|Entry||Database: EMDB / ID: 8582|
|Title||Structure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM|
|Source||Human immunodeficiency virus 1 / virus / HIV|
|Map data||CryoEM structure of HIV-1 capsid protein and spacer peptide-1 (CA-SP1)|
|Method||helical reconstruction, at 9 Å resolution|
|Authors||Zhang P / Randall S|
|Citation||Nat Commun, 2017, 8, 1779-1779|
Nat Commun, 2017, 8, 1779-1779 Yorodumi Papers
|Validation Report||PDB-ID: 5up4|
SummaryFull reportAbout validation report
|Date||Deposition: Feb 1, 2017 / Header (metadata) release: Jul 12, 2017 / Map release: Dec 6, 2017 / Last update: Dec 13, 2017|
Downloads & links
|File||emd_8582.map.gz (map file in CCP4 format, 488096 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.1 Å|
CCP4 map header:
-Entire HIV-1 CA-SP1
|Entire||Name: HIV-1 CA-SP1 / Number of components: 2|
-Component #1: protein, HIV-1 CA-SP1
|Protein||Name: HIV-1 CA-SP1 / Recombinant expression: No|
|Source||Species: Human immunodeficiency virus 1 / virus / HIV|
|Source (engineered)||Expression System: Escherichia coli / bacteria / /|
-Component #2: protein, HIV-1 Capsid Protein and spacer peptide 1
|Protein||Name: HIV-1 Capsid Protein and spacer peptide 1 / Recombinant expression: No|
|Mass||Theoretical: 24.654268 kDa|
|Source (engineered)||Expression System: Human immunodeficiency virus 1 / virus / HIV|
|Specimen state||helical array|
|Helical parameters||Axial symmetry: C1 (asymmetric) / Delta z: 13.46 Å / Delta phi: 128.88 deg.|
|Sample solution||Specimen conc.: 2.2 mg/ml / pH: 8|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 90 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 23 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 59000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm|
|Specimen Holder||Model: OTHER|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 200|
|Processing||Method: helical reconstruction|
|3D reconstruction||Software: FREALIGN / Resolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution assessment)|
-Atomic model buiding
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
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