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Yorodumi- PDB-8kc3: Cryo-EM structure of human C-terminally bound ATG9A-ATG2A-WIPI4 c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8kc3 | |||||||||
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Title | Cryo-EM structure of human C-terminally bound ATG9A-ATG2A-WIPI4 complex | |||||||||
Components |
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Keywords | LIPID TRANSPORT/MEMBRANE PROTEIN / Lipid transfer / ATG9A-ATG2A-WIPI4 complex / single particle cryo-EM / autophagy / LIPID TRANSPORT-MEMBRANE PROTEIN complex | |||||||||
Function / homology | Function and homology information phagophore / protein lipidation / lipid transfer activity / organelle membrane contact site / glycophagy / phosphatidylinositol phosphate binding / phospholipid scramblase activity / nucleophagy / programmed necrotic cell death / positive regulation of autophagosome assembly ...phagophore / protein lipidation / lipid transfer activity / organelle membrane contact site / glycophagy / phosphatidylinositol phosphate binding / phospholipid scramblase activity / nucleophagy / programmed necrotic cell death / positive regulation of autophagosome assembly / autophagy of mitochondrion / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phosphatidylinositol-3-phosphate binding / phagophore assembly site / bone morphogenesis / phosphatidylinositol-3,5-bisphosphate binding / reticulophagy / Macroautophagy / extrinsic component of membrane / autophagosome assembly / autophagosome / protein-membrane adaptor activity / cellular response to starvation / lipid droplet / mitochondrial membrane / trans-Golgi network / recycling endosome / autophagy / recycling endosome membrane / late endosome / late endosome membrane / endosome / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein kinase binding / Golgi apparatus / mitochondrion / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å | |||||||||
Authors | Wang, Y. / Stjepanovic, G. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Structural basis for lipid transfer by the ATG2A-ATG9A complex Authors: Wang, Y. / Stjepanovic, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kc3.cif.gz | 461.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kc3.ent.gz | 319.6 KB | Display | PDB format |
PDBx/mmJSON format | 8kc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kc3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8kc3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8kc3_validation.xml.gz | 86.1 KB | Display | |
Data in CIF | 8kc3_validation.cif.gz | 132.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/8kc3 ftp://data.pdbj.org/pub/pdb/validation_reports/kc/8kc3 | HTTPS FTP |
-Related structure data
Related structure data | 37091MC 8kbxC 8kbyC 8kbzC 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: 94551.031 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATG9A, APG9L1 / Production host: Homo sapiens (human) / References: UniProt: Q7Z3C6 #2: Protein | | Mass: 39916.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR45, WDRX1, WDRXI4, WIPI4, JM5 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q9Y484 #3: Protein | | Mass: 213100.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATG2A, KIAA0404 / Production host: Homo sapiens (human) / References: UniProt: Q2TAZ0 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: C-terminally bound ATG9A-ATG2A-WIPI4 complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.536 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1900 nm / Nominal defocus min: 1400 nm / C2 aperture diameter: 100 µm |
Image recording | Electron dose: 65.17 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116475 / Symmetry type: POINT |