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Yorodumi- PDB-4ngh: Crystal structure of the HIV-1 neutralizing antibody 4E10 Fab fra... -
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-Basic information
Entry | Database: PDB / ID: 4ngh | ||||||
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Title | Crystal structure of the HIV-1 neutralizing antibody 4E10 Fab fragment in complex with a hydrocarbon-stapled peptide containing the 4e10 epitope on gp41 and a tethered phosphate moiety. | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / BETA-SANDWICH / 4E10 FAB / ANTIBODY-EPITOPE COMPLEX / GP41 HIV-1 / HYDROCARBON STAPLE | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Stapled peptide (ACE)NWFNITN(DIV)LW(MK8)I(LYV)KKK Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||
Authors | Irimia, A. / Wilson, I.A. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2014 Title: Stapled HIV-1 peptides recapitulate antigenic structures and engage broadly neutralizing antibodies. Authors: Bird, G.H. / Irimia, A. / Ofek, G. / Kwong, P.D. / Wilson, I.A. / Walensky, L.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ngh.cif.gz | 195.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ngh.ent.gz | 155.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ngh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ngh_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 4ngh_full_validation.pdf.gz | 451 KB | Display | |
Data in XML | 4ngh_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 4ngh_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/4ngh ftp://data.pdbj.org/pub/pdb/validation_reports/ng/4ngh | HTTPS FTP |
-Related structure data
Related structure data | 4nhcC 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
#1: Antibody | Mass: 23395.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO cells |
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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) / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO cells |
#3: Protein/peptide | |
#4: Water | ChemComp-HOH / |
Compound details | THE STAPLED PEPTIDES IN THE STRUCTURE WAS OBTAINED BY INCORPORATION OF (R)-2-(((9H-FLUOREN-9-YL) ...THE STAPLED PEPTIDES IN THE STRUCTURE WAS OBTAINED BY INCORPORAT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.02 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Reservoir solution:0.2 M MgCl2, 0.1 M MES pH5.5, 40% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2011 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→49.04 Å / Num. all: 18601 / Num. obs: 18587 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 20.7 % / Biso Wilson estimate: 52 Å2 / Rsym value: 0.093 / Net I/σ(I): 28 |
Reflection shell | Resolution: 2.68→2.75 Å / Redundancy: 20.3 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 1335 / Rsym value: 0.597 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FX7 Resolution: 2.68→49.04 Å / SU ML: 0.79 / σ(F): 1.37 / Phase error: 22.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.257 Å2 / ksol: 0.359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.68→49.04 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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