[English] 日本語
![](img/lk-miru.gif)
- PDB-5ies: Crystal structure of VRC01c-HuGL2 Fab from an HIV-1 naive donor i... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5ies | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of VRC01c-HuGL2 Fab from an HIV-1 naive donor in complex with with a germline-targeting gp120 engineered outer domain eOD-GT8 at 2.16 A | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM/ VIRAL PROTEIN / HIV-1 gp120 / engineered outer domain (eOD) / germline targeting / CD4 binding site / VRC01-class naive human germline antibody / immune system / viral-protein complex / IMMUNE SYSTEM-VIRAL PROTEIN complex / IMMUNE SYSTEM- VIRAL PROTEIN complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sarkar, A. / Wilson, I.A. | ||||||
![]() | ![]() Title: HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen. Authors: Jardine, J.G. / Kulp, D.W. / Havenar-Daughton, C. / Sarkar, A. / Briney, B. / Sok, D. / Sesterhenn, F. / Ereno-Orbea, J. / Kalyuzhniy, O. / Deresa, I. / Hu, X. / Spencer, S. / Jones, M. / ...Authors: Jardine, J.G. / Kulp, D.W. / Havenar-Daughton, C. / Sarkar, A. / Briney, B. / Sok, D. / Sesterhenn, F. / Ereno-Orbea, J. / Kalyuzhniy, O. / Deresa, I. / Hu, X. / Spencer, S. / Jones, M. / Georgeson, E. / Adachi, Y. / Kubitz, M. / deCamp, A.C. / Julien, J.P. / Wilson, I.A. / Burton, D.R. / Crotty, S. / Schief, W.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 250.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 200.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 476.2 KB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 34.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5idlC ![]() 5if0C ![]() 5ifaC ![]() 4jpkS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 23614.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Antibody | Mass: 23816.408 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein / Sugars , 2 types, 3 molecules C![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#3: Protein | Mass: 19889.307 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#5: Sugar |
-Non-polymers , 2 types, 190 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.73 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M citric acid (pH 4.0), 20% (w/v) PEG6000 with an overall pH 5.0 of the solution, cryo-protected with 25% glycerol |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1542→46.45 Å / Num. obs: 52709 / % possible obs: 92.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 48.7 Å2 / CC1/2: 0.902 / Rsym value: 0.067 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.16→2.1933 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 1.9 / % possible all: 89.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4JPK Resolution: 2.16→46.448 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.16→46.448 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|