|Entry||Database: EMDB / ID: 6251|
|Title||CH106 Fab in complex with BG505 SOSIP.664 Trimer|
|Map data||CH106 Fab in complex with BG505 SOSIP.664 Trimer|
|Sample||Fab of CH106 human monoclonal antibody bound to HIV-1 Env gp140 BG505 SOSIP.664:|
Soluble HIV-1 Envelope glycoprotein / Fab of CH106 human monoclonal antibody
|Keywords||HIV-1 / Fab / Env trimer|
|Source||Human immunodeficiency virus 1 (HIV-1) / Homo sapiens (human)|
|Method||single particle reconstruction / negative staining / 19 Å resolution|
|Authors||Ozorowski G / Derking R / Sanders RW / Ward AB|
|Citation||Journal: PLoS Pathog. / Year: 2015|
Title: Comprehensive antigenic map of a cleaved soluble HIV-1 envelope trimer.
Authors: Ronald Derking / Gabriel Ozorowski / Kwinten Sliepen / Anila Yasmeen / Albert Cupo / Jonathan L Torres / Jean-Philippe Julien / Jeong Hyun Lee / Thijs van Montfort / Steven W de Taeye / Mark Connors / Dennis R Burton / Ian A Wilson / Per-Johan Klasse / Andrew B Ward / John P Moore / Rogier W Sanders
|Date||Deposition: Jan 19, 2015 / Header (metadata) release: Mar 11, 2015 / Map release: Mar 11, 2015 / Last update: Aug 26, 2015|
|Structure viewer||EM map: |
Downloads & links
|File||emd_6251.map.gz (map file in CCP4 format, 16001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 2.05 Å|
CCP4 map header:
-Entire Fab of CH106 human monoclonal antibody bound to HIV-1 Env gp140 B...
|Entire||Name: Fab of CH106 human monoclonal antibody bound to HIV-1 Env gp140 BG505 SOSIP.664|
Details: Size-exclusion-chromatography-purified gp140 trimers were used.
Number of components: 2
Oligomeric State: One Fab molecule binds to one BG505 SOSIP.664 gp140 monomer
|Mass||Theoretical: 570 kDa|
-Component #1: protein, Soluble HIV-1 Envelope glycoprotein
|Protein||Name: Soluble HIV-1 Envelope glycoprotein / a.k.a: SOSIP / Oligomeric Details: Trimer / Number of Copies: 1 / Recombinant expression: Yes|
|Mass||Theoretical: 420 kDa|
|Source||Species: Human immunodeficiency virus 1 (HIV-1) / Strain: BG505|
|Source (engineered)||Expression System: Homo sapiens (human) / Vector: pPPI4 / Cell of expression system: HEK293F|
-Component #2: protein, Fab of CH106 human monoclonal antibody
|Protein||Name: Fab of CH106 human monoclonal antibody / Oligomeric Details: dimer (heavy chain + light chain) / Recombinant expression: Yes / Number of Copies: 3|
|Mass||Theoretical: 50 kDa|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Homo sapiens (human) / Cell of expression system: HEK293F|
|Specimen||Specimen state: particle / Method: negative staining|
|Sample solution||Specimen conc.: 0.01 mg/ml / Buffer solution: 50 mM Tris-HCl, pH 7.4, 150 mM NaCl / pH: 7.4|
|Support film||400 Cu mesh grid with carbon support, plasma-cleaned|
|Staining||3 uL of protein was applied and blotted; then 2% w/v uranyl formate was applied for 45 seconds.|
|Vitrification||Instrument: NONE / Cryogen name: NONE|
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 12 / Date: Sep 29, 2014|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 52000 X (nominal), 52000 X (calibrated)|
Astigmatism: Objective lens astigmatism was corrected at 52,000x magnification.
Imaging mode: BRIGHT FIELD / Defocus: 1000 nm
|Specimen Holder||Model: SIDE ENTRY, EUCENTRIC / Tilt Angle: -50 - 0 deg.|
|Camera||Detector: TVIPS TEMCAM-F416 (4k x 4k)|
|Image acquisition||Number of digital images: 143|
|Processing||Method: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 27144|
Details: The particles were selected using an automatic selection program. Class averages with 3 Fabs bound to one gp140 trimer were placed into a substack and used for 3D reconstruction.
|3D reconstruction||Algorithm: Cross-common lines, projection matching / Software: EMAN2, SPARX / Resolution: 19 Å / Resolution method: FSC 0.5, semi-independent|
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