[English] 日本語
Yorodumi- PDB-2qad: Structure of tyrosine-sulfated 412d antibody complexed with HIV-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qad | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4 | ||||||
Components |
| ||||||
Keywords | viral protein/immune system / viral protein-immune system complex | ||||||
Function / homology | Function and homology information 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 / immunoglobulin complex / regulation of T cell activation / extracellular matrix structural constituent / T cell receptor complex / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Dectin-2 family / 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 / immunoglobulin mediated immune response / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / 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 calcium-mediated signaling / positive regulation of interleukin-2 production / protein tyrosine kinase binding / host cell endosome membrane / clathrin-coated endocytic vesicle membrane / antigen binding / Vpu mediated degradation of CD4 / calcium-mediated signaling / transmembrane signaling receptor activity / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of T cell activation / Clathrin-mediated endocytosis / virus receptor activity / Downstream TCR signaling / MHC class II protein complex binding / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / clathrin-dependent endocytosis of virus by host cell / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / blood microparticle / cell surface receptor signaling pathway / positive regulation of viral entry into host cell / early endosome / viral protein processing / cell adhesion / positive regulation of protein phosphorylation / membrane raft / immune response / 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 / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / virion attachment to host cell / protein kinase binding / apoptotic process / enzyme binding / structural molecule activity / host cell plasma membrane / virion membrane / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Huang, C.-C. / Tang, M. / Robinson, J. / Wyatt, R. / Kwong, P.D. | ||||||
Citation | Journal: Science / Year: 2007 Title: Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4 Authors: Huang, C.-C. / Lam, S.N. / Acharya, P. / Tang, M. / Xiang, S.-H. / Hussan, S.S. / Stanfield, R.L. / Robinson, J. / Sodroski, J. / Wilson, I.A. / Wyatt, R. / Bewley, C.A. / Kwong, P.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2qad.cif.gz | 778.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qad.ent.gz | 651.8 KB | Display | PDB format |
PDBx/mmJSON format | 2qad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/2qad ftp://data.pdbj.org/pub/pdb/validation_reports/qa/2qad | HTTPS FTP |
---|
-Related structure data
Related structure data | 2rllC 1rzgS 1rzkS 412dS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
| ||||||||
Details | this entry contains the crystallographic asymmetric unit which consists of two gp120/cd4/412d complexes. chain A, B, C, and D form one complex, and chain E, F, G, and H form the other. |
-Components
-Protein , 2 types, 4 molecules AEBF
#1: Protein | Mass: 36062.059 Da / Num. of mol.: 2 / Fragment: CORE WITH V3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: YU2 / Gene: env / Plasmid: CMVR / Cell line (production host): EMBRYONIC CELL LINE 293 / Production host: Homo sapiens (human) / References: UniProt: P35961 #2: Protein | Mass: 20129.896 Da / Num. of mol.: 2 Fragment: D1D2, IG-LIKE V-TYPE AND IG-LIKE C2-TYPE 1 DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Production host: Escherichia coli (E. coli) / References: UniProt: P01730 |
---|
-Antibody , 2 types, 4 molecules CGDH
#3: Antibody | Mass: 23483.066 Da / Num. of mol.: 2 / Fragment: FAB, ANTIGEN-BINDING FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Lymphocryptovirus / Production host: Human herpesvirus 4 (Epstein-Barr virus) / Strain (production host): Epstein-barr virus / References: UniProt: Q6GMX8 #4: Antibody | Mass: 24839.684 Da / Num. of mol.: 2 / Fragment: FAB, ANTIGEN-BINDING FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Lymphocryptovirus / Production host: Human herpesvirus 4 (Epstein-Barr virus) / Strain (production host): Epstein-barr virus / References: UniProt: A4F255 |
---|
-Sugars , 1 types, 31 molecules
#5: Sugar | ChemComp-NAG / |
---|
-Non-polymers , 2 types, 11 molecules
#6: Chemical | ChemComp-MLA / #7: Chemical | ChemComp-EDO / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.27 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 17-19% polyethylene glycol (PEG) 1500, 0.1 M Na cacodylate pH 6.5, 0.2 M Na malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 20, 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→50 Å / Num. obs: 25816 / % possible obs: 67.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 1.3 / Num. unique all: 595 / % possible all: 16.2 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: YU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG Resolution: 3.3→20 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: TLS refinement was performed with PHENIX. The anisotropic B-factor in ANISOU records is the total B-factor (B_tls + B_individual). The isotropic equivalent B-factor in ATOM records is the ...Details: TLS refinement was performed with PHENIX. The anisotropic B-factor in ANISOU records is the total B-factor (B_tls + B_individual). The isotropic equivalent B-factor in ATOM records is the mean of the trace of the ANISOU matrix divided by 10000 and multiplied by 8*pi^2 and represents the isotropic equivalent of the total B-factor (B_tls + B_individual). To obtain the individual B-factors, one needs to compute the TLS component (B_tls) using the TLS records in the PDB file header and then subtract it from the total B-factors (on the ANISOU records).
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 156 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|