3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Molecular Structure of the Native HIV-1 gp120 trimer bound to b12: Spike region
by subtomogram averaging, at 20 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
#3: Surface view with fitted model, atomic models: PDB-3dnl, Surface level: 1, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5018 |
|---|---|
| Title | Molecular Structure of the Native HIV-1 gp120 trimer bound to b12: Spike region |
| Map | b12-bound HIV-1 BaL spike |
| Sample | HIV-1 BaL virus |
| Keywords |  HIV-1, envelope glycoprotein. immunodeficiency virus, gp120 |
| Authors | Bartesaghi A, Borgnia M, Liu J, Sapiro G, Subramaniam S |
| Date | Deposition: 2008-06-29, Header release: 2008-07-03, Map release: 2009-05-05, Last update: 2011-08-02 |
| 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 #3: Surface view with fitted model, atomic models: PDB-3dnl, 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 Fit: output model of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | Nature, Vol. 455, Issue 7209, Page 109-13, Year 2008 |
|---|---|
| Title | Molecular architecture of native HIV-1 gp120 trimers. |
| Authors | Jun Liu, Alberto Bartesaghi, Mario J Borgnia, Guillermo Sapiro, Sriram Subramaniam Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA. |
| Keywords | Antigens, CD4 (chemistry), Cryoelectron Microscopy, HIV Envelope Protein gp120 (chemistry), HIV-1 (chemistry), Immunoglobulin Fab Fragments (chemistry), Models, Molecular, Protein Binding, Protein Structure, Quaternary, Protein Subunits (chemistry) |
| Links | DOI: 10.1038/nature07159, PubMed: 18668044, PMC: PMC2610422 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5018.map ( map file in CCP4 format, 4002 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: 410 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 4.1 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | b12-bound HIV-1 BaL spike | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | HIV-1 BaL virus |
|---|---|
| Number of Components | 1 |
| Details | Structures determined by cryo-electron tomography combined with 3D averaging |
| Component #1: virus - HIV-1 surface spike | |
| Scientific name | HIV-1 envelope glycoprotein |
| Common Name | HIV-1 surface spike |
| Scientific Name of Species | HIV-1 envelope glycoprotein |
| Common Name of Species | HIV-1 surface spike |
| Empty | No |
| Enveloped | Yes |
| Isolate | STRAIN |
| Class | VIRION |
| Natural Source | NCBI taxonomy: 9606 Host Species: Homo sapiens Host Category: VERTEBRATES |
 Experiment | |
| Sample Preparation | |
| Specimen Support Details | home-made holey carbon |
|---|---|
| Buffer | Details: 0.01 M Tris, 0.1 M NaCl, 1 mM EDTA pH: 7.2 |
| Vitrification | |
| Method | Blot and plunge |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Vitrobot |
| Humidity | 100 |
| Instrument | FEI VITROBOT |
| Temperature | 77 Kelvin |
| Imaging | |
| Microscope | FEI POLARA 300 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 80 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 34000 |
| Nominal Cs | 2.2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 2000 nm - 4000 nm |
| Energy Filter | Energy Filter: Gatan , Energy Window: 0-20 eV |
| Specimen Holder | |
| Holder | Cartridge |
| Model | GATAN LIQUID NITROGEN |
| Tilt Angle | -70 degrees - 70 degrees |
| Temperature | 77 K |
| Camera | |
| Detector | CCD |
 Processing | |
| Method | subtomogram averaging |
|---|---|
| 3D reconstruction | |
| Software | IMOD and in-house procedures |
| Resolution By Author | 20 A |
| Resolution Method | FSC at 0.5 cut-off |
| Subtomogram Averaging | |
| Details | Average number of tilts used in the 3D reconstructions: 400. Average tomographic tilt angle increment: 1. |
| Atomic Model Fitting | |
| Model #0 | |
| Target Criteria | correlation coefficient |
| Details | Automated fitting procedures |
| Software | Chimera |
| Refinement Space | REAL |
| PDB Entry ID | 1GC1 |
| Fitted Coordinate | |
| PDB entry ID | |
Top
Gallery
List
Diagram
Statistics
Documents
PDBj
EM Navigator
Detail page - EMDB-5018
Z (Sec.)
Y (Row.)
X (Col.)
Contact