+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37088 | |||||||||
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Title | Cryo-EM structure of human ATG9A in LMNG micelles | |||||||||
Map data | The autophagy relate transmembrane protein ATG9A, lipid scramblase | |||||||||
Sample |
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Keywords | Lipid scramblase / ATG9A / single particle cryo-EM / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information phospholipid scramblase activity / programmed necrotic cell death / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / bone morphogenesis / reticulophagy / Macroautophagy / autophagosome assembly ...phospholipid scramblase activity / programmed necrotic cell death / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / bone morphogenesis / reticulophagy / Macroautophagy / autophagosome assembly / autophagosome / trans-Golgi network / mitochondrial membrane / recycling endosome / recycling endosome membrane / late endosome / late endosome membrane / endosome / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.97 Å | |||||||||
Authors | Yang W / Goran S | |||||||||
Funding support | China, 2 items
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Citation | Journal: To Be Published Title: Structural basis for lipid transfer by the ATG2A-ATG9A complex Authors: Yang W / Goran S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37088.map.gz | 726.9 MB | EMDB map data format | |
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Header (meta data) | emd-37088-v30.xml emd-37088.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37088_fsc.xml | 20 KB | Display | FSC data file |
Images | emd_37088.png | 68.6 KB | ||
Filedesc metadata | emd-37088.cif.gz | 5.6 KB | ||
Others | emd_37088_half_map_1.map.gz emd_37088_half_map_2.map.gz | 764.8 MB 764.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37088 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37088 | HTTPS FTP |
-Validation report
Summary document | emd_37088_validation.pdf.gz | 633.7 KB | Display | EMDB validaton report |
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Full document | emd_37088_full_validation.pdf.gz | 633.2 KB | Display | |
Data in XML | emd_37088_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | emd_37088_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37088 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37088 | HTTPS FTP |
-Related structure data
Related structure data | 8kbzMC 8kbxC 8kbyC 8kc3C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_37088.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | The autophagy relate transmembrane protein ATG9A, lipid scramblase | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A of ATG9A
File | emd_37088_half_map_1.map | ||||||||||||
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Annotation | Half map A of ATG9A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of ATG9A
File | emd_37088_half_map_2.map | ||||||||||||
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Annotation | Half map B of ATG9A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ATG9A trimer
Entire | Name: ATG9A trimer |
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Components |
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-Supramolecule #1: ATG9A trimer
Supramolecule | Name: ATG9A trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 283 KDa |
-Macromolecule #1: Autophagy-related protein 9A
Macromolecule | Name: Autophagy-related protein 9A / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 94.551031 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAQFDTEYQR LEASYSDSPP GEEDLLVHVA EGSKSPWHHI ENLDLFFSRV YNLHQKNGFT CMLIGEIFEL MQFLFVVAFT TFLVSCVDY DILFANKMVN HSLHPTEPVK VTLPDAFLPA QVCSARIQEN GSLITILVIA GVFWIHRLIK FIYNICCYWE I HSFYLHAL ...String: MAQFDTEYQR LEASYSDSPP GEEDLLVHVA EGSKSPWHHI ENLDLFFSRV YNLHQKNGFT CMLIGEIFEL MQFLFVVAFT TFLVSCVDY DILFANKMVN HSLHPTEPVK VTLPDAFLPA QVCSARIQEN GSLITILVIA GVFWIHRLIK FIYNICCYWE I HSFYLHAL RIPMSALPYC TWQEVQARIV QTQKEHQICI HKRELTELDI YHRILRFQNY MVALVNKSLL PLRFRLPGLG EA VFFTRGL KYNFELILFW GPGSLFLNEW SLKAEYKRGG QRLELAQRLS NRILWIGIAN FLLCPLILIW QILYAFFSYA EVL KREPGA LGARCWSLYG RCYLRHFNEL EHELQSRLNR GYKPASKYMN CFLSPLLTLL AKNGAFFAGS ILAVLIALTI YDED VLAVE HVLTTVTLLG VTVTVCRSFI PDQHMVFCPE QLLRVILAHI HYMPDHWQGN AHRSQTRDEF AQLFQYKAVF ILEEL LSPI VTPLILIFCL RPRALEIIDF FRNFTVEVVG VGDTCSFAQM DVRQHGHPQW LSAGQTEASV YQQAEDGKTE LSLMHF AIT NPGWQPPRES TAFLGFLKEQ VQRDGAAASL AQGGLLPENA LFTSIQSLQS ESEPLSLIAN VVAGSSCRGP PLPRDLQ GS RHRAEVASAL RSFSPLQPGQ APTGRAHSTM TGSGVDARTA SSGSSVWEGQ LQSLVLSEYA STEMSLHALY MHQLHKQQ A QAEPERHVWH RRESDESGES APDEGGEGAR APQSIPRSAS YPCAAPRPGA PETTALHGGF QRRYGGITDP GTVPRVPSH FSRLPLGGWA EDGQSASRHP EPVPEEGSED ELPPQVHKV UniProtKB: Autophagy-related protein 9A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.17 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |