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- EMDB-52662: Cryo-EM structure of NDUFA4 bound complex IV within the respiraso... -

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Basic information

Entry
Database: EMDB / ID: EMD-52662
TitleCryo-EM structure of NDUFA4 bound complex IV within the respirasome complex
Map data
Sample
  • Cell: NDUFA4 bound complex IV
    • Protein or peptide: x 14 types
  • Ligand: x 7 types
KeywordsMitochondria / human / respirasome / cytochrome c oxidase / complex IV / NDUFA4 / assembly / 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 / mitochondrial electron transport, NADH to ubiquinone / response to electrical stimulus / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / 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 / protein-containing complex binding / mitochondrion / nucleoplasm / metal ion binding / membrane / cytosol
Similarity search - Function
NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / 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 ...NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / 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 NDUFA4 / 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 NDUFA4 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsNguyen MD / Singh V / Rorbach J
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation02305053 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 / Rorbach J
History
DepositionFeb 2, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52662.png

Downloads & links

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Map

FileDownload / File: emd_52662.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.08
Minimum - Maximum-33.845640000000003 - 50.317883000000002
Average (Standard dev.)0.000000000000403 (±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 °

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Supplemental data

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Half map: #2

Fileemd_52662_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_52662_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : NDUFA4 bound complex IV

EntireName: NDUFA4 bound complex IV
Components
  • Cell: NDUFA4 bound complex IV
    • 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
    • Protein or peptide: Cytochrome c oxidase subunit NDUFA4
  • Ligand: COPPER (II) ION
  • Ligand: MAGNESIUM ION
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: HEME-A
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: ZINC ION
  • Ligand: CARDIOLIPIN

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Supramolecule #1: NDUFA4 bound complex IV

SupramoleculeName: NDUFA4 bound complex IV / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Homo sapiens (human)

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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: 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

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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: 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

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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: 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

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

MacromoleculeName: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
type: protein_or_peptide / ID: 4 / 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

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

MacromoleculeName: Cytochrome c oxidase subunit 5A, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: 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

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Macromolecule #6: Cytochrome c oxidase subunit 5B, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 5B, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: 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

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Macromolecule #7: Cytochrome c oxidase subunit 6A1, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 6A1, mitochondrial / type: protein_or_peptide / ID: 7 / 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

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Macromolecule #8: Cytochrome c oxidase subunit 6B1

MacromoleculeName: Cytochrome c oxidase subunit 6B1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.204382 KDa
SequenceString:
MAEDMETKIK NYKTAPFDSR FPNQNQTRNC WQNYLDFHRC QKAMTAKGGD ISVCEWYQRV YQSLCPTSWV TDWDEQRAEG TFPGKI

UniProtKB: Cytochrome c oxidase subunit 6B1

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Macromolecule #9: Cytochrome c oxidase subunit 6C

MacromoleculeName: Cytochrome c oxidase subunit 6C / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.798474 KDa
SequenceString:
MAPEVLPKPR MRGLLARRLR NHMAVAFVLS LGVAALYKFR VADQRKKAYA DFYRNYDVMK DFEEMRKAGI FQSVK

UniProtKB: Cytochrome c oxidase subunit 6C

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Macromolecule #10: Cytochrome c oxidase subunit 7A2, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7A2, mitochondrial / type: protein_or_peptide / ID: 10 / 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

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Macromolecule #11: Cytochrome c oxidase subunit 7B, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7B, mitochondrial / type: protein_or_peptide / ID: 11 / 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

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Macromolecule #12: Cytochrome c oxidase subunit 7C, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7C, mitochondrial / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.256501 KDa
SequenceString:
MLGQSIRRFT TSVVRRSHYE EGPGKNLPFS VENKWSLLAK MCLYFGSAFA TPFLVVRHQL LKT

UniProtKB: Cytochrome c oxidase subunit 7C, mitochondrial

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Macromolecule #13: Cytochrome c oxidase subunit 8A, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 8A, mitochondrial / type: protein_or_peptide / ID: 13 / 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

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Macromolecule #14: Cytochrome c oxidase subunit NDUFA4

MacromoleculeName: Cytochrome c oxidase subunit NDUFA4 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.38184 KDa
SequenceString:
MLRQIIGQAK KHPSLIPLFV FIGTGATGAT LYLLRLALFN PDVCWDRNNP EPWNKLGPND QYKFYSVNVD YSKLKKERPD F

UniProtKB: Cytochrome c oxidase subunit NDUFA4

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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

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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: (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: 17 / 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

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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

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Macromolecule #19: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 19 / 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

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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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Macromolecule #21: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 21 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5z62

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109624
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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