3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
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
#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 / ID | EM DATA BANK (EMDB) / 1970 |
|---|---|
| Title | Negative stained image reconstruction of HIV spike protein in complex with PGT128 Fab at 14 Angstrom resolution |
| Map | HIV Envelope protein in complex with Fab PGT128 |
| Sample | HIV spike protein 664G construct in complex with Fab fragment of PGT128 monoclonal antibody |
| Keywords |  HIV, broadly neutralizing antibody, glycan shield |
| Authors | Khayat R, Pejchal R, Julien J-P, Wilson IA |
| Date | Deposition: 2011-09-25, Header release: 2011-10-20, Map release: 2011-10-21, Last update: 2011-10-21 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie 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 | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Map | |||||||||||||||||||||||||
| File |  EMD-1970.map ( map file in CCP4 format, 16386 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||
| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
| ||||||||||||||||||||||||
| Unit Cell | A= B= C: 348.8 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 2.18 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | HIV Envelope protein in complex with Fab PGT128 | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | HIV spike protein 664G construct in complex with Fab fragment of PGT128 monoclonal antibody |
|---|---|
| Number of Components | 2 |
| Oligomeric State | One trimer binds to three Fabs |
| Details | The sample was monodisperse |
| Mass-estimation Method | Size exclusion chromatography and light scattering |
| Experimental Mass | 0.445MDa |
| Component #1: protein - Spike protein | |
| Scientific name | Human immunodeficiency virus envelope protein |
| Common Name | Spike protein |
| Details | The PGT128 Fab was complexed to the spike protein, partially deglycosylated, purified using size exclusion chromatography, and concentrated. |
| Oligomeric Details | Trimer |
| Number of Copies | 3 |
| Scientific Name of Species | Human immunodeficiency virus |
| Common Name of Species | Spike protien |
| NCBI taxonomy | 12721 |
| Strain | KNH1144 SOSIP 664G |
| Recombinant expression | Yes |
| Engineered Source | Expression system: 293S Vector: pP14 |
| Component #2: protein - Fab fragment | |
| Scientific name | PGT128 monoclonal antibody fragment |
| Common Name | Fab fragment |
| Oligomeric Details | Monomer |
| Scientific Name of Species | Homo sapiens |
| Common Name of Species | Human |
| NCBI taxonomy | 9606 |
| Recombinant expression | No |
 Experiment | |
| Sample Preparation | |
| Staining | 2% Uranyl Formate for 30 seconds |
|---|---|
| Specimen Conc | 0.1 mg/ml |
| Specimen Support Details | 400 mesh copper grid |
| Specimen State | particle |
| Buffer | Details: 20 mM HEPES pH 7.5, 50 mM NaCl pH: 7.5 |
| Vitrification | |
| Cryogen Name | NONE |
| Instrument | NONE |
| Imaging | |
| Microscope | FEI TECNAI F20 |
| Date | 11-AUG-2011 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 120 kV |
| Electron Dose | 16 e/A**2 |
| Electron Beam Tilt Params | -2 mrad |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 100000 |
| Astigmatism | Objective lens astigmatism was corrected at 100,000 times magnification |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 400 nm - 950 nm |
| Specimen Holder | |
| Holder | eucentric |
| Model | SIDE ENTRY, EUCENTRIC |
| Tilt Angle | 0 degrees - 55 degrees |
| Temperature | 293 K ( 293 - 293 K) |
| Camera | |
| Detector | Gatan 4kx4k |
| Image Acquisition | |
| Number of Digital Images | 357 |
| Sampling Size | 0.109 |
| Quant Bit Number | 16 |
| Details | Data collected on CCD |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | Cros-common lines |
| Euler Angles Details | SPIDER:theta 90 degrees, phi 120 degrees |
| Software | Sparx |
| CTF Correction | Micrograph and each particle |
| Resolution By Author | 14 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| 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. |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1970.xml (8.9 KB) | ||
|---|---|---|---|
| Map data | emd_1970.map.gz (14.1 MB) | ||
| Images |  1970.png (246.8 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1970 | ||
| Movie files | |||
| movie #1 |
| ||
| movie #2 |
| ||
Top
Gallery
List
Diagram
Statistics
Documents
PDBj
EM Navigator
Detail page - EMDB-1970
Article
Z (Sec.)
Y (Row.)
X (Col.)
Contact