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- EMDB-6251: CH106 Fab in complex with BG505 SOSIP.664 Trimer -

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Basic information

Database: EMDB / ID: 6251
TitleCH106 Fab in complex with BG505 SOSIP.664 Trimer
Map dataCH106 Fab in complex with BG505 SOSIP.664 Trimer
SampleFab 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
KeywordsHIV-1 / Fab / Env trimer
SourceHuman immunodeficiency virus 1 (HIV-1) / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / 19 Å resolution
AuthorsOzorowski G / Derking R / Sanders RW / Ward AB
CitationJournal: 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
DateDeposition: Jan 19, 2015 / Header (metadata) release: Mar 11, 2015 / Map release: Mar 11, 2015 / Last update: Aug 26, 2015

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 14
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 14
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_6251.map.gz (map file in CCP4 format, 16001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
2.05 Å/pix.
= 328. Å
160 pix
2.05 Å/pix.
= 328. Å
160 pix
2.05 Å/pix.
= 328. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Contour Level:14 (by author), 14 (movie #1):
Minimum - Maximum-29.90282059 - 78.88714600
Average (Standard dev.)0.36066312 (5.82088995)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 328.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-29.90378.8870.361

Supplemental data

Sample components

Entire Fab of CH106 human monoclonal antibody bound to HIV-1 Env gp140 B...

EntireName: 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
MassTheoretical: 570 kDa

Component #1: protein, Soluble HIV-1 Envelope glycoprotein

ProteinName: Soluble HIV-1 Envelope glycoprotein / a.k.a: SOSIP / Oligomeric Details: Trimer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 420 kDa
SourceSpecies: 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

ProteinName: Fab of CH106 human monoclonal antibody / Oligomeric Details: dimer (heavy chain + light chain) / Recombinant expression: Yes / Number of Copies: 3
MassTheoretical: 50 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293F

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.01 mg/ml / Buffer solution: 50 mM Tris-HCl, pH 7.4, 150 mM NaCl / pH: 7.4
Support film400 Cu mesh grid with carbon support, plasma-cleaned
Staining3 uL of protein was applied and blotted; then 2% w/v uranyl formate was applied for 45 seconds.
VitrificationInstrument: NONE / Cryogen name: NONE

Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12 / Date: Sep 29, 2014
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 52000 X (nominal), 52000 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 52,000x magnification.
Imaging mode: BRIGHT FIELD / Defocus: 1000 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC / Tilt Angle: -50 - 0 deg.
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 143

Image processing

ProcessingMethod: 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 reconstructionAlgorithm: Cross-common lines, projection matching / Software: EMAN2, SPARX / Resolution: 19 Å / Resolution method: FSC 0.5, semi-independent

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