+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ai1 | ||||||
---|---|---|---|---|---|---|---|
Title | HIV-1 V3 LOOP MIMIC | ||||||
![]() |
| ||||||
![]() | COMPLEX (ANTIBODY/PEPTIDE) / COMPLEX (ANTIBODY-PEPTIDE) / ANTIBODY / CONSTRAINED HIV-1 V3 LOOP PEPTIDE / IMMUNOGLOBULIN / COMPLEX (ANTIBODY-PEPTIDE) complex | ||||||
Function / homology | ![]() humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / Dectin-2 family / immunoglobulin mediated immune response / positive regulation of plasma membrane raft polarization / positive regulation of phagocytosis ...humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / Dectin-2 family / immunoglobulin mediated immune response / positive regulation of plasma membrane raft polarization / positive regulation of phagocytosis / positive regulation of receptor clustering / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of establishment of T cell polarity / B cell differentiation / host cell endosome membrane / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / viral protein processing / blood microparticle / defense response to bacterium / fusion of virus membrane with host plasma membrane / external side of plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ghiara, J.B. / Wilson, I.A. | ||||||
![]() | ![]() Title: Structure-based design of a constrained peptide mimic of the HIV-1 V3 loop neutralization site. Authors: Ghiara, J.B. / Ferguson, D.C. / Satterthwait, A.C. / Dyson, H.J. / Wilson, I.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 94.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 74.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 454.9 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1acyS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Antibody | Mass: 23675.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#2: Antibody | Mass: 24208.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein/peptide | Mass: 2828.366 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE PEPTIDE IS NUMBERED ACCORDING TO THE BH10 ISOLATE References: UniProt: P05877 |
Compound details | THE PEPTIDE IS NUMBERED ACCORDING TO THE BH10 ISOLATE SEQUENCE (L.RATNER ET AL., NATURE 313:277-284 (1985)). |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.16 Å3/Da / Density % sol: 70.4 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, sitting drop / PH range low: 6.75 / PH range high: 5 | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 287 K |
---|---|
Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.8 Å / Num. obs: 19192 / % possible obs: 92 % / Rsym value: 0.08 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 90 |
Reflection | *PLUS Num. measured all: 50028 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 90 % |
-
Processing
Software |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1ACY Resolution: 2.8→12 Å / σ(F): 0
| |||||||||||||||
Displacement parameters | Biso mean: 30 Å2 | |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→12 Å
| |||||||||||||||
Software | *PLUS Name: ![]() | |||||||||||||||
Refine LS restraints | *PLUS
|