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Yorodumi- PDB-7a3q: Crystal structure of dengue 4 virus envelope glycoprotein in comp... -
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-Basic information
Entry | Database: PDB / ID: 7a3q | ||||||
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Title | Crystal structure of dengue 4 virus envelope glycoprotein in complex with the scFv fragment of the broadly neutralizing human antibody EDE1 C10 | ||||||
Components |
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Keywords | VIRAL PROTEIN / FLAVIVIRUS / CLASS 2 FUSION PROTEIN / DENGUE / Antibody | ||||||
Function / homology | Function and homology information membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / extracellular region Similarity search - Function | ||||||
Biological species | Dengue virus 4 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Sharma, A. / Vaney, M.C. / Guardado-Calvo, P. / Duquerroy, S. / Rouvinski, A. / Rey, F.A. | ||||||
Funding support | France, 1items
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Citation | Journal: Cell / Year: 2021 Title: The epitope arrangement on flavivirus particles contributes to Mab C10's extraordinary neutralization breadth across Zika and dengue viruses. Authors: Arvind Sharma / Xiaokang Zhang / Wanwisa Dejnirattisai / Xinghong Dai / Danyang Gong / Wiyada Wongwiwat / Stéphane Duquerroy / Alexander Rouvinski / Marie-Christine Vaney / Pablo Guardado- ...Authors: Arvind Sharma / Xiaokang Zhang / Wanwisa Dejnirattisai / Xinghong Dai / Danyang Gong / Wiyada Wongwiwat / Stéphane Duquerroy / Alexander Rouvinski / Marie-Christine Vaney / Pablo Guardado-Calvo / Ahmed Haouz / Patrick England / Ren Sun / Z Hong Zhou / Juthathip Mongkolsapaya / Gavin R Screaton / Felix A Rey / Abstract: The human monoclonal antibody C10 exhibits extraordinary cross-reactivity, potently neutralizing Zika virus (ZIKV) and the four serotypes of dengue virus (DENV1-DENV4). Here we describe a comparative ...The human monoclonal antibody C10 exhibits extraordinary cross-reactivity, potently neutralizing Zika virus (ZIKV) and the four serotypes of dengue virus (DENV1-DENV4). Here we describe a comparative structure-function analysis of C10 bound to the envelope (E) protein dimers of the five viruses it neutralizes. We demonstrate that the C10 Fab has high affinity for ZIKV and DENV1 but not for DENV2, DENV3, and DENV4. We further show that the C10 interaction with the latter viruses requires an E protein conformational landscape that limits binding to only one of the three independent epitopes per virion. This limited affinity is nevertheless counterbalanced by the particle's icosahedral organization, which allows two different dimers to be reached by both Fab arms of a C10 immunoglobulin. The epitopes' geometric distribution thus confers C10 its exceptional neutralization breadth. Our results highlight the importance not only of paratope/epitope complementarity but also the topological distribution for epitope-focused vaccine design. #1: Journal: Nature / Year: 2016 Title: Structural basis of potent Zika-dengue virus antibody cross-neutralization. Authors: Barba-Spaeth, G. / Dejnirattisai, W. / Rouvinski, A. / Vaney, M.C. / Medits, I. / Sharma, A. / Simon-Loriere, E. / Sakuntabhai, A. / Cao-Lormeau, V.M. / Haouz, A. / England, P. / Stiasny, K. ...Authors: Barba-Spaeth, G. / Dejnirattisai, W. / Rouvinski, A. / Vaney, M.C. / Medits, I. / Sharma, A. / Simon-Loriere, E. / Sakuntabhai, A. / Cao-Lormeau, V.M. / Haouz, A. / England, P. / Stiasny, K. / Mongkolsapaya, J. / Heinz, F.X. / Screaton, G.R. / Rey, F.A. #2: Journal: Nature / Year: 2015 Title: Recognition determinants of broadly neutralizing human antibodies against dengue viruses. Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / 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.C. / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a3q.cif.gz | 489.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a3q.ent.gz | 405.3 KB | Display | PDB format |
PDBx/mmJSON format | 7a3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a3q_validation.pdf.gz | 515.3 KB | Display | wwPDB validaton report |
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Full document | 7a3q_full_validation.pdf.gz | 528.4 KB | Display | |
Data in XML | 7a3q_validation.xml.gz | 41.3 KB | Display | |
Data in CIF | 7a3q_validation.cif.gz | 57.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/7a3q ftp://data.pdbj.org/pub/pdb/validation_reports/a3/7a3q | HTTPS FTP |
-Related structure data
Related structure data | 7a3nC 7a3oC 7a3pC 7a3rC 7a3sC 7a3tC 7a3uC 7cthC 3fkuS 3uajS 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
-Antibody , 2 types, 4 molecules HILM
#2: Antibody | Mass: 15679.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: variable domain from the heavy chain of broadly neutralising antibody EDE1 C10 Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly) #3: Antibody | Mass: 15632.767 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: variable domain from the light chain of broadly neutralising antibody EDE1 C10 Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly) |
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-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 43335.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: DENGUE VIRUS SEROTYPE 4 ENVELOPE PROTEIN ECTODOMAIN Source: (gene. exp.) Dengue virus 4 / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: S5S2D1 #4: Sugar | |
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-Non-polymers , 2 types, 42 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.74 Å3/Da / Density % sol: 55.14 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 100 mM CAPSO pH 9.6, 16.7% (w/v) PEG 8,000, 200 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.254 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.254 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. obs: 43980 / % possible obs: 99.1 % / Redundancy: 3.19 % / CC1/2: 0.998 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4614 / CC1/2: 0.688 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UAJ, 3FKU Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.9309 / Cor.coef. Fo:Fc free: 0.9158 / SU R Cruickshank DPI: 0.731 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.618 / SU Rfree Blow DPI: 0.287 / SU Rfree Cruickshank DPI: 0.299
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Displacement parameters | Biso max: 181.89 Å2 / Biso mean: 81.58 Å2 / Biso min: 19.97 Å2
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Refine analyze | Luzzati coordinate error obs: 0.503 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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