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- EMDB-16491: Cytochrome c oxidase from Schizosaccharomyces pombe -

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Basic information

Entry
Database: EMDB / ID: EMD-16491
TitleCytochrome c oxidase from Schizosaccharomyces pombe
Map data
Sample
  • Complex: Cytochrome c oxidase
    • Protein or peptide: x 13 types
  • Ligand: x 7 types
Function / homology
Function and homology information


mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex IV / 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 / proton transmembrane transport ...mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex IV / 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 / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / 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 c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase subunit VIIc ...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 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 7 / Cytochrome c oxidase subunit 13, mitochondrial / Cytochrome c oxidase polypeptide 5, mitochondrial / Cytochrome c oxidase subunit 12, mitochondrial / Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 4, mitochondrial / Respiratory supercomplex factor 2 homolog C1565.01 ...Cytochrome c oxidase subunit 7 / Cytochrome c oxidase subunit 13, mitochondrial / Cytochrome c oxidase polypeptide 5, mitochondrial / Cytochrome c oxidase subunit 12, mitochondrial / Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 4, mitochondrial / Respiratory supercomplex factor 2 homolog C1565.01 / Cytochrome c oxidase polypeptide VIII, mitochondrial / Cytochrome c oxidase subunit 6, mitochondrial
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast) / fission yeast (fission yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsMoe A / Adelroth P / Brzezinski P / Nasvik Ojemyr L
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Commun Chem / Year: 2023
Title: Cryo-EM structure and function of S. pombe complex IV with bound respiratory supercomplex factor.
Authors: Agnes Moe / Pia Ädelroth / Peter Brzezinski / Linda Näsvik Öjemyr /
Abstract: Fission yeast Schizosaccharomyces pombe serves as model organism for studying higher eukaryotes. We combined the use of cryo-EM and spectroscopy to investigate the structure and function of affinity ...Fission yeast Schizosaccharomyces pombe serves as model organism for studying higher eukaryotes. We combined the use of cryo-EM and spectroscopy to investigate the structure and function of affinity purified respiratory complex IV (CIV) from S. pombe. The reaction sequence of the reduced enzyme with O proceeds over a time scale of µs-ms, similar to that of the mammalian CIV. The cryo-EM structure of CIV revealed eleven subunits as well as a bound hypoxia-induced gene 1 (Hig1) domain of respiratory supercomplex factor 2 (Rcf2). These results suggest that binding of Rcf2 does not require the presence of a CIII-CIV supercomplex, i.e. Rcf2 is a component of CIV. An AlphaFold-Multimer model suggests that the Hig1 domains of both Rcf1 and Rcf2 bind at the same site of CIV suggesting that their binding is mutually exclusive. Furthermore, the differential functional effect of Rcf1 or Rcf2 is presumably caused by interactions of CIV with their different non-Hig1 domain parts.
History
DepositionJan 20, 2023-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 1, 2023-
Current statusMar 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16491.png

Downloads & links

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Map

FileDownload / File: emd_16491.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8617 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.3698189 - 2.105153
Average (Standard dev.)0.007634901 (±0.084462985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.5952 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16491_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16491_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cytochrome c oxidase

EntireName: Cytochrome c oxidase
Components
  • Complex: Cytochrome c oxidase
    • 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: HEME-A
  • Ligand: COPPER (II) ION
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM IONCalcium
  • Ligand: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
  • Ligand: DINUCLEAR COPPER ION
  • Ligand: ZINC ION

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Supramolecule #1: Cytochrome c oxidase

SupramoleculeName: Cytochrome c oxidase / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 246 KDa

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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 / EC number: cytochrome-c oxidase
Source (natural)Organism: fission yeast (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

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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 / EC number: cytochrome-c oxidase
Source (natural)Organism: fission yeast (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

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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 / EC number: cytochrome-c oxidase
Source (natural)Organism: fission yeast (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

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Macromolecule #4: Cytochrome c oxidase subunit 4, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 4, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fission yeast (fission yeast)
Molecular weightTheoretical: 17.624094 KDa
SequenceString:
MFMNSMLRVS RQRAAVRSTV SLYRGFVSAS IRRNEQNVVK AAAQELANAK EPSDLIGPGG RDGEVPTDLE QATGLERYEL LSELSGRDA FDMKPLDASR KGTLTDPIMV TSLDPYRHIG CTGSPSGSHN LIWMTVYKDK LRRCPECGSV YKLKFMGDPN

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Macromolecule #5: Cytochrome c oxidase polypeptide 5, mitochondrial

MacromoleculeName: Cytochrome c oxidase polypeptide 5, mitochondrial / type: protein_or_peptide / ID: 5 / 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

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Macromolecule #6: Cytochrome c oxidase subunit 6, mitochondrial

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

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Macromolecule #7: Cytochrome c oxidase subunit 7

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

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Macromolecule #8: Cytochrome c oxidase polypeptide VIII, mitochondrial

MacromoleculeName: Cytochrome c oxidase polypeptide VIII, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fission yeast (fission yeast)
Molecular weightTheoretical: 7.512846 KDa
SequenceString:
MLRYSLQARS ALRGVRFSSS HSAPKPGSTI PFYINKKPLP TLLYFGTFGV IFSIPFIVVK YHNRNL

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Macromolecule #9: Cytochrome c oxidase subunit 9, mitochondrial

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

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Macromolecule #10: Cytochrome c oxidase subunit 12, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 12, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fission yeast (fission yeast)
Molecular weightTheoretical: 10.275406 KDa
SequenceString:
MSEQEDQEAP KQFTFGTVGF DARFPNTNQT KHCFQSYIDY FRCIKAKGED FVPCKQFWHA YQSLCPMEWV ERWDEQRENG TFPAPI

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Macromolecule #11: Cytochrome c oxidase subunit 13, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 13, mitochondrial / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fission yeast (fission yeast)
Molecular weightTheoretical: 15.224184 KDa
SequenceString:
MSMMNRNIGF LSRTLKTSVP KRAGLLSFRA YSNEAKVNWL EEVQAEEEHA KRSSEFWKKV TYYIGGPALI LASANAYYIY CKHQEHAKH VEDTDPGYSF ENLRFKKYPW GDGSKTLFWN DKVNHLKKDD E

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Macromolecule #12: Respiratory supercomplex factor 2 homolog C1565.01

MacromoleculeName: Respiratory supercomplex factor 2 homolog C1565.01 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fission yeast (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

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Macromolecule #13: Unknown polypeptide

MacromoleculeName: Unknown polypeptide / type: protein_or_peptide / ID: 13 / 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)

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Macromolecule #14: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 14 / 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 #15: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 15 / 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 #16: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 16 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #17: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 17 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #18: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 18 / Number of copies: 4 / Formula: PEF
Molecular weightTheoretical: 691.959 Da
Chemical component information

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

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Macromolecule #19: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

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Macromolecule #20: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 20 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration4 mg/mL
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

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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 / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127659
FSC plot (resolution estimation)

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