[English] 日本語
![](img/lk-miru.gif)
- EMDB-5324: Molecular structure of soluble trimeric HIV-1 glycoprotein gp140 ... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-5324 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Molecular structure of soluble trimeric HIV-1 glycoprotein gp140 JR-FL with sCD4 and 17b | |||||||||
![]() | Molecular structure of soluble trimeric HIV-1 glycoprotein gp140 JR-FL with sCD4 and 17b | |||||||||
![]() |
| |||||||||
![]() | HIV/AIDS vaccine / immunogen / HIV glycoprotein structure / gp140 trimer / cryo-electron tomography / sub-tomogram averaging / cryo-electron microscopy | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 20.0 Å | |||||||||
![]() | Harris A / Borgnia MJ / Shi D / Bartesaghi A / He H / Pejchal R / Kang YK / Depetris R / Marozsan AJ / Sanders RW ...Harris A / Borgnia MJ / Shi D / Bartesaghi A / He H / Pejchal R / Kang YK / Depetris R / Marozsan AJ / Sanders RW / Klasse PJ / Milne JL / Wilson IA / Olson WC / Moore JP / Subramaniam S | |||||||||
![]() | ![]() Title: Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures. Authors: Audray Harris / Mario J Borgnia / Dan Shi / Alberto Bartesaghi / Haifeng He / Robert Pejchal / Yun Kenneth Kang / Rafael Depetris / Andre J Marozsan / Rogier W Sanders / Per Johan Klasse / ...Authors: Audray Harris / Mario J Borgnia / Dan Shi / Alberto Bartesaghi / Haifeng He / Robert Pejchal / Yun Kenneth Kang / Rafael Depetris / Andre J Marozsan / Rogier W Sanders / Per Johan Klasse / Jacqueline L S Milne / Ian A Wilson / William C Olson / John P Moore / Sriram Subramaniam / ![]() Abstract: The initial step in HIV-1 infection occurs with the binding of cell surface CD4 to trimeric HIV-1 envelope glycoproteins (Env), a heterodimer of a transmembrane glycoprotein (gp41) and a surface ...The initial step in HIV-1 infection occurs with the binding of cell surface CD4 to trimeric HIV-1 envelope glycoproteins (Env), a heterodimer of a transmembrane glycoprotein (gp41) and a surface glycoprotein (gp120). The design of soluble versions of trimeric Env that display structural and functional properties similar to those observed on intact viruses is highly desirable from the viewpoint of designing immunogens that could be effective as vaccines against HIV/AIDS. Using cryoelectron tomography combined with subvolume averaging, we have analyzed the structure of SOSIP gp140 trimers, which are cleaved, solubilized versions of the ectodomain of trimeric HIV-1 Env. We show that unliganded gp140 trimers adopt a quaternary arrangement similar to that displayed by native unliganded trimers on the surface of intact HIV-1 virions. When complexed with soluble CD4, Fab 17b, which binds to gp120 at its chemokine coreceptor binding site, or both soluble CD4 and 17b Fab, gp140 trimers display an open conformation in which there is an outward rotation and displacement of each gp120 protomer. We demonstrate that the molecular arrangements of gp120 trimers in the closed and open conformations of the soluble trimer are the same as those observed for the closed and open states, respectively, of trimeric gp120 on intact HIV-1 BaL virions, establishing that soluble gp140 trimers can be designed to mimic the quaternary structural transitions displayed by native trimeric Env. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 2.8 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 8.3 KB 8.3 KB | Display Display | ![]() |
Images | ![]() | 30 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 77.2 KB | Display | |
Data in XML | ![]() | 493 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1930C ![]() 5320C ![]() 5321C ![]() 5322C ![]() 5323C ![]() 5325C C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Molecular structure of soluble trimeric HIV-1 glycoprotein gp140 JR-FL with sCD4 and 17b | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : SOSIP gp140 JR-FL sCD4 17b
Entire | Name: SOSIP gp140 JR-FL sCD4 17b |
---|---|
Components |
|
-Supramolecule #1000: SOSIP gp140 JR-FL sCD4 17b
Supramolecule | Name: SOSIP gp140 JR-FL sCD4 17b / type: sample / ID: 1000 / Oligomeric state: trimeric / Number unique components: 4 |
---|
-Macromolecule #1: SOSIP gp140 JR-FL sCD4 17b
Macromolecule | Name: SOSIP gp140 JR-FL sCD4 17b / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes / Database: NCBI |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | subtomogram averaging |
Aggregation state | particle |
-
Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
---|
-
Electron microscopy
Microscope | FEI POLARA 300 |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
-
Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF |
---|
-Atomic model buiding 1
Initial model | PDB ID: |
---|---|
Software | Name: ![]() |
Refinement | Space: REAL |