[English] 日本語
![](img/lk-miru.gif)
- PDB-4s1q: Crystal structure of a VRC01-lineage antibody, 45-VRC01.H03+06.D-... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4s1q | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a VRC01-lineage antibody, 45-VRC01.H03+06.D-001739, in complex with clade A/E HIV-1 gp120 core | ||||||
![]() |
| ||||||
![]() | VIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 / neutralizing antibodies / VRC01-lineage / antibody maturation / evolutionary rate / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kwon, Y.D. / Yang, Y. / Zhang, B. / Kwong, P.D. | ||||||
![]() | ![]() Title: Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection. Authors: Wu, X. / Zhang, Z. / Schramm, C.A. / Joyce, M.G. / Do Kwon, Y. / Zhou, T. / Sheng, Z. / Zhang, B. / O'Dell, S. / McKee, K. / Georgiev, I.S. / Chuang, G.Y. / Longo, N.S. / Lynch, R.M. / ...Authors: Wu, X. / Zhang, Z. / Schramm, C.A. / Joyce, M.G. / Do Kwon, Y. / Zhou, T. / Sheng, Z. / Zhang, B. / O'Dell, S. / McKee, K. / Georgiev, I.S. / Chuang, G.Y. / Longo, N.S. / Lynch, R.M. / Saunders, K.O. / Soto, C. / Srivatsan, S. / Yang, Y. / Bailer, R.T. / Louder, M.K. / Mullikin, J.C. / Connors, M. / Kwong, P.D. / Mascola, J.R. / Shapiro, L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 445.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 370.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 483.8 KB | Display | |
Data in XML | ![]() | 30.3 KB | Display | |
Data in CIF | ![]() | 41.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4s1rC ![]() 4s1sC ![]() 4xmpC ![]() 4xnyC ![]() 4xnzC ![]() 4xvsC ![]() 4xvtC ![]() 3se8S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 39211.434 Da / Num. of mol.: 1 / Fragment: residue 44-492 / Mutation: V1V2 and V3 deletion Source method: isolated from a genetically manipulated source Details: HIV-1 gp120 core / Source: (gene. exp.) ![]() ![]() ![]() | ||
---|---|---|---|
#2: Antibody | Mass: 25264.580 Da / Num. of mol.: 1 Fragment: Fab of VRC01-lineage antibody,45-VRC01.H03+06.D-001739 heavy chain Source method: isolated from a genetically manipulated source Details: codon-optimized VRC01-lineage antibody, 45-VRC01.H03+06.D-001739, heavy chain Source: (gene. exp.) ![]() ![]() | ||
#3: Antibody | Mass: 23089.572 Da / Num. of mol.: 1 / Fragment: Fab of VRC01 light chain / Mutation: N72T Source method: isolated from a genetically manipulated source Details: codon-optimized human antibody VRC01 light chain / Source: (gene. exp.) ![]() ![]() | ||
#4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 10% PEG 8000, 0.1M Tris-HCl 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 40685 / Num. obs: 39180 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.113 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.63 / Rsym value: 0.515 / % possible all: 80.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3SE8 Resolution: 2.4→41.355 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 29.51 / 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: 2.4→41.355 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|