[English] 日本語
Yorodumi
- EMDB-52654: Cryo-EM structure of HIGD2A bound complex IV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52654
TitleCryo-EM structure of HIGD2A bound complex IV
Map dataThis is focus map on complex IV of state 1
Sample
  • Cell: Complex IV
    • Protein or peptide: x 14 types
  • Ligand: x 7 types
KeywordsHuman mitochondria / respirasome complex / assembly / cytochrome c oxidase / complex IV / HIGD2A / MEMBRANE PROTEIN
Function / homology
Function and homology information


Complex IV assembly / respiratory chain complex IV assembly / Respiratory electron transport / mitochondrial respirasome assembly / respiratory gaseous exchange by respiratory system / cellular respiration / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / mitochondrial electron transport, cytochrome c to oxygen ...Complex IV assembly / respiratory chain complex IV assembly / Respiratory electron transport / mitochondrial respirasome assembly / respiratory gaseous exchange by respiratory system / cellular respiration / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / response to copper ion / response to electrical stimulus / ATP synthesis coupled electron transport / enzyme regulator activity / lactation / response to nutrient / substantia nigra development / Mitochondrial protein degradation / aerobic respiration / cerebellum development / central nervous system development / respiratory electron transport chain / TP53 Regulates Metabolic Genes / generation of precursor metabolites and energy / Cytoprotection by HMOX1 / mitochondrial intermembrane space / mitochondrial membrane / response to oxidative stress / response to hypoxia / oxidoreductase activity / electron transfer activity / mitochondrial inner membrane / mitochondrial matrix / copper ion binding / heme binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / metal ion binding / membrane / cytosol
Similarity search - Function
: / Hypoxia induced protein, domain / Hypoxia induced protein conserved region / HIG1 domain profile. / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII ...: / Hypoxia induced protein, domain / Hypoxia induced protein conserved region / HIG1 domain profile. / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome C oxidase chain VIIB / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxin
Similarity search - Domain/homology
Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 8A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6A1, mitochondrial / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 7A2, mitochondrial / Cytochrome c oxidase subunit 6B1 ...Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 8A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6A1, mitochondrial / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 7A2, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / HIG1 domain family member 2A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsNguyen MD / Rorbach J / Singh V
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: To Be Published
Title: Structural basis for late maturation steps of mitochondrial respiratory chain complex IV within the human respirasome
Authors: Nguyen MD / Singh V / Rorbach J
History
DepositionJan 30, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52654.png

Downloads & links

-
Map

FileDownload / File: emd_52654.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is focus map on complex IV of state 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 600 pix.
= 504. Å		0.84 Å/pix.
x 600 pix.
= 504. Å		0.84 Å/pix.
x 600 pix.
= 504. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-37.883299999999998 - 59.083754999999996
Average (Standard dev.)-0.000000000001248 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 503.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_52654_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_52654_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Complex IV

EntireName: Complex IV
Components
  • Cell: Complex IV
    • Protein or peptide: HIG1 domain family member 2A, mitochondrial
    • 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 6A1, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 6B1
    • Protein or peptide: Cytochrome c oxidase subunit 6C
    • Protein or peptide: Cytochrome c oxidase subunit 7A2, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 7B, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 7C, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 8A, mitochondrial
  • Ligand: COPPER (II) ION
  • Ligand: MAGNESIUM ION
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: HEME-A
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: CARDIOLIPIN
  • Ligand: ZINC ION

+
Supramolecule #1: Complex IV

SupramoleculeName: Complex IV / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: HIG1 domain family member 2A, mitochondrial

MacromoleculeName: HIG1 domain family member 2A, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.542502 KDa
SequenceString:
MATPGPVIPE VPFEPSKPPV IEGLSPTVYR NPESFKEKFV RKTRENPVVP IGCLATAAAL TYGLYSFHRG NSQRSQLMMR TRIAAQGFT VAAILLGLAV TAMKSRP

UniProtKB: HIG1 domain family member 2A, mitochondrial

+
Macromolecule #2: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.10493 KDa
SequenceString: (FME)FADRWLFST NHKDIGTLYL LFGAWAGVLG TALSLLIRAE LGQPGNLLGN DHIYNVIVTA HAFVMIFFMV MPIMIG GFG NWLVPLMIGA PDMAFPRMNN MSFWLLPPSL LLLLASAMVE AGAGTGWTVY PPLAGNYSHP GASVDLTIFS LHLAGVS SI LGAINFITTI ...String:
(FME)FADRWLFST NHKDIGTLYL LFGAWAGVLG TALSLLIRAE LGQPGNLLGN DHIYNVIVTA HAFVMIFFMV MPIMIG GFG NWLVPLMIGA PDMAFPRMNN MSFWLLPPSL LLLLASAMVE AGAGTGWTVY PPLAGNYSHP GASVDLTIFS LHLAGVS SI LGAINFITTI INMKPPAMTQ YQTPLFVWSV LITAVLLLLS LPVLAAGITM LLTDRNLNTT FFDPAGGGDP ILYQHLFW F FGHPEVYILI LPGFGMISHI VTYYSGKKEP FGYMGMVWAM MSIGFLGFIV WAHHMFTVGM DVDTRAYFTS ATMIIAIPT GVKVFSWLAT LHGSNMKWSA AVLWALGFIF LFTVGGLTGI VLANSSLDIV LHDTYYVVAH FHYVLSMGAV FAIMGGFIHW FPLFSGYTL DQTYAKIHFT IMFIGVNLTF FPQHFLGLSG MPRRYSDYPD AYTTWNILSS VGSFISLTAV MLMIFMIWEA F ASKRKVLM VEEPSMNLEW LYGCPPPYHT FEEPVYMKS

UniProtKB: Cytochrome c oxidase subunit 1

+
Macromolecule #3: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.5809 KDa
SequenceString: MAHAAQVGLQ DATSPIMEEL ITFHDHALMI IFLICFLVLY ALFLTLTTKL TNTNISDAQE METVWTILPA IILVLIALPS LRILYMTDE VNDPSLTIKS IGHQWYWTYE YTDYGGLIFN SYMLPPLFLE PGDLRLLDVD NRVVLPIEAP IRMMITSQDV L HSWAVPTL ...String:
MAHAAQVGLQ DATSPIMEEL ITFHDHALMI IFLICFLVLY ALFLTLTTKL TNTNISDAQE METVWTILPA IILVLIALPS LRILYMTDE VNDPSLTIKS IGHQWYWTYE YTDYGGLIFN SYMLPPLFLE PGDLRLLDVD NRVVLPIEAP IRMMITSQDV L HSWAVPTL GLKTDAIPGR LNQTTFTATR PGVYYGQCSE ICGANHSFMP IVLELIPLKI FEMGPVFTL

UniProtKB: Cytochrome c oxidase subunit 2

+
Macromolecule #4: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.003678 KDa
SequenceString: (FME)THQSHAYHM VKPSPWPLTG ALSALLMTSG LAMWFHFHSM TLLMLGLLTN TLTMYQWWRD VTRESTYQGH HTPPVQ KGL RYGMILFITS EVFFFAGFFW AFYHSSLAPT PQLGGHWPPT GITPLNPLEV PLLNTSVLLA SGVSITWAHH SLMENNR NQ MIQALLITIL ...String:
(FME)THQSHAYHM VKPSPWPLTG ALSALLMTSG LAMWFHFHSM TLLMLGLLTN TLTMYQWWRD VTRESTYQGH HTPPVQ KGL RYGMILFITS EVFFFAGFFW AFYHSSLAPT PQLGGHWPPT GITPLNPLEV PLLNTSVLLA SGVSITWAHH SLMENNR NQ MIQALLITIL LGLYFTLLQA SEYFESPFTI SDGIYGSTFF VATGFHGLHV IIGSTFLTIC FIRQLMFHFT SKHHFGFE A AAWYWHFVDV VWLFLYVSIY WWGS

UniProtKB: Cytochrome c oxidase subunit 3

+
Macromolecule #5: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.609758 KDa
SequenceString:
MLATRVFSLV GKRAISTSVC VRAHESVVKS EDFSLPAYMD RRDHPLPEVA HVKHLSASQK ALKEKEKASW SSLSMDEKVE LYRIKFKES FAEMNRGSNE WKTVVGGAMF FIGFTALVIM WQKHYVYGPL PQSFDKEWVA KQTKRMLDMK VNPIQGLASK W DYEKNEWK K

UniProtKB: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

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

MacromoleculeName: Cytochrome c oxidase subunit 5A, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.785178 KDa
SequenceString:
MLGAALRRCA VAATTRADPR GLLHSARTPG PAVAIQSVRC YSHGSQETDE EFDARWVTYF NKPDIDAWEL RKGINTLVTY DMVPEPKII DAALRACRRL NDFASTVRIL EVVKDKAGPH KEIYPYVIQE LRPTLNELGI STPEELGLDK V

UniProtKB: Cytochrome c oxidase subunit 5A, mitochondrial

+
Macromolecule #7: Cytochrome c oxidase subunit 5B, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 5B, mitochondrial / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.714709 KDa
SequenceString:
MASRLLRGAG TLAAQALRAR GPSGAAAMRS MASGGGVPTD EEQATGLERE IMLAAKKGLD PYNVLAPKGA SGTREDPNLV PSISNKRIV GCICEEDNTS VVWFWLHKGE AQRCPRCGAH YKLVPQQLAH

UniProtKB: Cytochrome c oxidase subunit 5B, mitochondrial

+
Macromolecule #8: Cytochrome c oxidase subunit 6A1, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 6A1, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.173858 KDa
SequenceString:
MAVVGVSSVS RLLGRSRPQL GRPMSSGAHG EEGSARMWKT LTFFVALPGV AVSMLNVYLK SHHGEHERPE FIAYPHLRIR TKPFPWGDG NHTLFHNPHV NPLPTGYEDE

UniProtKB: Cytochrome c oxidase subunit 6A1, mitochondrial

+
Macromolecule #9: Cytochrome c oxidase subunit 6B1

MacromoleculeName: Cytochrome c oxidase subunit 6B1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.204382 KDa
SequenceString:
MAEDMETKIK NYKTAPFDSR FPNQNQTRNC WQNYLDFHRC QKAMTAKGGD ISVCEWYQRV YQSLCPTSWV TDWDEQRAEG TFPGKI

UniProtKB: Cytochrome c oxidase subunit 6B1

+
Macromolecule #10: Cytochrome c oxidase subunit 6C

MacromoleculeName: Cytochrome c oxidase subunit 6C / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.798474 KDa
SequenceString:
MAPEVLPKPR MRGLLARRLR NHMAVAFVLS LGVAALYKFR VADQRKKAYA DFYRNYDVMK DFEEMRKAGI FQSVK

UniProtKB: Cytochrome c oxidase subunit 6C

+
Macromolecule #11: Cytochrome c oxidase subunit 7A2, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7A2, mitochondrial / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.409977 KDa
SequenceString:
MLRNLLALRQ IGQRTISTAS RRHFKNKVPE KQKLFQEDDE IPLYLKGGVA DALLYRATMI LTVGGTAYAI YELAVASFPK KQE

UniProtKB: Cytochrome c oxidase subunit 7A2, mitochondrial

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

MacromoleculeName: Cytochrome c oxidase subunit 7B, mitochondrial / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.172496 KDa
SequenceString:
MFPLVKSALN RLQVRSIQQT MARQSHQKRT PDFHDKYGNA VLASGATFCI VTWTYVATQV GIEWNLSPVG RVTPKEWRNQ

UniProtKB: Cytochrome c oxidase subunit 7B, mitochondrial

+
Macromolecule #13: Cytochrome c oxidase subunit 7C, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7C, mitochondrial / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.256501 KDa
SequenceString:
MLGQSIRRFT TSVVRRSHYE EGPGKNLPFS VENKWSLLAK MCLYFGSAFA TPFLVVRHQL LKT

UniProtKB: Cytochrome c oxidase subunit 7C, mitochondrial

+
Macromolecule #14: Cytochrome c oxidase subunit 8A, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 8A, mitochondrial / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.589089 KDa
SequenceString:
MSVLTPLLLR GLTGSARRLP VPRAKIHSLP PEGKLGIMEL AVGLTSCFVT FLLPAGWILS HLETYRRPE

UniProtKB: Cytochrome c oxidase subunit 8A, mitochondrial

+
Macromolecule #15: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 15 / Number of copies: 3 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

+
Macromolecule #16: MAGNESIUM ION

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

+
Macromolecule #17: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 17 / Number of copies: 4 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

+
Macromolecule #18: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 18 / Number of copies: 2 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

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

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

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

+
Macromolecule #20: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 20 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

+
Macromolecule #21: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 21 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMKClpotassium chloride
25.0 mMC8H18N2O4SHepes
20.0 mMMg(CH3COO)2Magnesium acetate
0.01 %C47H88O22LMNG

Details: 25 mM HEPES-KOH pH=7.5, 50 mM KCl, 20 mM Mg(OAc)2, 0.01% (v/v) LMNG, 0.001 % cardiolipin, 0.001 % GD, 0.1mM DTT
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 17476 / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5xte

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129242
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

-
Atomic model buiding 1

Initial modelPDB ID:

5z62


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9i6f:
Cryo-EM structure of HIGD2A bound complex IV

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more