa
SequenceString: MSFWKNLFTS AFTPISAEAD ELIKEDRKQF EENTPSKKNF ETQSPDEPSP KTTDSTGARD ANLSLKTQEP IVSADDAKGA QGKGADEKE EKKETIQPPE EVKTEPPQPE EKEGKEAKEP EEPPKEEAEE PQEGGEEEEE EEEEEEITDP LEKMTQECMD A PDCKEVKH ...String:
MSFWKNLFTS AFTPISAEAD ELIKEDRKQF EENTPSKKNF ETQSPDEPSP KTTDSTGARD ANLSLKTQEP IVSADDAKGA QGKGADEKE EKKETIQPPE EVKTEPPQPE EKEGKEAKEP EEPPKEEAEE PQEGGEEEEE EEEEEEITDP LEKMTQECMD A PDCKEVKH HFEECTARVT KKVEQGDKSE DCIEEFFHLY HCARDCADPK VFKVLV

UniProtKB: Cytochrome b-c1 complex subunit 6

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Macromolecule #7: Cytochrome b-c1 complex subunit 7

MacromoleculeName: Cytochrome b-c1 complex subunit 7 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 16.058521 KDa
SequenceString:
MKPVSLAKYI QKSPFLTKLL LPISNAYVHL SGYRKYGLRY DDLMLEENDD TQKALSRLPK MESYDRVYRI RRAMQLSIEN KILPKSEWT KPEEDYHYLR PVLAEVIAER KEREAFDALI VKKPETQAHA TSSPAHAH

UniProtKB: Cytochrome b-c1 complex subunit 7

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Macromolecule #8: Cytochrome b-c1 complex subunit 8

MacromoleculeName: Cytochrome b-c1 complex subunit 8 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 10.48107 KDa
SequenceString:
MGGAAGGKTY LGWWGHLGGP KQKGIITYSL SPFQQRPMAG FFKTSTQNMF RRVMTEGLYV AIPFGIAYYI YCWGKERNEF LNSKHGRHL VEE

UniProtKB: Cytochrome b-c1 complex subunit 8

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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: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 7.807629 KDa
SequenceString:
MASSTIYNIF FRRNSSFYAT IFVSAFFAKI GFDVFTDSVW KRANAGLTWD EVKPRFLNKD EDAEDDE

UniProtKB: Cytochrome b-c1 complex subunit 9

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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: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 9.136762 KDa
SequenceString:
MISFFPNKPM YHVQPHISFI TPERTMKTIP AFSRWAFAAV AGVFVFAMQV PKVKTTILQP IAFIGDHFKD KTPEEDKWL

UniProtKB: Cytochrome b-c1 complex subunit 10

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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: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 59.60768 KDa
SequenceString: MNSWWTYVNR WIFSTNAKDI AILYLLFGLV SGIIGSVFSF IIRMELSAPG SQFLSGNGQL YNVAISAHGI LMIFFFIIPA LFGAFGNYL VPLMIGAPDV AYPRVNNFTF WLLPPALMLL LISALTEEGP GGGWTVYPPL SSITSHSGPA IDLAILSLQL T GISSTLGS ...String:
MNSWWTYVNR WIFSTNAKDI AILYLLFGLV SGIIGSVFSF IIRMELSAPG SQFLSGNGQL YNVAISAHGI LMIFFFIIPA LFGAFGNYL VPLMIGAPDV AYPRVNNFTF WLLPPALMLL LISALTEEGP GGGWTVYPPL SSITSHSGPA IDLAILSLQL T GISSTLGS VNLIATMINM RAPGLSLYQM PLFAWAIMIT SILLLLTLPV LAGGLFMLFS DRNLNTSFYA PEGGGDPVLY QH LFWFFGH PEVYILIMPA FGVVSHIIPS LAHKPIFGKE GMLWAMLSIA LLGLMVWSHH LFTVGLDVDT RAYFSAATMV IAI PTGIKI FSWLATLTGG AIQWSRVPML YAIGFLILFT IGGLTGVILS NSVLDIAFHD TYFVVAHFHY VLSMGALFGL CGAY YYWSP KMFGLMYNET LASIQFWILF IGVNIVFGPQ HFLGLNGMPR RIPDYPEAFV GWNFVSSIGS VISILSLFLF MYVMY DQFT SNRVVKTNPY LIPSYFDDNV IFVNEKLGVA QSIEWLLHSP VHEHAFNTLP TKSI

UniProtKB: Cytochrome c oxidase subunit 1

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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: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 28.139258 KDa
SequenceString: MLFFNSILND APSSWALYFQ DGASPSYLGV THLNDYLMFY LTFIFIGVIY AICKAVIEYN YNSHPIAAKY TTHGSIVEFI WTLIPALIL ILVALPSFKL LYLLDEVQKP SMTVKAIGRQ WFWTYELNDF VTNENEPVSF DSYMVPEEDL EEGSLRQLEV D NRLVLPID ...String:
MLFFNSILND APSSWALYFQ DGASPSYLGV THLNDYLMFY LTFIFIGVIY AICKAVIEYN YNSHPIAAKY TTHGSIVEFI WTLIPALIL ILVALPSFKL LYLLDEVQKP SMTVKAIGRQ WFWTYELNDF VTNENEPVSF DSYMVPEEDL EEGSLRQLEV D NRLVLPID TRIRLILTSG DVIHSWAVPS LGIKCDCIPG RLNQVSLSID REGLFYGQCS ELCGVLHSSM PIVVQGVSLE DF LAWLEEN S

UniProtKB: Cytochrome c oxidase subunit 2

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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: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 30.432148 KDa
SequenceString: MNLSTKFQGH PYHIVSASPW PFFLSVVLFF NCLAATLYLH GYKHSSVFFG ISFLGLLATM YLWFRDMSTE ANIHGAHTKA VTKGLKIGF MLFLISETFL FASIFWAFFH SSLSPTFELG AVWPPVGIAD KTIDPLEVPL LNTVILLTSG ASLTYAHYSL I ARNRENAL ...String:
MNLSTKFQGH PYHIVSASPW PFFLSVVLFF NCLAATLYLH GYKHSSVFFG ISFLGLLATM YLWFRDMSTE ANIHGAHTKA VTKGLKIGF MLFLISETFL FASIFWAFFH SSLSPTFELG AVWPPVGIAD KTIDPLEVPL LNTVILLTSG ASLTYAHYSL I ARNRENAL KGLYMTIALS FLFLGGQAYE YWNAPFTISD SVYGASFYFA TGLHGIHIIV GTILLLAATY NIYTYHLTNT HH NGFECGI YYWHFCDVVW LFLYLTIYIW GS

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: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 17.624094 KDa
SequenceString:
MFMNSMLRVS RQRAAVRSTV SLYRGFVSAS IRRNEQNVVK AAAQELANAK EPSDLIGPGG RDGEVPTDLE QATGLERYEL LSELSGRDA FDMKPLDASR KGTLTDPIMV TSLDPYRHIG CTGSPSGSHN LIWMTVYKDK LRRCPECGSV YKLKFMGDPN

UniProtKB: Cytochrome c oxidase subunit 4, mitochondrial

+
Macromolecule #15: Cytochrome c oxidase polypeptide 5, mitochondrial

MacromoleculeName: Cytochrome c oxidase polypeptide 5, mitochondrial / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 24.933271 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe (fission yeast)
SequenceString: MYLSKIICKK VPMKLLCTRN AATVSAAATN ALQKEQPSGE AMIARPRLVD LDKRWGIMSQ EEKDGLITDL YARQKQPWTT LSIEEKKAA YWIAFGEHGP RAFSHISQKT VFWGTVAGLT IGVVLFGLIR TQAAPSPRTM TREWQEKSNE YMKENKINPI S GEASEGFK ...String:
MYLSKIICKK VPMKLLCTRN AATVSAAATN ALQKEQPSGE AMIARPRLVD LDKRWGIMSQ EEKDGLITDL YARQKQPWTT LSIEEKKAA YWIAFGEHGP RAFSHISQKT VFWGTVAGLT IGVVLFGLIR TQAAPSPRTM TREWQEKSNE YMKENKINPI S GEASEGFK GRGQISGGIF SPSEKDKKEN LYFQGGGGGG SAWSHPQFEK GGGSGGGSGG SAWSHPQFEK

UniProtKB: Cytochrome c oxidase polypeptide 5, mitochondrial

+
Macromolecule #16: Cytochrome c oxidase subunit 6, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 6, mitochondrial / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 15.958173 KDa
SequenceString:
MKAVQRIFQT GRFSVAAGPS VRFQAGFLAA NRQVRFSSNH GVSLEEINTK YNDFFSNVQD QFELQRGLNN CFAYDIVPSS DVIEQALRA ARRVNDFPTA VRIFEGIKVK LPTKEQYQAY VKELKPVCNE LGIVLKEDLF K

UniProtKB: Cytochrome c oxidase subunit 6, mitochondrial

+
Macromolecule #17: Cytochrome c oxidase subunit 7

MacromoleculeName: Cytochrome c oxidase subunit 7 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 6.741878 KDa
SequenceString:
MKNTIVQQQR FLQSIHKPTY LQRPGSFALV YPYYAVMAGL GLYSLYASGR VIFGKKDAF

UniProtKB: Cytochrome c oxidase subunit 7

+
Macromolecule #18: Cytochrome c oxidase polypeptide VIII, mitochondrial

MacromoleculeName: Cytochrome c oxidase polypeptide VIII, mitochondrial / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 7.512846 KDa
SequenceString:
MLRYSLQARS ALRGVRFSSS HSAPKPGSTI PFYINKKPLP TLLYFGTFGV IFSIPFIVVK YHNRNL

UniProtKB: Cytochrome c oxidase polypeptide VIII, mitochondrial

+
Macromolecule #19: Cytochrome c oxidase subunit 9, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 9, mitochondrial / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 6.652764 KDa
SequenceString:
MAVGPVTGMF KRRIVTDFSV TMILGTLGAC YWWFGYHKPA ARQREEFYVK LAAEKNAE

UniProtKB: Cytochrome c oxidase subunit 9, mitochondrial

+
Macromolecule #20: Cytochrome c oxidase subunit 12, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 12, mitochondrial / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 10.275406 KDa
SequenceString:
MSEQEDQEAP KQFTFGTVGF DARFPNTNQT KHCFQSYIDY FRCIKAKGED FVPCKQFWHA YQSLCPMEWV ERWDEQRENG TFPAPI

UniProtKB: Cytochrome c oxidase subunit 12, mitochondrial

+
Macromolecule #21: Cytochrome c oxidase subunit 13, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 13, mitochondrial / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 15.224184 KDa
SequenceString:
MSMMNRNIGF LSRTLKTSVP KRAGLLSFRA YSNEAKVNWL EEVQAEEEHA KRSSEFWKKV TYYIGGPALI LASANAYYIY CKHQEHAKH VEDTDPGYSF ENLRFKKYPW GDGSKTLFWN DKVNHLKKDD E

UniProtKB: Cytochrome c oxidase subunit 13, mitochondrial

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Macromolecule #22: Respiratory supercomplex factor 2 homolog C1565.01

MacromoleculeName: Respiratory supercomplex factor 2 homolog C1565.01 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 27.084996 KDa
SequenceString: MKLSTPEEVK AFNRNTYSAL FKGALVGSSL GIAGWLIGNR YSAGFRRLPF SLKSWLVIGS GSGASIIFAD KAGLKFEAER YGKFDQIDY STKGLPWNQR ALYYFNEHKW PIILGTWAST MGLSLYAASR NRYDTAPQKL IQARMYAQGV TVVVLLGSVY L STLANRLE ...String:
MKLSTPEEVK AFNRNTYSAL FKGALVGSSL GIAGWLIGNR YSAGFRRLPF SLKSWLVIGS GSGASIIFAD KAGLKFEAER YGKFDQIDY STKGLPWNQR ALYYFNEHKW PIILGTWAST MGLSLYAASR NRYDTAPQKL IQARMYAQGV TVVVLLGSVY L STLANRLE PLEREVLVTD PSNPTKLVAF KQRKERYPGE LQWEVLVSQD EERLRKLNLP LREPHGSTGP MSTPTPALNS SR SA

UniProtKB: Respiratory supercomplex factor 2 homolog C1565.01

+
Macromolecule #23: Unknown polypeptide

MacromoleculeName: Unknown polypeptide / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 2.230741 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

+
Macromolecule #24: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 24 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #25: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 25 / Number of copies: 6 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / type: ligand / ID: 26 / Number of copies: 4 / Formula: PCF
Molecular weightTheoretical: 734.039 Da
Chemical component information

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

+
Macromolecule #27: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 27 / Number of copies: 10 / Formula: PEF
Molecular weightTheoretical: 691.959 Da
Chemical component information

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

+
Macromolecule #28: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 28 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

+
Macromolecule #29: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 29 / Number of copies: 2 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10 / Coenzyme Q10

+
Macromolecule #30: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 30 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

+
Macromolecule #31: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 31 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

+
Macromolecule #32: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 32 / 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 #33: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 33 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION / Copper

+
Macromolecule #34: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 34 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #35: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 35 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #36: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 36 / Number of copies: 1 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / 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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 125752
FSC plot (resolution estimation)

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