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Yorodumi- PDB-2fx9: Crystal structure of hiv-1 neutralizing human fab 4e10 in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fx9 | ||||||
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Title | Crystal structure of hiv-1 neutralizing human fab 4e10 in complex with a thioether-linked peptide encompassing the 4e10 epitope on gp41 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin fold / beta-sandwich / antibody-epitope complex | ||||||
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 / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cardoso, R.M.F. / Brunel, F.M. / Ferguson, S. / Burton, D.R. / Dawson, P.E. / Wilson, I.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural basis of enhanced binding of extended and helically constrained peptide epitopes of the broadly neutralizing HIV-1 antibody 4E10. Authors: Cardoso, R.M. / Brunel, F.M. / Ferguson, S. / Zwick, M. / Burton, D.R. / Dawson, P.E. / Wilson, I.A. #1: Journal: Immunity / Year: 2005 Title: Broadly neutralizing anti-HIV antibody 4E10 recognizes a helical conformation of a highly conserved fusion-associated motif in gp41 Authors: Cardoso, R.M.F. / Zwick, M.B. / Stanfield, R.L. / Kunert, R. / Binley, J.M. / Katinger, H. / Burton, D.R. / Wilson, I.A. | ||||||
History |
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Remark 999 | No database reference is currently available for Chains L, M, H, I, P, and Q. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fx9.cif.gz | 191.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fx9.ent.gz | 151.2 KB | Display | PDB format |
PDBx/mmJSON format | 2fx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fx9_validation.pdf.gz | 471.3 KB | Display | wwPDB validaton report |
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Full document | 2fx9_full_validation.pdf.gz | 491.8 KB | Display | |
Data in XML | 2fx9_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 2fx9_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/2fx9 ftp://data.pdbj.org/pub/pdb/validation_reports/fx/2fx9 | HTTPS FTP |
-Related structure data
Related structure data | 2fx7C 2fx8C 1tzgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23292.705 Da / Num. of mol.: 2 / Fragment: Light Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 23860.848 Da / Num. of mol.: 2 / Fragment: Heavy Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #3: Protein/peptide | Mass: 1941.385 Da / Num. of mol.: 2 / Fragment: Peptide Epitope of 4E10 / Source method: obtained synthetically Details: This sequence includes a fragment of the HIV envelope protein gp41 References: UniProt: P05880*PLUS #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.71 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 0.2 M ammonium nitrate, pH no buffer, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.95369 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 5, 2005 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 51978 / Num. obs: 51614 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 31.6 Å2 / Rsym value: 0.094 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3779 / Rsym value: 0.324 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PBD ENTRY 1TZG Resolution: 2.1→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 46.1188 Å2 / ksol: 0.343825 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.316 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell |
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