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Yorodumi- EMDB-27629: Helical reconstruction of A92E HIV capsid in presence of FG mutan... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27629 | |||||||||
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Title | Helical reconstruction of A92E HIV capsid in presence of FG mutant CPSF6 construct | |||||||||
Map data | Helical reconstruction of A92E HIV capsid in presence of FG mutant CPSF6 construct | |||||||||
Sample |
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Keywords | Complex / VIRAL PROTEIN | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 7.0 Å | |||||||||
Authors | Iqbal N / Asturias F / Kvaratskhelia M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Helical reconstruction of A92E HIV capsid in presence of FG mutant CPSF6 construct Authors: Iqbal N / Asturias F / Kvaratskhelia M | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27629.map.gz | 80.4 MB | EMDB map data format | |
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Header (meta data) | emd-27629-v30.xml emd-27629.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27629_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_27629.png | 64.4 KB | ||
Others | emd_27629_half_map_1.map.gz emd_27629_half_map_2.map.gz | 80.8 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27629 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27629 | HTTPS FTP |
-Validation report
Summary document | emd_27629_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_27629_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_27629_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | emd_27629_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27629 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27629 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27629.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Helical reconstruction of A92E HIV capsid in presence of FG mutant CPSF6 construct | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map 1
File | emd_27629_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_27629_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HIV Capsid Protein Hexamer
Entire | Name: HIV Capsid Protein Hexamer |
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Components |
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-Supramolecule #1: HIV Capsid Protein Hexamer
Supramolecule | Name: HIV Capsid Protein Hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
-Macromolecule #1: HIV Capsid
Macromolecule | Name: HIV Capsid / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: PIVQNLQGQM VHQCISPRTL NAWVKVVEEK AFSPEVIPMF SALSCGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAGP IAPGQMREPR GSDIAGTTST LQEQIGWMTH NPPIPVGEIY KRWIILGLNK IVRMYSPTSI LDIRQGPKEP FRDYVDRFYK ...String: PIVQNLQGQM VHQCISPRTL NAWVKVVEEK AFSPEVIPMF SALSCGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAGP IAPGQMREPR GSDIAGTTST LQEQIGWMTH NPPIPVGEIY KRWIILGLNK IVRMYSPTSI LDIRQGPKEP FRDYVDRFYK TLRAEQASQE VKNAATETLL VQNANPDCKT ILKALGPGAT LEEMMTACQG VGGPGHKARV L |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | 3D array |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 8 / Details: 1M NaCl, 50mM Tris pH 8, 0.2mM IP6 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 2157 / Average electron dose: 45.65 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 28000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 28000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |