|Entry||Database: EMDB / ID: 1970|
|Title||Negative stained image reconstruction of HIV spike protein in complex with PGT128 Fab at 14 Angstrom resolution|
|Keywords||HIV / broadly neutralizing antibody / glycan shield|
|Sample||HIV spike protein 664G construct in complex with Fab fragment of PGT128 monoclonal antibody|
|Source||Human immunodeficiency virus / virus / Spike protien|
Homo sapiens / human
|Map data||HIV Envelope protein in complex with Fab PGT128|
|Method||single particle reconstruction, at 14 Å resolution|
|Authors||Khayat R / Pejchal R / Julien J-P / Wilson IA|
|Citation||Science, 2011, 334, 1097-1103|
Science, 2011, 334, 1097-1103 Yorodumi Papers
|Date||Deposition: Sep 25, 2011 / Header (metadata) release: Oct 20, 2011 / Map release: Oct 21, 2011 / Last update: Oct 21, 2011|
Downloads & links
|File||emd_1970.map.gz (map file in CCP4 format, 16001 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.18 Å|
CCP4 map header:
-Entire HIV spike protein 664G construct in complex with Fab fragment of ...
|Entire||Name: HIV spike protein 664G construct in complex with Fab fragment of PGT128 monoclonal antibody|
Details: The sample was monodisperse / Number of components: 2 / Oligomeric State: One trimer binds to three Fabs
|Mass||Experimental: 445 kDa|
Measured by: Size exclusion chromatography and light scattering
-Component #1: protein, Human immunodeficiency virus envelope protein
|Protein||Name: Human immunodeficiency virus envelope protein / a.k.a: Spike protein / Oligomeric Details: Trimer|
Details: The PGT128 Fab was complexed to the spike protein, partially deglycosylated, purified using size exclusion chromatography, and concentrated.
Number of Copies: 3 / Recombinant expression: Yes
|Source||Species: Human immunodeficiency virus / virus / Spike protien|
Strain: KNH1144 SOSIP 664G
|Source (engineered)||Expression System: 293s / Vector: pP14|
-Component #2: protein, PGT128 monoclonal antibody fragment
|Protein||Name: PGT128 monoclonal antibody fragment / a.k.a: Fab fragment / Oligomeric Details: Monomer / Recombinant expression: No|
|Source||Species: Homo sapiens / human|
|Sample solution||Specimen conc.: 0.1 mg/ml / Buffer solution: 20 mM HEPES pH 7.5, 50 mM NaCl / pH: 7.5|
|Support film||400 mesh copper grid|
|Staining||2% Uranyl Formate for 30 seconds|
|Vitrification||Instrument: NONE / Cryogen name: NONE|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20 / Date: Aug 11, 2011|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 16 e/Å2 / Electron beam tilt params: -2 mrad / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 100000 X (nominal)|
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 400 - 950 nm
|Specimen Holder||Holder: eucentric / Model: SIDE ENTRY, EUCENTRIC / Tilt Angle: 0 - 55 deg. / Temperature: 293 K ( 293 - 293 K)|
|Camera||Detector: GENERIC GATAN (4k x 4k)|
|Image acquisition||Number of digital images: 357 / Sampling size: 0.109 microns / Bit depth: 16 / Details: Data collected on CCD|
|Processing||Method: single particle reconstruction / Number of class averages: 62 / Number of projections: 12824|
Details: The particles were selected using an DoG Picker, and cleaned using reference free class averaging.
Applied symmetry: C3 (3 fold cyclic)
|3D reconstruction||Algorithm: Cros-common lines / Euler angles: SPIDER:theta 90 degrees, phi 120 degrees / Software: Sparx / CTF correction: Micrograph and each particle / Resolution: 14 Å / Resolution method: FSC 0.5|
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