[English] 日本語
![](img/lk-miru.gif)
- PDB-2b4c: Crystal structure of HIV-1 JR-FL gp120 core protein containing th... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2b4c | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody | |||||||||
![]() |
| |||||||||
![]() | Viral protein/Immune system / HIV-1 / gp120 / JRFL / V3 / X5 / CD4 induced antibody / Viral protein-Immune system COMPLEX | |||||||||
Function / homology | ![]() helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / positive regulation of kinase activity / regulation of T cell activation / T cell receptor complex / extracellular matrix structural constituent / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of calcium ion transport / macrophage differentiation / Generation of second messenger molecules / T cell differentiation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / positive regulation of calcium-mediated signaling / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of establishment of T cell polarity / T cell activation / positive regulation of interleukin-2 production / protein tyrosine kinase binding / host cell endosome membrane / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / positive regulation of T cell activation / MHC class II protein complex binding / Clathrin-mediated endocytosis / virus receptor activity / signaling receptor activity / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / early endosome / viral protein processing / cell adhesion / positive regulation of protein phosphorylation / immune response / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / virion attachment to host cell / endoplasmic reticulum membrane / protein kinase binding / host cell plasma membrane / structural molecule activity / positive regulation of DNA-templated transcription / virion membrane / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Huang, C. / Tang, M. / Zhang, M.Y. / Majeed, S. / Montabana, E. / Stanfield, R.L. / Dimitrov, D.S. / Korber, B. / Sodroski, J. / Wilson, I.A. ...Huang, C. / Tang, M. / Zhang, M.Y. / Majeed, S. / Montabana, E. / Stanfield, R.L. / Dimitrov, D.S. / Korber, B. / Sodroski, J. / Wilson, I.A. / Wyatt, R. / Kwong, P.D. | |||||||||
![]() | ![]() Title: Structure of a V3-containing HIV-1 gp120 core. Authors: Huang, C.C. / Tang, M. / Zhang, M.Y. / Majeed, S. / Montabana, E. / Stanfield, R.L. / Dimitrov, D.S. / Korber, B. / Sodroski, J. / Wilson, I.A. / Wyatt, R. / Kwong, P.D. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 205.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 160.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 747.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 774.1 KB | Display | |
Data in XML | ![]() | 36.8 KB | Display | |
Data in CIF | ![]() | 49.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
2 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 2 types, 2 molecules GC
#1: Protein | Mass: 38452.652 Da / Num. of mol.: 1 / Fragment: CORE with V3 / Mutation: N301Q, T389A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 20129.896 Da / Num. of mol.: 1 / Fragment: D1D2, N-TERMINAL TWO DOMAIN FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Antibody , 2 types, 2 molecules LH
#3: Antibody | Mass: 23267.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#4: Antibody | Mass: 24990.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 3 types, 7 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/XYL.gif)
![](data/chem/img/XYL.gif)
#5: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
---|---|---|---|
#6: Sugar | #8: Sugar | |
-Non-polymers , 1 types, 5 molecules ![](data/chem/img/SO4.gif)
#7: Chemical | ChemComp-SO4 / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 5.5 Details: ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 12, 2004 |
Radiation | Monochromator: SI (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→20 Å / Num. obs: 19372 / % possible obs: 86.6 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.505 / % possible all: 20.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RHH AND 1RZK Resolution: 3.3→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 8776198.43 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 126.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.3→3.51 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
|