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- PDB-4ut7: CRYSTAL STRUCTURE OF THE SCFV FRAGMENT OF THE BROADLY NEUTRALIZIN... -
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Basic information
Entry | Database: PDB / ID: 4ut7 | ||||||
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Title | CRYSTAL STRUCTURE OF THE SCFV FRAGMENT OF THE BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11 | ||||||
![]() | (BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11) x 2 | ||||||
![]() | IMMUNE SYSTEM / BROADLY NEUTRALIZING ANTIBODY / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX / VIRAL PROTEIN / MEMBRANE FUSION / CLASS 2 FUSION PROTEIN / DENGUE VIRUS / SCFV FRAGMENT | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Rey, F.A. | ||||||
![]() | ![]() Title: Recognition Determinants of Broadly Neutralizing Human Antibodies Against Dengue Viruses. Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. / ...Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. / Petres, S. / Shepard, W.E. / Despres, P. / Arenzana-Seisdedos, F. / Dussart, P. / Mongkolsapaya, J. / Screaton, G.R. / Rey, F.A. #1: ![]() Title: A new class of highly potent, broadly neutralizing antibodies isolated from viremic patients infected with dengue virus. Authors: Wanwisa Dejnirattisai / Wiyada Wongwiwat / Sunpetchuda Supasa / Xiaokang Zhang / Xinghong Dai / Alexander Rouvinski / Amonrat Jumnainsong / Carolyn Edwards / Nguyen Than Ha Quyen / Thaneeya ...Authors: Wanwisa Dejnirattisai / Wiyada Wongwiwat / Sunpetchuda Supasa / Xiaokang Zhang / Xinghong Dai / Alexander Rouvinski / Amonrat Jumnainsong / Carolyn Edwards / Nguyen Than Ha Quyen / Thaneeya Duangchinda / Jonathan M Grimes / Wen-Yang Tsai / Chih-Yun Lai / Wei-Kung Wang / Prida Malasit / Jeremy Farrar / Cameron P Simmons / Z Hong Zhou / Felix A Rey / Juthathip Mongkolsapaya / Gavin R Screaton / ![]() ![]() ![]() ![]() ![]() ![]() Abstract: Dengue is a rapidly emerging, mosquito-borne viral infection, with an estimated 400 million infections occurring annually. To gain insight into dengue immunity, we characterized 145 human monoclonal ...Dengue is a rapidly emerging, mosquito-borne viral infection, with an estimated 400 million infections occurring annually. To gain insight into dengue immunity, we characterized 145 human monoclonal antibodies (mAbs) and identified a previously unknown epitope, the envelope dimer epitope (EDE), that bridges two envelope protein subunits that make up the 90 repeating dimers on the mature virion. The mAbs to EDE were broadly reactive across the dengue serocomplex and fully neutralized virus produced in either insect cells or primary human cells, with 50% neutralization in the low picomolar range. Our results provide a path to a subunit vaccine against dengue virus and have implications for the design and monitoring of future vaccine trials in which the induction of antibody to the EDE should be prioritized. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 115.7 KB | Display | ![]() |
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PDB format | ![]() | 90 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.9 KB | Display | ![]() |
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Full document | ![]() | 427 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ut6C ![]() 4ut9C ![]() 4utaC ![]() 4utbC ![]() 4utcC ![]() 4ut8 C: citing same article ( |
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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 on special symmetry positions |
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Components
#1: Antibody | Mass: 15962.392 Da / Num. of mol.: 1 / Fragment: SCFV HEAVY CHAIN DOMAIN, RESIDUES 1-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 15740.104 Da / Num. of mol.: 1 / Fragment: SCFV LIGHT CHAIN DOMAIN, RESIDUES 1-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | Details: 0.1 M MES 6.5 25% (V/V) PEG 550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2013 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS |
Radiation | Monochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→29.52 Å / Num. obs: 28835 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.6 / % possible all: 95.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: FAB A11 FROM THE COMPLEX DENGUE 2 FAB A11 Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.9321 / Cor.coef. Fo:Fc free: 0.9128 / SU R Cruickshank DPI: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.096 / SU Rfree Blow DPI: 0.093 / SU Rfree Cruickshank DPI: 0.091
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Displacement parameters | Biso mean: 22.18 Å2
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Refine analyze | Luzzati coordinate error obs: 0.178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Total num. of bins used: 14
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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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