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Yorodumi- PDB-8dpm: Structure of EBOV GP lacking the mucin-like domain with 9.20.1A2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dpm | |||||||||
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Title | Structure of EBOV GP lacking the mucin-like domain with 9.20.1A2 Fab and 6D6 scFv bound | |||||||||
Components |
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Keywords | VIRAL PROTEIN/Immune System / Antibody / Viral protein / glycoprotein / immune system / Ebola virus / VIRAL PROTEIN-Immune System complex | |||||||||
Function / homology | Function and homology information host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell plasma membrane / virion membrane / extracellular region / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Ebola virus - Mayinga Zaire 1976 Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
Authors | Yu, X. / Saphire, E.O. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell Rep / Year: 2023 Title: The evolution and determinants of neutralization of potent head-binding antibodies against Ebola virus. Authors: Xiaoying Yu / Kathryn M Hastie / Carl W Davis / Ruben Diaz Avalos / Dewight Williams / Diptiben Parekh / Sean Hui / Colin Mann / Chitra Hariharan / Ayato Takada / Rafi Ahmed / Erica Ollmann Saphire / Abstract: Monoclonal antibodies against the Ebola virus (EBOV) surface glycoprotein are effective treatments for EBOV disease. Antibodies targeting the EBOV glycoprotein (GP) head epitope have potent ...Monoclonal antibodies against the Ebola virus (EBOV) surface glycoprotein are effective treatments for EBOV disease. Antibodies targeting the EBOV glycoprotein (GP) head epitope have potent neutralization and Fc effector function activity and thus are of high interest as therapeutics and for vaccine design. Here we focus on the head-binding antibodies 1A2 and 1D5, which have been identified previously in a longitudinal study of survivors of EBOV infection. 1A2 and 1D5 have the same heavy- and light-chain germlines despite being isolated from different individuals and at different time points after recovery from infection. Cryoelectron microscopy analysis of each antibody in complex with the EBOV surface GP reveals key amino acid substitutions in 1A2 that contribute to greater affinity, improved neutralization potency, and enhanced breadth as well as two strategies for antibody evolution from a common site. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dpm.cif.gz | 434.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dpm.ent.gz | 344.5 KB | Display | PDB format |
PDBx/mmJSON format | 8dpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dpm_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8dpm_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8dpm_validation.xml.gz | 67.9 KB | Display | |
Data in CIF | 8dpm_validation.cif.gz | 99.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/8dpm ftp://data.pdbj.org/pub/pdb/validation_reports/dp/8dpm | HTTPS FTP |
-Related structure data
Related structure data | 27638MC 8dplC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Glycoprotein ... , 2 types, 6 molecules FAKGBL
#1: Protein | Mass: 31297.158 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Strain: Mayinga-76 / Gene: GP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q05320 #2: Protein | Mass: 15335.362 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Gene: GP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A0E3H7K2 |
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-Antibody , 3 types, 9 molecules HCMIDNJEO
#3: Antibody | Mass: 25853.459 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) #4: Antibody | Mass: 13340.016 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #5: Antibody | Mass: 11985.138 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
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-Sugars , 2 types, 6 molecules
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81175 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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