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Yorodumi- PDB-4xcf: Crystal structure of human 4E10 Fab in complex with its peptide e... -
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-Basic information
Entry | Database: PDB / ID: 4xcf | ||||||
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Title | Crystal structure of human 4E10 Fab in complex with its peptide epitope on HIV-1 gp41; crystals cryoprotected with phosphatidylcholine (03:0 PC) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / 4E10 Fab anti HIV-1 gp41 / phosphatidylcholine / membrane lipid | ||||||
Function / homology | Function and homology information Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Irimia, A. / Stanfield, R.L. / Wilson, I.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Immunity / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xcf.cif.gz | 211.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xcf.ent.gz | 167.8 KB | Display | PDB format |
PDBx/mmJSON format | 4xcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/4xcf ftp://data.pdbj.org/pub/pdb/validation_reports/xc/4xcf | HTTPS FTP |
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-Related structure data
Related structure data | 4xawC 4xbeC 4xbgC 4xbpC 4xc1C 4xc3C 4xccC 4xceC 4xcnC 4xcyC 2fx7S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23395.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDR12 / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human) | ||
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#2: Antibody | Mass: 23990.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDR12 / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human) | ||
#3: Protein/peptide | Mass: 2226.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P05877*PLUS | ||
#4: Chemical | ChemComp-43Y / [( #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 53.7 % |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.03317 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 22, 2011 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→35.93 Å / Num. obs: 93375 / % possible obs: 93.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.043 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.43→1.45 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 1.5 / % possible all: 53.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FX7 Resolution: 1.43→35.93 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.47 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→35.93 Å
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Refine LS restraints |
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LS refinement shell |
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