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- EMDB-15691: Cryo-EM structure of heme A synthase trimer from Aquifex aeolicus -

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Basic information

Entry
Database: EMDB / ID: EMD-15691
TitleCryo-EM structure of heme A synthase trimer from Aquifex aeolicus
Map data
Sample
  • Complex: Heme A synthase with cofactor Heme B
    • Protein or peptide: Heme O oxygenase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
KeywordsHeme A synthase / Oligomerization / Function / Heme A / MEMBRANE PROTEIN
Function / homologyCOX15/CtaA family / Cytochrome oxidase assembly protein / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / heme A biosynthetic process / membrane / Heme O oxygenase
Function and homology information
Biological speciesAquifex aeolicus VF5 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHui Z / Guoliang Z
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Max Planck Society
CitationJournal: To Be Published
Title: Cryo-EM structure of heme A synthase trimer from Aquifex aeolicus
Authors: Hui Z / Guoliang Z
History
DepositionAug 29, 2022-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15691.png

Downloads & links

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Map

FileDownload / File: emd_15691.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 256 pix.
= 314.88 Å		1.23 Å/pix.
x 256 pix.
= 314.88 Å		1.23 Å/pix.
x 256 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0488
Minimum - Maximum-0.14577729 - 0.30360663
Average (Standard dev.)0.00014899936 (±0.004071076)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15691_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15691_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15691_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Heme A synthase with cofactor Heme B

EntireName: Heme A synthase with cofactor Heme B
Components
  • Complex: Heme A synthase with cofactor Heme B
    • Protein or peptide: Heme O oxygenase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate

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Supramolecule #1: Heme A synthase with cofactor Heme B

SupramoleculeName: Heme A synthase with cofactor Heme B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)

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Macromolecule #1: Heme O oxygenase

MacromoleculeName: Heme O oxygenase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria) / Strain: VF5
Molecular weightTheoretical: 34.984523 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GMNTNLKSSP LKTLVLASVV LTYVLMVFGG IVTSTGSGLG CPDWPLCHGQ LLPFQLKEQI PTPPAPVVAP TPLQPWIEQT HRILGGITG IVLLATLFYA FKRGTSFVKK ALVFIFIALI LEALLGMRVV ITEAPLLREL LHYVYTSAHL ILSVFILSTI T ITYYYVKF ...String:
GMNTNLKSSP LKTLVLASVV LTYVLMVFGG IVTSTGSGLG CPDWPLCHGQ LLPFQLKEQI PTPPAPVVAP TPLQPWIEQT HRILGGITG IVLLATLFYA FKRGTSFVKK ALVFIFIALI LEALLGMRVV ITEAPLLREL LHYVYTSAHL ILSVFILSTI T ITYYYVKF FGERPKEYIP YADALYVATM FQILLGIFVR YVKALEYNQF VYYLHITYAG FLVILSLFIM FKEFNKYSLI TF LLMTAQI LAGVATVISG FFLPYLFLHI AIGFFIVLWV SYLVAPSVLK TYTEFRGELA RNSSAWSHPQ FEK

UniProtKB: Heme O oxygenase

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 3 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 3 / Number of copies: 9 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration3.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaclsodium chloride
20.0 mMTris-HClTris hydrochloride
GridModel: Homemade / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsCalibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 165000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 462000
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6a2j

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72435
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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