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- PDB-8aw5: Cryo-EM structure of heme A synthase trimer from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 8aw5
TitleCryo-EM structure of heme A synthase trimer from Aquifex aeolicus
ComponentsHeme O oxygenase
KeywordsMEMBRANE PROTEIN / Heme A synthase / Oligomerization / Function / Heme A
Function / homologyCOX15/CtaA family / Cytochrome oxidase assembly protein / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / heme A biosynthetic process / membrane / PROTOPORPHYRIN IX CONTAINING FE / Chem-POV / Heme O oxygenase
Function and homology information
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHui, Z. / Guoliang, Z.
Funding support China, 2items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme O oxygenase
B: Heme O oxygenase
C: Heme O oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,64415
Polymers104,9543
Non-polymers8,69012
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area12430 Å2
ΔGint-149 kcal/mol
Surface area35850 Å2

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Components

#1: Protein Heme O oxygenase


Mass: 34984.523 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: ctaA, aq_153 / Production host: Escherichia coli (E. coli) / References: UniProt: O66543
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C42H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Heme A synthase with cofactor Heme B / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Top10
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNacl1
220 mMTris hydrochlorideTris-HCl1
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Homemade
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1100 nm / Calibrated defocus min: 1200 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 70 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 462000
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72435 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047221
ELECTRON MICROSCOPYf_angle_d0.6639792
ELECTRON MICROSCOPYf_dihedral_angle_d15.3422667
ELECTRON MICROSCOPYf_chiral_restr0.0371128
ELECTRON MICROSCOPYf_plane_restr0.0031068

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