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- PDB-4orz: HIV-1 Nef protein in complex with single domain antibody sdAb19 a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4orz | ||||||
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Title | HIV-1 Nef protein in complex with single domain antibody sdAb19 and an engineered Hck SH3 domain | ||||||
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![]() | TRANSFERASE/APOPTOSIS/IMMUNE SYSTEM / SH3 domain / immunglobolin fold / Antibodies / Epitopes / HIV Antibodies / HIV Accessory Proteins / PxxP motif / Complementarity Determining Regions / TRANSFERASE-APOPTOSIS-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / regulation of podosome assembly / suppression by virus of host autophagy / regulation of phagocytosis / FLT3 signaling through SRC family kinases ...leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / regulation of podosome assembly / suppression by virus of host autophagy / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / activation of transmembrane receptor protein tyrosine kinase activity / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / host cell Golgi membrane / mesoderm development / FCGR activation / localization / type II interferon-mediated signaling pathway / Signaling by CSF3 (G-CSF) / lipopolysaccharide-mediated signaling pathway / transport vesicle / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / cell surface receptor protein tyrosine kinase signaling pathway / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / virion component / caveola / cell projection / integrin-mediated signaling pathway / Regulation of signaling by CBL / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / endocytosis involved in viral entry into host cell / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / SH3 domain binding / peptidyl-tyrosine phosphorylation / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / regulation of inflammatory response / protein tyrosine kinase activity / protein autophosphorylation / cell differentiation / lysosome / cytoskeleton / cell adhesion / intracellular signal transduction / inflammatory response / protein phosphorylation / intracellular membrane-bounded organelle / innate immune response / focal adhesion / signaling receptor binding / virus-mediated perturbation of host defense response / lipid binding / positive regulation of cell population proliferation / GTP binding / negative regulation of apoptotic process / host cell plasma membrane / Golgi apparatus / extracellular region / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Geyer, M. / Lulf, S. | ||||||
![]() | ![]() Title: Structural basis for the inhibition of HIV-1 Nef by a high-affinity binding single-domain antibody. Authors: Lulf, S. / Matz, J. / Rouyez, M.C. / Jarviluoma, A. / Saksela, K. / Benichou, S. / Geyer, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 55.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.4 KB | Display | ![]() |
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Full document | ![]() | 449 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rbbS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 7614.431 Da / Num. of mol.: 1 / Fragment: SH3 domain, UNP residues 77-138 / Mutation: E90Y, A91S, I92P, H93F, H94S, E95W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P08631, non-specific protein-tyrosine kinase |
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#2: Protein | Mass: 16817.979 Da / Num. of mol.: 1 / Fragment: Nef protein, UNP residues 45-210 / Mutation: I47M, T48A, C59S, C210A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Antibody | Mass: 13007.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: About 0.1 micro L of protein solution at 10 mg/ml concentration was mixed with 0.1 micro L of reservoir solution from a 70 L reservoir in 96-well Hampton 3553 crystallization plates. Initial ...Details: About 0.1 micro L of protein solution at 10 mg/ml concentration was mixed with 0.1 micro L of reservoir solution from a 70 L reservoir in 96-well Hampton 3553 crystallization plates. Initial crystals of NefSF2 sdAb19 SH3B6 could be obtained in 0.2 M potassium formate and 20% polyethylene glycol (PEG) 3350. Crystal conditions were optimized to 0.2 M potassium formate, 17.5% polyethylene glycol (PEG) 3350 and 0.35 M ammonium chloride grown by hanging-drop vapor diffusion in Linbro crystallization plates. , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2012 |
Radiation | Monochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2→41.75 Å / Num. obs: 47918 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.1→2.15 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3RBB Resolution: 2→41.75 Å / SU ML: 0.21 / σ(F): 2.04 / Phase error: 24.91 / Stereochemistry target values: MLHL
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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→41.75 Å
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Refine LS restraints |
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LS refinement shell |
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