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Negative stained image reconstruction of HIV spike protein in complex with PGT128 Fab at 14 Angstrom resolution

by single particle reconstruction, at 14.0 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1970
AuthorsKhayat R, Pejchal R, Julien J-P, Wilson IA
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1, Made by UCSF CHIMERA

Supplemental images

1970.png
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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Diagram

EMDB-2305

EMDB-2304

EMDB-2173

EMDB-1977
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleScience, Vol. 334, Issue 6059, Page 1097-103, Year 2011
TitleA potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield.
AuthorsRobert 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
Department of Molecular Biology, Skaggs Institute for Chemical Biology and International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, nhe Scripps Research Institute, La Jolla, CA 92037, USA.
KeywordsAntibodies, Neutralizing (chemistry), Antibody Specificity, Binding Sites, Antibody, Carbohydrate Conformation, Cell Line, Crystallography, X-Ray, Disaccharides (chemistry), Epitopes, Glycosylation, HIV Antibodies (chemistry), HIV Envelope Protein gp120 (chemistry), HIV-1 (immunology), Humans, Hydrogen Bonding, Immunoglobulin Fab Fragments (chemistry), Mannose (chemistry, 31103-86-3), Mannosides (chemistry), Models, Molecular, Mutation, Oligosaccharides (chemistry), Polysaccharides (chemistry), Protein Conformation, Protein Structure, Tertiary, mannosyl alpha(1-6)-mannoside
LinksDOI: 10.1126/science.1213256, PubMed: 21998254, PMC: PMC3280215
Map
FileEMD-1970.map ( map file in CCP4 format, 16386 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:1.0 (by author), 1 (movie #1):
Minimum - Maximum: -1.63715 - 3.57025
Average (Standard dev.): 0.0105322 (0.257004)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 160 160 160
Origin : 0 0 0
Limit : 159 159 159
Spacing : 160 160 160
Unit CellA = 348.8 A , B = 348.8 A , C = 348.8 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 2.18 A , Y = 2.18 A , Z = 2.18 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.6373.5700.011
Annotation DetailsHIV Envelope protein in complex with Fab PGT128
Supplement
Images
Images

1970.png
Sample
NameHIV spike protein 664G construct in complex with Fab fragment of PGT128 monoclonal antibody
Number of Components2
Oligomeric StateOne trimer binds to three Fabs
DetailsThe sample was monodisperse
Mass-estimation MethodSize exclusion chromatography and light scattering
Experimental Mass0.445 MDa
Component #1: protein - Spike protein
Scientific nameHuman immunodeficiency virus envelope protein
Common NameSpike protein
DetailsThe PGT128 Fab was complexed to the spike protein, partially deglycosylated, purified using size exclusion chromatography, and concentrated.
Oligomeric DetailsTrimer
Number of Copies3
Scientific Name of SpeciesHuman immunodeficiency virus (NCBI Taxonomy: 12721)
Common Name of SpeciesSpike protien
StrainKNH1144 SOSIP 664G
Recombinant expressionYes
Engineered SourceExp System: 293S
Vector: pP14
Component #2: protein - Fab fragment
Scientific namePGT128 monoclonal antibody fragment
Common NameFab fragment
Oligomeric DetailsMonomer
Scientific Name of SpeciesHomo sapiens (NCBI Taxonomy: 9606)
Common Name of SpeciesHuman
Recombinant expressionNo
Experiment
Sample Preparation
Staining2% Uranyl Formate for 30 seconds
Specimen Conc0.1 mg/ml
Specimen Support Details400 mesh copper grid
Specimen Stateparticle
BufferDetails: 20 mM HEPES pH 7.5, 50 mM NaCl
pH: 7.5
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI F20
Date11-AUG-2011
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Electron Dose16 e/A**2
Electron Beam Tilt Params-2 mrad
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 100000 X,
AstigmatismObjective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs2.0 mm
Imaging ModeBRIGHT FIELD
Defocus400 nm - 950 nm
Specimen Holder
Holdereucentric ( SIDE ENTRY, EUCENTRIC )
Tilt Angle0 degrees - 55 degrees
Temperature293 Kelvin ( 293 Kelvin - 293 Kelvin )
Camera
DetectorGatan 4kx4k
Image Acquisition
Number of Digital Images357
Sampling Size0.109 microns
Quant Bit Number16
DetailsData collected on CCD
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmCros-common lines
Euler Angles DetailsSPIDER:theta 90 degrees, phi 120 degrees
SoftwareSparx
CTF CorrectionMicrograph and each particle
Resolution By Author14.0
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Class Averages62
Number of Projections12824
DetailsThe particles were selected using an DoG Picker, and cleaned using reference free class averaging.
Download
Data from EMDB
Header (meta data in XML format)emd-1970.xml (8.9 KB)
Map dataemd_1970.map.gz (14.1 MB)
Images1970.png (246.8 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1970
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 4.1 MB
Session file for UCSF-Chimera, 26.7 KB