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Yorodumi- PDB-8aw5: Cryo-EM structure of heme A synthase trimer from Aquifex aeolicus -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aw5 | |||||||||
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Title | Cryo-EM structure of heme A synthase trimer from Aquifex aeolicus | |||||||||
Components | Heme O oxygenase | |||||||||
Keywords | MEMBRANE PROTEIN / Heme A synthase / Oligomerization / Function / Heme A | |||||||||
Function / homology | COX15/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 species | Aquifex aeolicus VF5 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Hui, Z. / Guoliang, Z. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Cryo-EM structure of heme A synthase trimer from Aquifex aeolicus Authors: Hui, Z. / Guoliang, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aw5.cif.gz | 162.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aw5.ent.gz | 130.4 KB | Display | PDB format |
PDBx/mmJSON format | 8aw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aw5_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8aw5_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8aw5_validation.xml.gz | 43.3 KB | Display | |
Data in CIF | 8aw5_validation.cif.gz | 56.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/8aw5 ftp://data.pdbj.org/pub/pdb/validation_reports/aw/8aw5 | HTTPS FTP |
-Related structure data
Related structure data | 15691MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 | #3: Chemical | ChemComp-POV / ( Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Heme A synthase with cofactor Heme B / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Source (natural) | Organism: Aquifex aeolicus VF5 (bacteria) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: Top10 | |||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Homemade | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1100 nm / Calibrated defocus min: 1200 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 70 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 462000 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72435 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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