|Entry||Database: PDB / ID: 3dik|
|Title||Pseudo-atomic model of the HIV-1 CA hexameric lattice|
|Descriptor||Capsid protein p24|
|Keywords||VIRAL PROTEIN / MATURE RETROVIRAL CAPSID / FULLERENE CONE / HEXAMER / AIDS / Aspartyl protease / Capsid maturation / Capsid protein / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Hydrolase / Lipoprotein / Magnesium / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / RNA-binding / RNA-directed DNA polymerase / Transferase / Viral nucleoprotein / Virion / Zinc-finger|
|Specimen source||Human immunodeficiency virus type 1 / virus|
|Method||Electron crystallography (9 Å resolution / 2d array / Crystallography)|
|Authors||Ganser-Pornillos, B.K. / Cheng, A. / Yeager, M.|
|Citation||Cell, 2007, 131, 70-79|
SummaryFull reportAbout validation report
|Date||Deposition: Jun 20, 2008 / Release: Sep 16, 2008|
Downloads & links
A: Capsid protein p24
Mass: 24498.084 Da / Num. of mol.: 1
Source: (gene. exp.) Human immunodeficiency virus type 1 / virus
References: UniProt: P12497
|Experiment||Method: ELECTRON CRYSTALLOGRAPHY|
|EM experiment||Aggregation state: 2D ARRAY / Reconstruction method: CRYSTALLOGRAPHY|
|Buffer solution||Name: 17.5%(w/v) PEG 20,000, 50mM Na Cacodylate, 100mM Calcium Acetate|
Details: 17.5%(w/v) PEG 20,000, 50mM Na Cacodylate, 100mM Calcium Acetate
|Specimen||Conc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Details: Carbon coated molybdenum grids|
|Vitrification||Cryogen name: ETHANE|
Details: Washed with 0.1M KCl, blotted briefly, and plunged into liquid ethane
Model: Tecnai F20 / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TECNAI F20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: OTHER|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 52000 / Nominal defocus max: 1500 nm / Nominal defocus min: 400 nm / Cs: 2 mm|
|Specimen holder||Temperature: 90 kelvins / Tilt angle max: 40.3 deg. / Tilt angle min: 0 deg.|
|Image recording||Electron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM|
|Radiation||Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: electron|
|Radiation wavelength||Relative weight: 1|
|3D reconstruction||Method: 2D crystallography / Resolution: 9 Å|
Details: THIS MODDEL CONTAINS CA ATOMS ONLY. THE TWO DOMAINS UNP RESIDUES 133-280 AND UNP RESIDUES 281-351 WERE ALLOWED TO MOVE INDEPENDENTLY. THAT IS WHY THE CONNECTIVITY BETWEEN THEM IS NOT WELL-PRESERVED. MRC AND CCP4 PROGRAMS WERE USED.
Symmetry type: 2D CRYSTAL
|Atomic model building||Details: REFINEMENT PROTOCOL--RIGID BODY / Ref protocol: RIGID BODY FIT / Ref space: REAL|
|Atomic model building|
|Number of atoms included #LAST||Protein: 219 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 219|
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