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- PDB-5cil: Crystal Structure of non-neutralizing version of 4E10 (WDWD) with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cil | |||||||||
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Title | Crystal Structure of non-neutralizing version of 4E10 (WDWD) with epitope bound | |||||||||
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Function / homology | ![]() Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Caaveiro, J.M.M. / Rujas, E. / Nieva, J.L. / Tsumoto, K. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10 Authors: Rujas, E. / Gulzar, N. / Morante, K. / Tsumoto, K. / Scott, J.K. / Nieva, J.L. / Caaveiro, J.M.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 | ![]() | 197.5 KB | Display | ![]() |
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PDB format | ![]() | 154.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5cinC ![]() 5cipC ![]() 4wy7S C: citing same article ( 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
-Protein/peptide , 1 types, 1 molecules P
#3: Protein/peptide | ![]() Mass: 2187.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 23590.473 Da / Num. of mol.: 1 / Mutation: W100D, W100(B)D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 23106.541 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 414 molecules ![](data/chem/img/GOL.gif)
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![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ![]() #5: Chemical | ![]() #6: Chemical | ChemComp-ACT / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.03 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 100mM TRIS-HCl, 200mM Ammonium acetate, 34%PEG 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.81→44.5 Å / Num. obs: 50189 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.81→1.91 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.8 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4WY7 Resolution: 1.81→44.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.852 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.386 Å2
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Refinement step | Cycle: 1 / Resolution: 1.81→44.5 Å
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