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Yorodumi- PDB-4xc1: Crystal structure of human 4E10 Fab in complex with its peptide e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xc1 | ||||||
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Title | Crystal structure of human 4E10 Fab in complex with its peptide epitope on HIV-1 GP41: crystals cryoprotected with sn-Glycerol 3-phosphate | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV-1 gp41 MPER / 4E10 Fab / lipid membrane | ||||||
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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 | 4xc1.cif.gz | 210 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xc1.ent.gz | 166.6 KB | Display | PDB format |
PDBx/mmJSON format | 4xc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xc1_validation.pdf.gz | 472.4 KB | Display | wwPDB validaton report |
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Full document | 4xc1_full_validation.pdf.gz | 475.3 KB | Display | |
Data in XML | 4xc1_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 4xc1_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/4xc1 ftp://data.pdbj.org/pub/pdb/validation_reports/xc/4xc1 | HTTPS FTP |
-Related structure data
Related structure data | 4xawC 4xbeC 4xbgC 4xbpC 4xc3C 4xccC 4xceC 4xcfC 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 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.) Human immunodeficiency virus 1 / References: UniProt: P05877*PLUS |
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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.) Homo sapiens (human) / Plasmid: pDR12 / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human) |
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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.) Homo sapiens (human) / Plasmid: pDR12 / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human) |
-Non-polymers , 3 types, 636 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 55.9 % |
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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: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→42.49 Å / Num. obs: 68582 / % possible obs: 98.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.07 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.63→1.67 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FX7 Resolution: 1.63→42.49 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.27 / 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: 1.63→42.49 Å
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Refine LS restraints |
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LS refinement shell |
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