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- PDB-4xc3: Crystal structure of human 4E10 Fab in complex with its peptide e... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xc3 | ||||||
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Title | Crystal structure of human 4E10 Fab in complex with its peptide epitope on HIV-1 gp41; crystals cryoprotected with rac-glycerol 1-phosphate | ||||||
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![]() | IMMUNE SYSTEM / HIV-1 gp41 MPER / 4E10 Fab / membrane lipid | ||||||
Function / homology | ![]() Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / : / viral envelope ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / : / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Irimia, A. / Stanfield, R.L. / Wilson, I.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystallographic Identification of Lipid as an Integral Component of the Epitope of HIV Broadly Neutralizing Antibody 4E10. Authors: Irimia, A. / Sarkar, A. / Stanfield, R.L. / Wilson, I.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 210.6 KB | Display | ![]() |
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PDB format | ![]() | 166.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.8 KB | Display | ![]() |
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Full document | ![]() | 464 KB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 43 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xawC ![]() 4xbeC ![]() 4xbgC ![]() 4xbpC ![]() 4xc1C ![]() 4xccC ![]() 4xceC ![]() 4xcfC ![]() 4xcnC ![]() 4xcyC C: citing same article ( |
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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 on special symmetry positions |
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Components
-Protein/peptide , 1 types, 1 molecules P
#3: Protein/peptide | Mass: 2201.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 23395.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 24180.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 3 types, 764 molecules 


#4: Chemical | #5: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #6: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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Nonpolymer details | ONE UNKNOWN LIGANDS (UNL) HAS BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTION ENVIRONMENTS, ...ONE UNKNOWN LIGANDS (UNL) HAS BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTIO |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: The complex grew from 1:1 protein:reservoir solution sitting drops equilibrated against 20% PEG 8000, 0.2 M sodium acetate, pH 5.5, 0.2 M sodium thiocyanate |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 12, 2011 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111), non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→32.796 Å / Num. obs: 67194 / % possible obs: 97.3 % / Redundancy: 4 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.045 / Net I/σ(I): 20.47 |
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.1 / % possible all: 74.2 |
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Processing
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Refinement | Resolution: 1.63→32.796 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→32.796 Å
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Refine LS restraints |
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LS refinement shell |
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