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- EMDB-1970: Negative stained image reconstruction of HIV spike protein in com... -

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Basic information

Entry
Database: EMDB / ID: 1970
TitleNegative stained image reconstruction of HIV spike protein in complex with PGT128 Fab at 14 Angstrom resolution
KeywordsHIV / broadly neutralizing antibody / glycan shield
SampleHIV spike protein 664G construct in complex with Fab fragment of PGT128 monoclonal antibody
SourceHuman immunodeficiency virus / virus / Spike protien
Homo sapiens / human
Map dataHIV Envelope protein in complex with Fab PGT128
Methodsingle particle reconstruction, at 14 A resolution
AuthorsKhayat R / Pejchal R / Julien J-P / Wilson IA
CitationScience, 2011, 334, 1097-1103

Science, 2011, 334, 1097-1103 StrPapers
A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield.
Robert Pejchal / Katie J Doores / Laura M Walker / Reza Khayat / Po-Ssu Huang / Sheng-Kai Wang / Robyn L Stanfield / Jean-Philippe Julien / Alejandra Ramos / Max Crispin / Rafael Depetris / Umesh Katpally / Andre Marozsan / Albert Cupo / Sebastien Maloveste / Yan Liu / Ryan McBride / Yukishige Ito / Rogier W Sanders / Cassandra Ogohara / James C Paulson / Ten Feizi / Christopher N Scanlan / Chi-Huey Wong / John P Moore / William C Olson / Andrew B Ward / Pascal Poignard / William R Schief / Dennis R Burton / Ian A Wilson

DateDeposition: Sep 25, 2011 / Header (metadata) release: Oct 20, 2011 / Map release: Oct 21, 2011 / Last update: Sep 25, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1970.map.gz (map file in CCP4 format, 16001 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
2.18 A/pix
= 348.8 A
160 pix
2.18 A/pix
= 348.8 A
160 pix
2.18 A/pix
= 348.8 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.18 A
Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-1.63715 - 3.57025
Average (Standard dev.)0.0105322 (0.257004)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin000
Limit159159159
Spacing160160160
CellA=B=C: 348.8 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.182.182.18
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z348.800348.800348.800
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-1.6373.5700.011

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Supplemental data

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Sample components

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Entire HIV spike protein 664G construct in complex with Fab fragment of ...

EntireName: 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
MassExperimental: 445 kDa
Measured by: Size exclusion chromatography and light scattering

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Component #1: protein, Human immunodeficiency virus envelope protein

ProteinName: 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
SourceSpecies: Human immunodeficiency virus / virus / Spike protien
Strain: KNH1144 SOSIP 664G
Source (engineered)Expression System: 293s / Vector: pP14

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Component #2: protein, PGT128 monoclonal antibody fragment

ProteinName: PGT128 monoclonal antibody fragment / a.k.a: Fab fragment / Oligomeric Details: Monomer / Recombinant expression: No
SourceSpecies: Homo sapiens / human

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml / Buffer solution: 20 mM HEPES pH 7.5, 50 mM NaCl / pH: 7.5
Support film400 mesh copper grid
Staining2% Uranyl Formate for 30 seconds
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20 / Date: Aug 11, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 16 e/A2 / Electron beam tilt params: -2 mrad / Illumination mode: FLOOD BEAM
LensMagnification: 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 HolderHolder: eucentric / Model: SIDE ENTRY, EUCENTRIC / Tilt Angle: 0 - 55 deg. / Temperature: 293 K ( 293 - 293 K)
CameraDetector: GENERIC GATAN (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 357 / Sampling size: 0.109 microns / Bit depth: 16 / Details: Data collected on CCD

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Image processing

ProcessingMethod: 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 reconstructionAlgorithm: Cros-common lines / Euler angles: SPIDER:theta 90 degrees, phi 120 degrees / Software: Sparx / CTF correction: Micrograph and each particle / Resolution: 14 A / Resolution method: FSC 0.5

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